[med-svn] [mothur] 01/06: New upstream version 1.39.0
Tomasz Buchert
tomasz at moszumanska.debian.org
Sun Feb 26 15:29:31 UTC 2017
This is an automated email from the git hooks/post-receive script.
tomasz pushed a commit to branch master
in repository mothur.
commit 4608f7ef05e68d89401ce8abf12cfa2dc0c691ac
Author: Tomasz Buchert <tomasz at debian.org>
Date: Fri Jan 27 07:05:15 2017 +0100
New upstream version 1.39.0
---
.gitignore | 1 +
Makefile | 7 +-
Mothur.xcodeproj/project.pbxproj | 133 +-
README.md | 2 +-
TestMothur/catch.hpp | 4392 ++-
TestMothur/dataset.h | 10 +-
TestMothur/distcdataset.cpp | 46955 ++++++++++++++++++++++++
TestMothur/distcdataset.h | 32 +
TestMothur/distpdataset.cpp | 2578 ++
TestMothur/distpdataset.h | 30 +
TestMothur/main.cpp | 7 +-
TestMothur/testclassifier/testphylotree.cpp | 129 +
TestMothur/testclassifier/testphylotree.hpp | 32 +
TestMothur/testcontainers/testfastqread.cpp | 5 +-
TestMothur/testcontainers/testoptimatrix.cpp | 101 +
TestMothur/testcontainers/testoptimatrix.h | 31 +
TestMothur/testopticluster.cpp | 132 +
TestMothur/testopticluster.h | 35 +
TestMothur/testtrimoligos.hpp | 4 +-
TestMothur/testvsearchfileparser.cpp | 6 +-
TestMothur/testvsearchfileparser.h | 1 -
makefile-internal | 6 +-
source/calculators/filters.h | 12 +
source/chimera/chimeracheckrdp.cpp | 2 +-
source/classifier/classify.cpp | 1 -
source/classifier/phylosummary.cpp | 38 +-
source/classifier/phylotree.cpp | 13 +-
source/classifier/phylotree.h | 5 +
source/classifier/taxonomyequalizer.cpp | 41 +-
source/cluster.cpp | 4 +-
source/cluster.hpp | 10 +-
source/commandfactory.cpp | 6 +-
source/commands/aligncommand.cpp | 2 +-
source/commands/aligncommand.h | 2 +-
source/commands/biominfocommand.cpp | 6 +
source/commands/catchallcommand.cpp | 4 +-
source/commands/chimeraperseuscommand.cpp | 6 +-
source/commands/chimeraperseuscommand.h | 9 +-
source/commands/chimeraslayercommand.cpp | 6 +-
source/commands/chimerauchimecommand.cpp | 34 +-
source/commands/chimerauchimecommand.h | 18 +-
source/commands/chimeravsearchcommand.cpp | 350 +-
source/commands/chimeravsearchcommand.h | 3 -
source/commands/classifyotucommand.cpp | 13 +-
source/commands/classifyseqscommand.cpp | 7 +-
source/commands/clustercommand.cpp | 247 +-
source/commands/clustercommand.h | 15 +-
source/commands/clustersplitcommand.cpp | 307 +-
source/commands/clustersplitcommand.h | 17 +-
source/commands/createdatabasecommand.cpp | 99 +-
source/commands/distancecommand.cpp | 2 +-
source/commands/getcommandinfocommand.cpp | 2 +-
source/commands/getcurrentcommand.cpp | 2 +
source/commands/getgroupscommand.cpp | 6 +-
source/commands/getlineagecommand.cpp | 16 +-
source/commands/getotulabelscommand.cpp | 9 +-
source/commands/getotuscommand.cpp | 432 -
source/commands/getotuscommand.h | 55 -
source/commands/getseqscommand.cpp | 8 +-
source/commands/listseqscommand.cpp | 7 +-
source/commands/makebiomcommand.cpp | 8 +-
source/commands/makecontigscommand.cpp | 150 +-
source/commands/makecontigscommand.h | 792 +-
source/commands/makefilecommand.cpp | 129 +-
source/commands/makefilecommand.h | 3 +
source/commands/mergetaxsummarycommand.cpp | 35 +-
source/commands/mgclustercommand.cpp | 20 +-
source/commands/mgclustercommand.h | 2 +-
source/commands/pcrseqscommand.cpp | 7 +-
source/commands/phylotypecommand.cpp | 30 +-
source/commands/phylotypecommand.h | 2 -
source/commands/preclustercommand.cpp | 170 +-
source/commands/preclustercommand.h | 84 +-
source/commands/removegroupscommand.cpp | 6 +-
source/commands/removelineagecommand.cpp | 15 +-
source/commands/removeotulabelscommand.cpp | 9 +-
source/commands/removeotuscommand.cpp | 439 -
source/commands/removeotuscommand.h | 52 -
source/commands/removeseqscommand.cpp | 8 +-
source/commands/renamefilecommand.cpp | 19 +-
source/commands/screenseqscommand.cpp | 45 +-
source/commands/screenseqscommand.h | 2 +-
source/commands/sensspeccommand.cpp | 58 +-
source/commands/sensspeccommand.h | 3 +-
source/commands/setcurrentcommand.cpp | 18 +-
source/commands/setcurrentcommand.h | 2 +-
source/commands/setdircommand.cpp | 39 +-
source/commands/setdircommand.h | 2 +-
source/commands/sffinfocommand.cpp | 12 +-
source/commands/sffmultiplecommand.cpp | 16 +-
source/commands/sharedcommand.cpp | 8 +-
source/commands/shhhercommand.cpp | 32 +-
source/commands/shhhseqscommand.cpp | 3 +-
source/commands/shhhseqscommand.h | 3 +-
source/commands/sortseqscommand.cpp | 8 +-
source/commands/sparcccommand.cpp | 8 +-
source/commands/splitgroupscommand.cpp | 7 +-
source/commands/sracommand.cpp | 6 +-
source/commands/sracommand.h | 2 +-
source/commands/subsamplecommand.cpp | 4 +-
source/commands/summarytaxcommand.cpp | 113 +-
source/commands/summarytaxcommand.h | 1 +
source/datastructures/alignmentdb.cpp | 6 +-
source/datastructures/alignmentdb.h | 2 +-
source/datastructures/blastalign.cpp | 3 +-
source/datastructures/blastdb.cpp | 18 +-
source/datastructures/counttable.h | 2 +-
source/datastructures/kmerdb.cpp | 2 +-
source/datastructures/optimatrix.cpp | 445 +
source/datastructures/optimatrix.h | 60 +
source/datastructures/sequencecountparser.cpp | 169 +-
source/datastructures/sequencecountparser.h | 12 +-
source/datastructures/sequencedb.cpp | 54 -
source/datastructures/sequencedb.h | 2 -
source/datastructures/sequenceparser.cpp | 275 +-
source/datastructures/sequenceparser.h | 6 +-
source/engine.cpp | 18 +-
source/linearalgebra.cpp | 2 +-
source/makefile | 171 -
source/mothur.cpp | 7 +-
source/mothurout.cpp | 203 +-
source/mothurout.h | 19 +-
source/opticluster.cpp | 632 +
source/opticluster.h | 66 +
source/optionparser.cpp | 26 +-
source/read/splitmatrix.cpp | 13 +-
source/read/splitmatrix.h | 4 +-
source/singlelinkage.cpp | 1 -
source/trimoligos.h | 6 +
source/validparameter.cpp | 10 +-
source/vsearchfileparser.cpp | 5 +-
131 files changed, 56870 insertions(+), 4186 deletions(-)
diff --git a/.gitignore b/.gitignore
index 4e1c84e..0ad40e5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -9,6 +9,7 @@ xcuserdata
project.xcworkspace
*.xcuserdata
TARGET_BUILD_DIRTARGET_BUILD_DIR
+DerivedData
*.xcuserdata
*.xml
nbproject/
diff --git a/Makefile b/Makefile
index 88e837f..196ac52 100644
--- a/Makefile
+++ b/Makefile
@@ -15,8 +15,8 @@ USEBOOST ?= yes
BOOST_LIBRARY_DIR="\"Enter_your_boost_library_path_here\""
BOOST_INCLUDE_DIR="\"Enter_your_boost_include_path_here\""
MOTHUR_FILES="\"Enter_your_default_path_here\""
-RELEASE_DATE = "\"8/9/2016\""
-VERSION = "\"1.38.1\""
+RELEASE_DATE = "\"1/23/2017\""
+VERSION = "\"1.39.0\""
ifeq ($(strip $(64BIT_VERSION)),yes)
CXXFLAGS += -DBIT_VERSION
@@ -27,6 +27,9 @@ ifeq ($(strip $(OPTIMIZE)),yes)
CXXFLAGS += -O3
endif
+#CPP_11
+ CXXFLAGS += -std=c++11
+
CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION} -O3
ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 48a38e6..6806724 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,12 +7,10 @@
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@@ -367,13 +365,15 @@
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- 4846AD8A1D3810DD00DE9913 /* testtrimoligos.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 4846AD881D3810DD00DE9913 /* testtrimoligos.cpp */; };
+ 48576EA11D05DBC600BBC9C0 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 2114A7671C654D7400D3D8D9 /* averagelinkage.cpp */; };
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487C5A871AB88B93002AF48A /* mimarksattributescommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 487C5A851AB88B93002AF48A /* mimarksattributescommand.cpp */; };
- 487D09EB1CB2CEF3007039BF /* vsearchfileparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 489B55701BCD7F0100FB7DC8 /* vsearchfileparser.cpp */; };
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@@ -381,11 +381,16 @@
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@@ -399,8 +404,10 @@
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48EDB76C1D1320DD00F76E93 /* chimeravsearchcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48EDB76A1D1320DD00F76E93 /* chimeravsearchcommand.cpp */; };
+ 48F06CCD1D74BEC4004A45DD /* testphylotree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48F06CCB1D74BEC4004A45DD /* testphylotree.cpp */; };
48F98E4D1A9CFD670005E81B /* completelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 48F98E4C1A9CFD670005E81B /* completelinkage.cpp */; };
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@@ -777,12 +784,12 @@
};
8DD76FAF0486AB0100D96B5E /* CopyFiles */ = {
isa = PBXCopyFilesBuildPhase;
- buildActionMask = 8;
- dstPath = Users/SarahsWork/desktop/debug;
+ buildActionMask = 12;
+ dstPath = "";
dstSubfolderSpec = 16;
files = (
);
- runOnlyForDeploymentPostprocessing = 1;
+ runOnlyForDeploymentPostprocessing = 0;
};
/* End PBXCopyFilesBuildPhase section */
@@ -810,6 +817,10 @@
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@@ -825,6 +836,14 @@
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+ 48F06CCC1D74BEC4004A45DD /* testphylotree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; name = testphylotree.hpp; path = testclassifier/testphylotree.hpp; sourceTree = "<group>"; };
48F98E4C1A9CFD670005E81B /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = completelinkage.cpp; path = source/completelinkage.cpp; sourceTree = SOURCE_ROOT; };
7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; name = classifysvmsharedcommand.cpp; path = source/commands/classifysvmsharedcommand.cpp; sourceTree = SOURCE_ROOT; };
7B2181FF17AD777B00286E6A /* classifysvmsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; name = classifysvmsharedcommand.h; path = source/commands/classifysvmsharedcommand.h; sourceTree = SOURCE_ROOT; };
@@ -1658,6 +1679,8 @@
A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */,
A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */,
A7E9B77012D37EC400DA6239 /* observable.h */,
+ 48910D4C1D58CBFC00F60EDB /* opticluster.h */,
+ 48910D451D58CAD700F60EDB /* opticluster.cpp */,
A7E9B77512D37EC400DA6239 /* optionparser.cpp */,
A7E9B77612D37EC400DA6239 /* optionparser.h */,
A7E9B77B12D37EC400DA6239 /* overlap.cpp */,
@@ -1718,10 +1741,17 @@
children = (
481FB5201AC0A6B60076CFF3 /* catch.hpp */,
481FB51B1AC0A63E0076CFF3 /* main.cpp */,
+ 48F06CCA1D74BC6F004A45DD /* testclassifier */,
48D6E9691CA4262A008DF76B /* dataset.cpp */,
48D6E96A1CA4262A008DF76B /* dataset.h */,
+ 48910D4F1D58E26C00F60EDB /* distcdataset.h */,
+ 48910D501D58E26C00F60EDB /* distcdataset.cpp */,
+ 48576EA61D05F59300BBC9C0 /* distpdataset.cpp */,
+ 48576EA71D05F59300BBC9C0 /* distpdataset.h */,
4827A4DA1CB3ED2100345170 /* fastqdataset.cpp */,
4827A4DB1CB3ED2100345170 /* fastqdataset.h */,
+ 48910D4D1D58E26C00F60EDB /* testopticluster.cpp */,
+ 48910D4E1D58E26C00F60EDB /* testopticluster.h */,
4846AD881D3810DD00DE9913 /* testtrimoligos.cpp */,
4846AD891D3810DD00DE9913 /* testtrimoligos.hpp */,
48D6E9661CA42389008DF76B /* testvsearchfileparser.cpp */,
@@ -1757,12 +1787,23 @@
children = (
480E8DAF1CAB12ED00A0D137 /* testfastqread.cpp */,
480E8DB01CAB12ED00A0D137 /* testfastqread.h */,
+ 48576EA31D05E8F600BBC9C0 /* testoptimatrix.cpp */,
+ 48576EA41D05E8F600BBC9C0 /* testoptimatrix.h */,
48C728641B66A77800D40830 /* testsequence.cpp */,
48C728761B6AB4EE00D40830 /* testsequence.h */,
);
name = testcontainers;
sourceTree = "<group>";
};
+ 48F06CCA1D74BC6F004A45DD /* testclassifier */ = {
+ isa = PBXGroup;
+ children = (
+ 48F06CCB1D74BEC4004A45DD /* testphylotree.cpp */,
+ 48F06CCC1D74BEC4004A45DD /* testphylotree.hpp */,
+ );
+ name = testclassifier;
+ sourceTree = "<group>";
+ };
7B17437A17AF6F02004C161B /* svm */ = {
isa = PBXGroup;
children = (
@@ -2319,6 +2360,8 @@
A7E9B76012D37EC400DA6239 /* nameassignment.hpp */,
48705ABE19BE32C50075E977 /* oligos.h */,
48705ABD19BE32C50075E977 /* oligos.cpp */,
+ 48910D491D58CBA300F60EDB /* optimatrix.cpp */,
+ 48910D4A1D58CBA300F60EDB /* optimatrix.h */,
A7E9B77712D37EC400DA6239 /* ordervector.cpp */,
A7E9B77812D37EC400DA6239 /* ordervector.hpp */,
A7E9B79F12D37EC400DA6239 /* qualityscores.cpp */,
@@ -2537,7 +2580,7 @@
08FB7793FE84155DC02AAC07 /* Project object */ = {
isa = PBXProject;
attributes = {
- LastUpgradeCheck = 0620;
+ LastUpgradeCheck = 0730;
ORGANIZATIONNAME = "Schloss Lab";
TargetAttributes = {
481FB5181AC0A63E0076CFF3 = {
@@ -2588,6 +2631,7 @@
481FB64E1AC1B7F40076CFF3 /* treenode.cpp in Sources */,
481FB5801AC1B6EA0076CFF3 /* weighted.cpp in Sources */,
481FB54F1AC1B63A0076CFF3 /* memeuclidean.cpp in Sources */,
+ 48910D511D58E26C00F60EDB /* testopticluster.cpp in Sources */,
481FB5611AC1B69B0076CFF3 /* sharedjsd.cpp in Sources */,
481FB5AF1AC1B7300076CFF3 /* createdatabasecommand.cpp in Sources */,
481FB5731AC1B6EA0076CFF3 /* simpsoneven.cpp in Sources */,
@@ -2695,6 +2739,7 @@
481FB6651AC1B8450076CFF3 /* overlap.cpp in Sources */,
481FB6841AC1B8B80076CFF3 /* trimoligos.cpp in Sources */,
481FB6401AC1B7EA0076CFF3 /* sequencedb.cpp in Sources */,
+ 48576EA81D05F59300BBC9C0 /* distpdataset.cpp in Sources */,
481FB5C81AC1B74F0076CFF3 /* getseqscommand.cpp in Sources */,
481FB6011AC1B7970076CFF3 /* reversecommand.cpp in Sources */,
481FB55E1AC1B66D0076CFF3 /* sharedjackknife.cpp in Sources */,
@@ -2730,12 +2775,12 @@
481FB6811AC1B8960076CFF3 /* subsample.cpp in Sources */,
481FB5521AC1B6450076CFF3 /* odum.cpp in Sources */,
481FB68E1AC1BA9E0076CFF3 /* kmernode.cpp in Sources */,
+ 48C1DDC71D25C1BC00B5BA9D /* (null) in Sources */,
481FB5CE1AC1B75C0076CFF3 /* homovacommand.cpp in Sources */,
481FB6551AC1B8100076CFF3 /* heatmap.cpp in Sources */,
481FB5E61AC1B77E0076CFF3 /* normalizesharedcommand.cpp in Sources */,
481FB5E71AC1B77E0076CFF3 /* nmdscommand.cpp in Sources */,
481FB52B1AC1B09F0076CFF3 /* setseedcommand.cpp in Sources */,
- 4846AD8A1D3810DD00DE9913 /* testtrimoligos.cpp in Sources */,
481FB5261AC0ADA00076CFF3 /* sequence.cpp in Sources */,
481FB5C61AC1B74F0076CFF3 /* getrelabundcommand.cpp in Sources */,
481FB6571AC1B8100076CFF3 /* inputdata.cpp in Sources */,
@@ -2791,11 +2836,14 @@
481FB63B1AC1B7EA0076CFF3 /* rabundvector.cpp in Sources */,
481FB5A91AC1B7300076CFF3 /* collectsharedcommand.cpp in Sources */,
481FB6211AC1B7BA0076CFF3 /* communitytype.cpp in Sources */,
+ 48910D521D58E26C00F60EDB /* distcdataset.cpp in Sources */,
+ 48C1DDC61D25C1BC00B5BA9D /* (null) in Sources */,
481FB5621AC1B69E0076CFF3 /* sharedkstest.cpp in Sources */,
481FB5E91AC1B77E0076CFF3 /* otuhierarchycommand.cpp in Sources */,
481FB5351AC1B5D90076CFF3 /* fasta.cpp in Sources */,
481FB6321AC1B7EA0076CFF3 /* groupmap.cpp in Sources */,
481FB5FF1AC1B7970076CFF3 /* removeseqscommand.cpp in Sources */,
+ 48F06CCD1D74BEC4004A45DD /* testphylotree.cpp in Sources */,
481FB6771AC1B88F0076CFF3 /* readcluster.cpp in Sources */,
481FB5831AC1B6FF0076CFF3 /* ccode.cpp in Sources */,
481FB5681AC1B6B20076CFF3 /* sharedochiai.cpp in Sources */,
@@ -2848,15 +2896,14 @@
481FB6621AC1B8450076CFF3 /* noalign.cpp in Sources */,
481FB5E31AC1B77E0076CFF3 /* mgclustercommand.cpp in Sources */,
481FB5491AC1B6220076CFF3 /* invsimpson.cpp in Sources */,
+ 48576EA51D05E8F600BBC9C0 /* testoptimatrix.cpp in Sources */,
481FB5821AC1B6FF0076CFF3 /* bellerophon.cpp in Sources */,
481FB6731AC1B8820076CFF3 /* seqnoise.cpp in Sources */,
481FB5DC1AC1B75C0076CFF3 /* makelookupcommand.cpp in Sources */,
481FB53D1AC1B5F80076CFF3 /* bstick.cpp in Sources */,
- 480E8DB31CAB1F7900A0D137 /* averagelinkage.cpp in Sources */,
481FB6681AC1B8450076CFF3 /* rarecalc.cpp in Sources */,
481FB60B1AC1B7AC0076CFF3 /* sffmultiplecommand.cpp in Sources */,
481FB59F1AC1B71B0076CFF3 /* classifyrfsharedcommand.cpp in Sources */,
- 487D09EB1CB2CEF3007039BF /* vsearchfileparser.cpp in Sources */,
481FB5F51AC1B77E0076CFF3 /* primerdesigncommand.cpp in Sources */,
481FB5B41AC1B7300076CFF3 /* distancecommand.cpp in Sources */,
481FB5391AC1B5E90076CFF3 /* ace.cpp in Sources */,
@@ -2903,6 +2950,7 @@
481FB5C21AC1B74F0076CFF3 /* getoturepcommand.cpp in Sources */,
481FB5D01AC1B75C0076CFF3 /* kruskalwalliscommand.cpp in Sources */,
48B662031BBB1B6600997EE4 /* testrenameseqscommand.cpp in Sources */,
+ 48E418561D08893A004C36AB /* (null) in Sources */,
481FB5511AC1B6410076CFF3 /* npshannon.cpp in Sources */,
481FB6471AC1B7EA0076CFF3 /* sparsematrix.cpp in Sources */,
481FB5871AC1B6FF0076CFF3 /* decalc.cpp in Sources */,
@@ -2979,6 +3027,8 @@
A7E9B89F12D37EC400DA6239 /* chimeraslayercommand.cpp in Sources */,
A7E9B8A012D37EC400DA6239 /* chopseqscommand.cpp in Sources */,
A7E9B8A112D37EC400DA6239 /* classify.cpp in Sources */,
+ 48576EA21D05DBCD00BBC9C0 /* vsearchfileparser.cpp in Sources */,
+ 48910D461D58CAD700F60EDB /* opticluster.cpp in Sources */,
A7E9B8A212D37EC400DA6239 /* classifyotucommand.cpp in Sources */,
A7E9B8A312D37EC400DA6239 /* classifyseqscommand.cpp in Sources */,
A7E9B8A412D37EC400DA6239 /* clearcut.cpp in Sources */,
@@ -3014,7 +3064,6 @@
A7E9B8C212D37EC400DA6239 /* engine.cpp in Sources */,
A7E9B8C312D37EC400DA6239 /* fasta.cpp in Sources */,
A7E9B8C412D37EC400DA6239 /* fastamap.cpp in Sources */,
- 2114A7681C654D7400D3D8D9 /* averagelinkage.cpp in Sources */,
A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */,
A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */,
A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */,
@@ -3131,7 +3180,6 @@
A7E9B93A12D37EC400DA6239 /* secondarystructurecommand.cpp in Sources */,
A7E9B93B12D37EC400DA6239 /* sensspeccommand.cpp in Sources */,
A7E9B93C12D37EC400DA6239 /* seqerrorcommand.cpp in Sources */,
- 489B55721BCD7F0100FB7DC8 /* vsearchfileparser.cpp in Sources */,
A7E9B93D12D37EC400DA6239 /* seqsummarycommand.cpp in Sources */,
A7E9B93E12D37EC400DA6239 /* sequence.cpp in Sources */,
A7E9B93F12D37EC400DA6239 /* sequencedb.cpp in Sources */,
@@ -3140,6 +3188,7 @@
A7E9B94212D37EC400DA6239 /* sffinfocommand.cpp in Sources */,
A7E9B94312D37EC400DA6239 /* shannon.cpp in Sources */,
483C952E188F0CAD0035E7B7 /* (null) in Sources */,
+ 48910D4B1D58CBA300F60EDB /* optimatrix.cpp in Sources */,
A7E9B94412D37EC400DA6239 /* shannoneven.cpp in Sources */,
A7E9B94512D37EC400DA6239 /* sharedace.cpp in Sources */,
A7E9B94612D37EC400DA6239 /* sharedanderbergs.cpp in Sources */,
@@ -3289,6 +3338,7 @@
A7496D2E167B531B00CC7D7C /* kruskalwalliscommand.cpp in Sources */,
A79EEF8616971D4A0006DEC1 /* filtersharedcommand.cpp in Sources */,
A74C06E916A9C0A9008390A3 /* primerdesigncommand.cpp in Sources */,
+ 48576EA11D05DBC600BBC9C0 /* averagelinkage.cpp in Sources */,
A7128B1D16B7002A00723BE4 /* getdistscommand.cpp in Sources */,
A7B0231516B8244C006BA09E /* removedistscommand.cpp in Sources */,
A799314B16CBD0CD0017E888 /* mergetaxsummarycommand.cpp in Sources */,
@@ -3320,8 +3370,8 @@
isa = XCBuildConfiguration;
buildSettings = {
ALWAYS_SEARCH_USER_PATHS = YES;
- CLANG_CXX_LANGUAGE_STANDARD = "compiler-default";
- CLANG_CXX_LIBRARY = "compiler-default";
+ CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
+ CLANG_CXX_LIBRARY = "libstdc++";
CLANG_WARN_CXX0X_EXTENSIONS = YES;
"CLANG_WARN_CXX0X_EXTENSIONS[arch=*]" = NO;
CLANG_WARN_UNREACHABLE_CODE = YES;
@@ -3332,10 +3382,10 @@
"DYLIB_CURRENT_VERSION[sdk=*]" = "";
GCC_DYNAMIC_NO_PIC = NO;
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.38.1\\\"\"",
- "RELEASE_DATE=\"\\\"08/9/2016\\\"\"",
+ "VERSION=\"\\\"1.39.0\\\"\"",
+ "RELEASE_DATE=\"\\\"1/20/2017\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3359,18 +3409,18 @@
isa = XCBuildConfiguration;
buildSettings = {
ALWAYS_SEARCH_USER_PATHS = YES;
- CLANG_CXX_LANGUAGE_STANDARD = "compiler-default";
- CLANG_CXX_LIBRARY = "compiler-default";
+ CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
+ CLANG_CXX_LIBRARY = "libstdc++";
CLANG_WARN_CXX0X_EXTENSIONS = YES;
CLANG_WARN_UNREACHABLE_CODE = YES;
DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
DEPLOYMENT_LOCATION = YES;
DSTROOT = TARGET_BUILD_DIR;
GCC_MODEL_TUNING = G5;
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.38.1\\\"\"",
- "RELEASE_DATE=\"\\\"8/9/2016\\\"\"",
+ "VERSION=\"\\\"1.39.0\\\"\"",
+ "RELEASE_DATE=\"\\\"1/20/2017\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_WARN_ABOUT_MISSING_PROTOTYPES = NO;
@@ -3393,13 +3443,16 @@
1DEB928A08733DD80010E9CD /* Debug */ = {
isa = XCBuildConfiguration;
buildSettings = {
+ CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
+ CLANG_CXX_LIBRARY = "libstdc++";
CLANG_WARN_UNREACHABLE_CODE = YES;
DEPLOYMENT_LOCATION = NO;
+ ENABLE_TESTABILITY = YES;
GCC_C_LANGUAGE_STANDARD = c11;
GCC_ENABLE_SSE3_EXTENSIONS = NO;
GCC_ENABLE_SSE41_EXTENSIONS = NO;
GCC_ENABLE_SSE42_EXTENSIONS = NO;
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
"VERSION=\"\\\"1.36.0\\\"\"",
@@ -3418,11 +3471,14 @@
LIBRARY_SEARCH_PATHS = "";
"LIBRARY_SEARCH_PATHS[arch=*]" = /usr/local/lib/;
MACH_O_TYPE = mh_execute;
+ MACOSX_DEPLOYMENT_TARGET = 10.12;
ONLY_ACTIVE_ARCH = YES;
OTHER_CPLUSPLUSFLAGS = (
"-DBIT_VERSION",
"-DUSE_BOOST",
"-DUNIT_TEST",
+ "-stdlib=libstdc++",
+ "-std=c++11",
"-DUSE_READLINE",
"$(OTHER_CFLAGS)",
);
@@ -3440,15 +3496,17 @@
1DEB928B08733DD80010E9CD /* Release */ = {
isa = XCBuildConfiguration;
buildSettings = {
+ CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
+ CLANG_CXX_LIBRARY = "libstdc++";
CLANG_WARN_UNREACHABLE_CODE = YES;
DEPLOYMENT_LOCATION = NO;
GCC_C_LANGUAGE_STANDARD = c11;
GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
GCC_MODEL_TUNING = "";
- GCC_OPTIMIZATION_LEVEL = 0;
+ GCC_OPTIMIZATION_LEVEL = 3;
GCC_PREPROCESSOR_DEFINITIONS = (
- "VERSION=\"\\\"1.38.1\\\"\"",
- "RELEASE_DATE=\"\\\"8/9/2016\\\"\"",
+ "VERSION=\"\\\"1.39.0\\\"\"",
+ "RELEASE_DATE=\"\\\"1/20/2017\\\"\"",
"MOTHUR_FILES=\"\\\"/Users/sarahwestcott/desktop/release\\\"\"",
);
GCC_VERSION = "";
@@ -3469,10 +3527,13 @@
LIBRARY_SEARCH_PATHS = "";
"LIBRARY_SEARCH_PATHS[arch=*]" = /usr/local/lib/;
MACH_O_TYPE = mh_execute;
+ MACOSX_DEPLOYMENT_TARGET = 10.12;
OTHER_CPLUSPLUSFLAGS = (
"-DUSE_READLINE",
"-DUSE_BOOST",
"-DUNIT_TEST",
+ "-std=c++11",
+ "-stdlib=libstdc++",
"-DBIT_VERSION",
"$(OTHER_CFLAGS)",
);
@@ -3491,8 +3552,8 @@
isa = XCBuildConfiguration;
buildSettings = {
ALWAYS_SEARCH_USER_PATHS = YES;
- CLANG_CXX_LANGUAGE_STANDARD = "compiler-default";
- CLANG_CXX_LIBRARY = "compiler-default";
+ CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
+ CLANG_CXX_LIBRARY = "libstdc++";
CLANG_ENABLE_MODULES = YES;
CLANG_ENABLE_OBJC_ARC = YES;
CLANG_WARN_BOOL_CONVERSION = NO;
@@ -3517,11 +3578,11 @@
GCC_WARN_ABOUT_RETURN_TYPE = YES_ERROR;
GCC_WARN_UNDECLARED_SELECTOR = YES;
GCC_WARN_UNINITIALIZED_AUTOS = NO;
- MACOSX_DEPLOYMENT_TARGET = 10.9;
+ MACOSX_DEPLOYMENT_TARGET = 10.12;
MTL_ENABLE_DEBUG_INFO = YES;
ONLY_ACTIVE_ARCH = YES;
PRODUCT_NAME = "$(TARGET_NAME)";
- SDKROOT = macosx10.9;
+ SDKROOT = macosx;
};
name = Debug;
};
@@ -3529,8 +3590,8 @@
isa = XCBuildConfiguration;
buildSettings = {
ALWAYS_SEARCH_USER_PATHS = YES;
- CLANG_CXX_LANGUAGE_STANDARD = "compiler-default";
- CLANG_CXX_LIBRARY = "compiler-default";
+ CLANG_CXX_LANGUAGE_STANDARD = "c++0x";
+ CLANG_CXX_LIBRARY = "libstdc++";
CLANG_ENABLE_MODULES = YES;
CLANG_ENABLE_OBJC_ARC = YES;
CLANG_WARN_BOOL_CONVERSION = NO;
@@ -3554,11 +3615,11 @@
GCC_WARN_ABOUT_RETURN_TYPE = YES_ERROR;
GCC_WARN_UNDECLARED_SELECTOR = YES;
GCC_WARN_UNINITIALIZED_AUTOS = NO;
- MACOSX_DEPLOYMENT_TARGET = 10.9;
+ MACOSX_DEPLOYMENT_TARGET = 10.12;
MTL_ENABLE_DEBUG_INFO = NO;
ONLY_ACTIVE_ARCH = YES;
PRODUCT_NAME = "$(TARGET_NAME)";
- SDKROOT = macosx10.9;
+ SDKROOT = macosx;
};
name = Release;
};
diff --git a/README.md b/README.md
index 430d72a..444e8bd 100644
--- a/README.md
+++ b/README.md
@@ -1,4 +1,4 @@
-[](https://travis-ci.org/mothur/mothur)
+[](https://travis-ci.org/mothur/mothur)
# README
diff --git a/TestMothur/catch.hpp b/TestMothur/catch.hpp
old mode 100755
new mode 100644
index fbc526f..5ee3b29
--- a/TestMothur/catch.hpp
+++ b/TestMothur/catch.hpp
@@ -1,6 +1,6 @@
/*
- * CATCH v1.0 build 53 (master branch)
- * Generated: 2014-08-20 08:08:19.533804
+ * Catch v1.6.0
+ * Generated: 2017-01-11 16:38:09.405017
* ----------------------------------------------------------
* This file has been merged from multiple headers. Please don't edit it directly
* Copyright (c) 2012 Two Blue Cubes Ltd. All rights reserved.
@@ -10,35 +10,44 @@
*/
#ifndef TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED
#define TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED
-#define UNIT_TEST
#define TWOBLUECUBES_CATCH_HPP_INCLUDED
-// #included from: internal/catch_suppress_warnings.h
+#ifdef __clang__
+# pragma clang system_header
+#elif defined __GNUC__
+# pragma GCC system_header
+#endif
-#define TWOBLUECUBES_CATCH_SUPPRESS_WARNINGS_H_INCLUDED
+// #included from: internal/catch_suppress_warnings.h
#ifdef __clang__
-#pragma clang diagnostic ignored "-Wglobal-constructors"
-#pragma clang diagnostic ignored "-Wvariadic-macros"
-#pragma clang diagnostic ignored "-Wc99-extensions"
-#pragma clang diagnostic ignored "-Wunused-variable"
-#pragma clang diagnostic push
-#pragma clang diagnostic ignored "-Wpadded"
-#pragma clang diagnostic ignored "-Wc++98-compat"
-#pragma clang diagnostic ignored "-Wc++98-compat-pedantic"
+# ifdef __ICC // icpc defines the __clang__ macro
+# pragma warning(push)
+# pragma warning(disable: 161 1682)
+# else // __ICC
+# pragma clang diagnostic ignored "-Wglobal-constructors"
+# pragma clang diagnostic ignored "-Wvariadic-macros"
+# pragma clang diagnostic ignored "-Wc99-extensions"
+# pragma clang diagnostic ignored "-Wunused-variable"
+# pragma clang diagnostic push
+# pragma clang diagnostic ignored "-Wpadded"
+# pragma clang diagnostic ignored "-Wc++98-compat"
+# pragma clang diagnostic ignored "-Wc++98-compat-pedantic"
+# pragma clang diagnostic ignored "-Wswitch-enum"
+# pragma clang diagnostic ignored "-Wcovered-switch-default"
+# endif
#elif defined __GNUC__
-#pragma GCC diagnostic ignored "-Wvariadic-macros"
-#pragma GCC diagnostic ignored "-Wunused-variable"
-#pragma GCC diagnostic push
-#pragma GCC diagnostic ignored "-Wpadded"
+# pragma GCC diagnostic ignored "-Wvariadic-macros"
+# pragma GCC diagnostic ignored "-Wunused-variable"
+# pragma GCC diagnostic push
+# pragma GCC diagnostic ignored "-Wpadded"
#endif
-
-#ifdef CATCH_CONFIG_MAIN
-# define CATCH_CONFIG_RUNNER
+#if defined(CATCH_CONFIG_MAIN) || defined(CATCH_CONFIG_RUNNER)
+# define CATCH_IMPL
#endif
-#ifdef CATCH_CONFIG_RUNNER
+#ifdef CATCH_IMPL
# ifndef CLARA_CONFIG_MAIN
# define CLARA_CONFIG_MAIN_NOT_DEFINED
# define CLARA_CONFIG_MAIN
@@ -51,84 +60,101 @@
// #included from: catch_common.h
#define TWOBLUECUBES_CATCH_COMMON_H_INCLUDED
-#define INTERNAL_CATCH_UNIQUE_NAME_LINE2( name, line ) name##line
-#define INTERNAL_CATCH_UNIQUE_NAME_LINE( name, line ) INTERNAL_CATCH_UNIQUE_NAME_LINE2( name, line )
-#define INTERNAL_CATCH_UNIQUE_NAME( name ) INTERNAL_CATCH_UNIQUE_NAME_LINE( name, __LINE__ )
-
-#define INTERNAL_CATCH_STRINGIFY2( expr ) #expr
-#define INTERNAL_CATCH_STRINGIFY( expr ) INTERNAL_CATCH_STRINGIFY2( expr )
-
-#include <sstream>
-#include <stdexcept>
-#include <algorithm>
-
// #included from: catch_compiler_capabilities.h
#define TWOBLUECUBES_CATCH_COMPILER_CAPABILITIES_HPP_INCLUDED
-// Much of the following code is based on Boost (1.53)
+// Detect a number of compiler features - mostly C++11/14 conformance - by compiler
+// The following features are defined:
+//
+// CATCH_CONFIG_CPP11_NULLPTR : is nullptr supported?
+// CATCH_CONFIG_CPP11_NOEXCEPT : is noexcept supported?
+// CATCH_CONFIG_CPP11_GENERATED_METHODS : The delete and default keywords for compiler generated methods
+// CATCH_CONFIG_CPP11_IS_ENUM : std::is_enum is supported?
+// CATCH_CONFIG_CPP11_TUPLE : std::tuple is supported
+// CATCH_CONFIG_CPP11_LONG_LONG : is long long supported?
+// CATCH_CONFIG_CPP11_OVERRIDE : is override supported?
+// CATCH_CONFIG_CPP11_UNIQUE_PTR : is unique_ptr supported (otherwise use auto_ptr)
+
+// CATCH_CONFIG_CPP11_OR_GREATER : Is C++11 supported?
+
+// CATCH_CONFIG_VARIADIC_MACROS : are variadic macros supported?
+// CATCH_CONFIG_COUNTER : is the __COUNTER__ macro supported?
+// ****************
+// Note to maintainers: if new toggles are added please document them
+// in configuration.md, too
+// ****************
+
+// In general each macro has a _NO_<feature name> form
+// (e.g. CATCH_CONFIG_CPP11_NO_NULLPTR) which disables the feature.
+// Many features, at point of detection, define an _INTERNAL_ macro, so they
+// can be combined, en-mass, with the _NO_ forms later.
+
+// All the C++11 features can be disabled with CATCH_CONFIG_NO_CPP11
+
+//inline std::string toString( std::nullptr_t null ) {
+// return "nullptr";
+//}
+
+#ifdef __cplusplus
+
+# if __cplusplus >= 201103L
+# define CATCH_CPP11_OR_GREATER
+# endif
+
+# if __cplusplus >= 201402L
+# define CATCH_CPP14_OR_GREATER
+# endif
+
+#endif
#ifdef __clang__
# if __has_feature(cxx_nullptr)
-# define CATCH_CONFIG_CPP11_NULLPTR
+# define CATCH_INTERNAL_CONFIG_CPP11_NULLPTR
# endif
# if __has_feature(cxx_noexcept)
-# define CATCH_CONFIG_CPP11_NOEXCEPT
+# define CATCH_INTERNAL_CONFIG_CPP11_NOEXCEPT
# endif
+# if defined(CATCH_CPP11_OR_GREATER)
+# define CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS _Pragma( "clang diagnostic ignored \"-Wparentheses\"" )
+# endif
+
#endif // __clang__
////////////////////////////////////////////////////////////////////////////////
// Borland
#ifdef __BORLANDC__
-#if (__BORLANDC__ > 0x582 )
-//#define CATCH_CONFIG_SFINAE // Not confirmed
-#endif
-
#endif // __BORLANDC__
////////////////////////////////////////////////////////////////////////////////
// EDG
#ifdef __EDG_VERSION__
-#if (__EDG_VERSION__ > 238 )
-//#define CATCH_CONFIG_SFINAE // Not confirmed
-#endif
-
#endif // __EDG_VERSION__
////////////////////////////////////////////////////////////////////////////////
// Digital Mars
#ifdef __DMC__
-#if (__DMC__ > 0x840 )
-//#define CATCH_CONFIG_SFINAE // Not confirmed
-#endif
-
#endif // __DMC__
////////////////////////////////////////////////////////////////////////////////
// GCC
#ifdef __GNUC__
-#if __GNUC__ < 3
-
-#if (__GNUC_MINOR__ >= 96 )
-//#define CATCH_CONFIG_SFINAE
-#endif
-
-#elif __GNUC__ >= 3
+# if __GNUC__ == 4 && __GNUC_MINOR__ >= 6 && defined(__GXX_EXPERIMENTAL_CXX0X__)
+# define CATCH_INTERNAL_CONFIG_CPP11_NULLPTR
+# endif
-// #define CATCH_CONFIG_SFINAE // Taking this out completely for now
+# if !defined(CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS) && defined(CATCH_CPP11_OR_GREATER)
+# define CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS _Pragma( "GCC diagnostic ignored \"-Wparentheses\"" )
+# endif
-#endif // __GNUC__ < 3
-
-#if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ >= 6 && defined(__GXX_EXPERIMENTAL_CXX0X__) )
-
-#define CATCH_CONFIG_CPP11_NULLPTR
-#endif
+// - otherwise more recent versions define __cplusplus >= 201103L
+// and will get picked up below
#endif // __GNUC__
@@ -136,33 +162,123 @@
// Visual C++
#ifdef _MSC_VER
-#if (_MSC_VER >= 1310 ) // (VC++ 7.0+)
-//#define CATCH_CONFIG_SFINAE // Not confirmed
+#if (_MSC_VER >= 1600)
+# define CATCH_INTERNAL_CONFIG_CPP11_NULLPTR
+# define CATCH_INTERNAL_CONFIG_CPP11_UNIQUE_PTR
+#endif
+
+#if (_MSC_VER >= 1900 ) // (VC++ 13 (VS2015))
+#define CATCH_INTERNAL_CONFIG_CPP11_NOEXCEPT
+#define CATCH_INTERNAL_CONFIG_CPP11_GENERATED_METHODS
+#define CATCH_INTERNAL_CONFIG_CPP11_SHUFFLE
#endif
#endif // _MSC_VER
+////////////////////////////////////////////////////////////////////////////////
+
// Use variadic macros if the compiler supports them
#if ( defined _MSC_VER && _MSC_VER > 1400 && !defined __EDGE__) || \
( defined __WAVE__ && __WAVE_HAS_VARIADICS ) || \
( defined __GNUC__ && __GNUC__ >= 3 ) || \
( !defined __cplusplus && __STDC_VERSION__ >= 199901L || __cplusplus >= 201103L )
-#ifndef CATCH_CONFIG_NO_VARIADIC_MACROS
-#define CATCH_CONFIG_VARIADIC_MACROS
+#define CATCH_INTERNAL_CONFIG_VARIADIC_MACROS
+
#endif
+// Use __COUNTER__ if the compiler supports it
+#if ( defined _MSC_VER && _MSC_VER >= 1300 ) || \
+ ( defined __GNUC__ && __GNUC__ >= 4 && __GNUC_MINOR__ >= 3 ) || \
+ ( defined __clang__ && __clang_major__ >= 3 )
+
+#define CATCH_INTERNAL_CONFIG_COUNTER
+
#endif
////////////////////////////////////////////////////////////////////////////////
// C++ language feature support
-// detect language version:
-#if (__cplusplus == 201103L)
-# define CATCH_CPP11
-# define CATCH_CPP11_OR_GREATER
-#elif (__cplusplus >= 201103L)
-# define CATCH_CPP11_OR_GREATER
+// catch all support for C++11
+#if defined(CATCH_CPP11_OR_GREATER)
+
+# if !defined(CATCH_INTERNAL_CONFIG_CPP11_NULLPTR)
+# define CATCH_INTERNAL_CONFIG_CPP11_NULLPTR
+# endif
+
+# ifndef CATCH_INTERNAL_CONFIG_CPP11_NOEXCEPT
+# define CATCH_INTERNAL_CONFIG_CPP11_NOEXCEPT
+# endif
+
+# ifndef CATCH_INTERNAL_CONFIG_CPP11_GENERATED_METHODS
+# define CATCH_INTERNAL_CONFIG_CPP11_GENERATED_METHODS
+# endif
+
+# ifndef CATCH_INTERNAL_CONFIG_CPP11_IS_ENUM
+# define CATCH_INTERNAL_CONFIG_CPP11_IS_ENUM
+# endif
+
+# ifndef CATCH_INTERNAL_CONFIG_CPP11_TUPLE
+# define CATCH_INTERNAL_CONFIG_CPP11_TUPLE
+# endif
+
+# ifndef CATCH_INTERNAL_CONFIG_VARIADIC_MACROS
+# define CATCH_INTERNAL_CONFIG_VARIADIC_MACROS
+# endif
+
+# if !defined(CATCH_INTERNAL_CONFIG_CPP11_LONG_LONG)
+# define CATCH_INTERNAL_CONFIG_CPP11_LONG_LONG
+# endif
+
+# if !defined(CATCH_INTERNAL_CONFIG_CPP11_OVERRIDE)
+# define CATCH_INTERNAL_CONFIG_CPP11_OVERRIDE
+# endif
+# if !defined(CATCH_INTERNAL_CONFIG_CPP11_UNIQUE_PTR)
+# define CATCH_INTERNAL_CONFIG_CPP11_UNIQUE_PTR
+# endif
+# if !defined(CATCH_INTERNAL_CONFIG_CPP11_SHUFFLE)
+# define CATCH_INTERNAL_CONFIG_CPP11_SHUFFLE
+# endif
+
+#endif // __cplusplus >= 201103L
+
+// Now set the actual defines based on the above + anything the user has configured
+#if defined(CATCH_INTERNAL_CONFIG_CPP11_NULLPTR) && !defined(CATCH_CONFIG_CPP11_NO_NULLPTR) && !defined(CATCH_CONFIG_CPP11_NULLPTR) && !defined(CATCH_CONFIG_NO_CPP11)
+# define CATCH_CONFIG_CPP11_NULLPTR
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_CPP11_NOEXCEPT) && !defined(CATCH_CONFIG_CPP11_NO_NOEXCEPT) && !defined(CATCH_CONFIG_CPP11_NOEXCEPT) && !defined(CATCH_CONFIG_NO_CPP11)
+# define CATCH_CONFIG_CPP11_NOEXCEPT
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_CPP11_GENERATED_METHODS) && !defined(CATCH_CONFIG_CPP11_NO_GENERATED_METHODS) && !defined(CATCH_CONFIG_CPP11_GENERATED_METHODS) && !defined(CATCH_CONFIG_NO_CPP11)
+# define CATCH_CONFIG_CPP11_GENERATED_METHODS
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_CPP11_IS_ENUM) && !defined(CATCH_CONFIG_CPP11_NO_IS_ENUM) && !defined(CATCH_CONFIG_CPP11_IS_ENUM) && !defined(CATCH_CONFIG_NO_CPP11)
+# define CATCH_CONFIG_CPP11_IS_ENUM
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_CPP11_TUPLE) && !defined(CATCH_CONFIG_CPP11_NO_TUPLE) && !defined(CATCH_CONFIG_CPP11_TUPLE) && !defined(CATCH_CONFIG_NO_CPP11)
+# define CATCH_CONFIG_CPP11_TUPLE
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_VARIADIC_MACROS) && !defined(CATCH_CONFIG_NO_VARIADIC_MACROS) && !defined(CATCH_CONFIG_VARIADIC_MACROS)
+# define CATCH_CONFIG_VARIADIC_MACROS
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_CPP11_LONG_LONG) && !defined(CATCH_CONFIG_CPP11_NO_LONG_LONG) && !defined(CATCH_CONFIG_CPP11_LONG_LONG) && !defined(CATCH_CONFIG_NO_CPP11)
+# define CATCH_CONFIG_CPP11_LONG_LONG
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_CPP11_OVERRIDE) && !defined(CATCH_CONFIG_CPP11_NO_OVERRIDE) && !defined(CATCH_CONFIG_CPP11_OVERRIDE) && !defined(CATCH_CONFIG_NO_CPP11)
+# define CATCH_CONFIG_CPP11_OVERRIDE
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_CPP11_UNIQUE_PTR) && !defined(CATCH_CONFIG_CPP11_NO_UNIQUE_PTR) && !defined(CATCH_CONFIG_CPP11_UNIQUE_PTR) && !defined(CATCH_CONFIG_NO_CPP11)
+# define CATCH_CONFIG_CPP11_UNIQUE_PTR
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_COUNTER) && !defined(CATCH_CONFIG_NO_COUNTER) && !defined(CATCH_CONFIG_COUNTER)
+# define CATCH_CONFIG_COUNTER
+#endif
+#if defined(CATCH_INTERNAL_CONFIG_CPP11_SHUFFLE) && !defined(CATCH_CONFIG_CPP11_NO_SHUFFLE) && !defined(CATCH_CONFIG_CPP11_SHUFFLE) && !defined(CATCH_CONFIG_NO_CPP11)
+# define CATCH_CONFIG_CPP11_SHUFFLE
+#endif
+
+#if !defined(CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS)
+# define CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS
#endif
// noexcept support:
@@ -174,11 +290,62 @@
# define CATCH_NOEXCEPT_IS(x)
#endif
+// nullptr support
+#ifdef CATCH_CONFIG_CPP11_NULLPTR
+# define CATCH_NULL nullptr
+#else
+# define CATCH_NULL NULL
+#endif
+
+// override support
+#ifdef CATCH_CONFIG_CPP11_OVERRIDE
+# define CATCH_OVERRIDE override
+#else
+# define CATCH_OVERRIDE
+#endif
+
+// unique_ptr support
+#ifdef CATCH_CONFIG_CPP11_UNIQUE_PTR
+# define CATCH_AUTO_PTR( T ) std::unique_ptr<T>
+#else
+# define CATCH_AUTO_PTR( T ) std::auto_ptr<T>
+#endif
+
+#define INTERNAL_CATCH_UNIQUE_NAME_LINE2( name, line ) name##line
+#define INTERNAL_CATCH_UNIQUE_NAME_LINE( name, line ) INTERNAL_CATCH_UNIQUE_NAME_LINE2( name, line )
+#ifdef CATCH_CONFIG_COUNTER
+# define INTERNAL_CATCH_UNIQUE_NAME( name ) INTERNAL_CATCH_UNIQUE_NAME_LINE( name, __COUNTER__ )
+#else
+# define INTERNAL_CATCH_UNIQUE_NAME( name ) INTERNAL_CATCH_UNIQUE_NAME_LINE( name, __LINE__ )
+#endif
+
+#define INTERNAL_CATCH_STRINGIFY2( expr ) #expr
+#define INTERNAL_CATCH_STRINGIFY( expr ) INTERNAL_CATCH_STRINGIFY2( expr )
+
+#include <sstream>
+#include <stdexcept>
+#include <algorithm>
+
namespace Catch {
+ struct IConfig;
+
+ struct CaseSensitive { enum Choice {
+ Yes,
+ No
+ }; };
+
class NonCopyable {
- NonCopyable( NonCopyable const& );
- void operator = ( NonCopyable const& );
+#ifdef CATCH_CONFIG_CPP11_GENERATED_METHODS
+ NonCopyable( NonCopyable const& ) = delete;
+ NonCopyable( NonCopyable && ) = delete;
+ NonCopyable& operator = ( NonCopyable const& ) = delete;
+ NonCopyable& operator = ( NonCopyable && ) = delete;
+#else
+ NonCopyable( NonCopyable const& info );
+ NonCopyable& operator = ( NonCopyable const& );
+#endif
+
protected:
NonCopyable() {}
virtual ~NonCopyable();
@@ -216,6 +383,7 @@ namespace Catch {
void toLowerInPlace( std::string& s );
std::string toLower( std::string const& s );
std::string trim( std::string const& str );
+ bool replaceInPlace( std::string& str, std::string const& replaceThis, std::string const& withThis );
struct pluralise {
pluralise( std::size_t count, std::string const& label );
@@ -231,13 +399,14 @@ namespace Catch {
SourceLineInfo();
SourceLineInfo( char const* _file, std::size_t _line );
SourceLineInfo( SourceLineInfo const& other );
-# ifdef CATCH_CPP11_OR_GREATER
+# ifdef CATCH_CONFIG_CPP11_GENERATED_METHODS
SourceLineInfo( SourceLineInfo && ) = default;
SourceLineInfo& operator = ( SourceLineInfo const& ) = default;
SourceLineInfo& operator = ( SourceLineInfo && ) = default;
# endif
bool empty() const;
bool operator == ( SourceLineInfo const& other ) const;
+ bool operator < ( SourceLineInfo const& other ) const;
std::string file;
std::size_t line;
@@ -252,6 +421,9 @@ namespace Catch {
void throwLogicError( std::string const& message, SourceLineInfo const& locationInfo );
+ void seedRng( IConfig const& config );
+ unsigned int rngSeed();
+
// Use this in variadic streaming macros to allow
// >> +StreamEndStop
// as well as
@@ -337,7 +509,7 @@ namespace Catch {
template<typename T>
class Ptr {
public:
- Ptr() : m_p( NULL ){}
+ Ptr() : m_p( CATCH_NULL ){}
Ptr( T* p ) : m_p( p ){
if( m_p )
m_p->addRef();
@@ -353,7 +525,7 @@ namespace Catch {
void reset() {
if( m_p )
m_p->release();
- m_p = NULL;
+ m_p = CATCH_NULL;
}
Ptr& operator = ( T* p ){
Ptr temp( p );
@@ -366,12 +538,11 @@ namespace Catch {
return *this;
}
void swap( Ptr& other ) { std::swap( m_p, other.m_p ); }
- T* get() { return m_p; }
- const T* get() const{ return m_p; }
+ T* get() const{ return m_p; }
T& operator*() const { return *m_p; }
T* operator->() const { return m_p; }
- bool operator !() const { return m_p == NULL; }
- operator SafeBool::type() const { return SafeBool::makeSafe( m_p != NULL ); }
+ bool operator !() const { return m_p == CATCH_NULL; }
+ operator SafeBool::type() const { return SafeBool::makeSafe( m_p != CATCH_NULL ); }
private:
T* m_p;
@@ -468,9 +639,13 @@ namespace Catch {
struct ITestCaseRegistry {
virtual ~ITestCaseRegistry();
virtual std::vector<TestCase> const& getAllTests() const = 0;
- virtual void getFilteredTests( TestSpec const& testSpec, IConfig const& config, std::vector<TestCase>& matchingTestCases ) const = 0;
-
+ virtual std::vector<TestCase> const& getAllTestsSorted( IConfig const& config ) const = 0;
};
+
+ bool matchTest( TestCase const& testCase, TestSpec const& testSpec, IConfig const& config );
+ std::vector<TestCase> filterTests( std::vector<TestCase> const& testCases, TestSpec const& testSpec, IConfig const& config );
+ std::vector<TestCase> const& getAllTestCasesSorted( IConfig const& config );
+
}
namespace Catch {
@@ -503,27 +678,32 @@ struct NameAndDesc {
const char* description;
};
+void registerTestCase
+ ( ITestCase* testCase,
+ char const* className,
+ NameAndDesc const& nameAndDesc,
+ SourceLineInfo const& lineInfo );
+
struct AutoReg {
- AutoReg( TestFunction function,
- SourceLineInfo const& lineInfo,
- NameAndDesc const& nameAndDesc );
+ AutoReg
+ ( TestFunction function,
+ SourceLineInfo const& lineInfo,
+ NameAndDesc const& nameAndDesc );
template<typename C>
- AutoReg( void (C::*method)(),
- char const* className,
- NameAndDesc const& nameAndDesc,
- SourceLineInfo const& lineInfo ) {
- registerTestCase( new MethodTestCase<C>( method ),
- className,
- nameAndDesc,
- lineInfo );
- }
-
- void registerTestCase( ITestCase* testCase,
- char const* className,
- NameAndDesc const& nameAndDesc,
- SourceLineInfo const& lineInfo );
+ AutoReg
+ ( void (C::*method)(),
+ char const* className,
+ NameAndDesc const& nameAndDesc,
+ SourceLineInfo const& lineInfo ) {
+
+ registerTestCase
+ ( new MethodTestCase<C>( method ),
+ className,
+ nameAndDesc,
+ lineInfo );
+ }
~AutoReg();
@@ -532,50 +712,70 @@ private:
void operator= ( AutoReg const& );
};
+void registerTestCaseFunction
+ ( TestFunction function,
+ SourceLineInfo const& lineInfo,
+ NameAndDesc const& nameAndDesc );
+
} // end namespace Catch
#ifdef CATCH_CONFIG_VARIADIC_MACROS
///////////////////////////////////////////////////////////////////////////////
+ #define INTERNAL_CATCH_TESTCASE2( TestName, ... ) \
+ static void TestName(); \
+ namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( &TestName, CATCH_INTERNAL_LINEINFO, Catch::NameAndDesc( __VA_ARGS__ ) ); }\
+ static void TestName()
#define INTERNAL_CATCH_TESTCASE( ... ) \
- static void INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )(); \
- namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( &INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), CATCH_INTERNAL_LINEINFO, Catch::NameAndDesc( __VA_ARGS__ ) ); }\
- static void INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )()
+ INTERNAL_CATCH_TESTCASE2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), __VA_ARGS__ )
///////////////////////////////////////////////////////////////////////////////
#define INTERNAL_CATCH_METHOD_AS_TEST_CASE( QualifiedMethod, ... ) \
namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( &QualifiedMethod, "&" #QualifiedMethod, Catch::NameAndDesc( __VA_ARGS__ ), CATCH_INTERNAL_LINEINFO ); }
///////////////////////////////////////////////////////////////////////////////
- #define INTERNAL_CATCH_TEST_CASE_METHOD( ClassName, ... )\
+ #define INTERNAL_CATCH_TEST_CASE_METHOD2( TestName, ClassName, ... )\
namespace{ \
- struct INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ) : ClassName{ \
+ struct TestName : ClassName{ \
void test(); \
}; \
- Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar ) ( &INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )::test, #ClassName, Catch::NameAndDesc( __VA_ARGS__ ), CATCH_INTERNAL_LINEINFO ); \
+ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar ) ( &TestName::test, #ClassName, Catch::NameAndDesc( __VA_ARGS__ ), CATCH_INTERNAL_LINEINFO ); \
} \
- void INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )::test()
+ void TestName::test()
+ #define INTERNAL_CATCH_TEST_CASE_METHOD( ClassName, ... ) \
+ INTERNAL_CATCH_TEST_CASE_METHOD2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), ClassName, __VA_ARGS__ )
+
+ ///////////////////////////////////////////////////////////////////////////////
+ #define INTERNAL_CATCH_REGISTER_TESTCASE( Function, ... ) \
+ Catch::AutoReg( Function, CATCH_INTERNAL_LINEINFO, Catch::NameAndDesc( __VA_ARGS__ ) );
#else
///////////////////////////////////////////////////////////////////////////////
+ #define INTERNAL_CATCH_TESTCASE2( TestName, Name, Desc ) \
+ static void TestName(); \
+ namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( &TestName, CATCH_INTERNAL_LINEINFO, Catch::NameAndDesc( Name, Desc ) ); }\
+ static void TestName()
#define INTERNAL_CATCH_TESTCASE( Name, Desc ) \
- static void INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )(); \
- namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( &INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), CATCH_INTERNAL_LINEINFO, Catch::NameAndDesc( Name, Desc ) ); }\
- static void INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )()
+ INTERNAL_CATCH_TESTCASE2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), Name, Desc )
///////////////////////////////////////////////////////////////////////////////
#define INTERNAL_CATCH_METHOD_AS_TEST_CASE( QualifiedMethod, Name, Desc ) \
namespace{ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar )( &QualifiedMethod, "&" #QualifiedMethod, Catch::NameAndDesc( Name, Desc ), CATCH_INTERNAL_LINEINFO ); }
///////////////////////////////////////////////////////////////////////////////
- #define INTERNAL_CATCH_TEST_CASE_METHOD( ClassName, TestName, Desc )\
+ #define INTERNAL_CATCH_TEST_CASE_METHOD2( TestCaseName, ClassName, TestName, Desc )\
namespace{ \
- struct INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ) : ClassName{ \
+ struct TestCaseName : ClassName{ \
void test(); \
}; \
- Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar ) ( &INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )::test, #ClassName, Catch::NameAndDesc( TestName, Desc ), CATCH_INTERNAL_LINEINFO ); \
+ Catch::AutoReg INTERNAL_CATCH_UNIQUE_NAME( autoRegistrar ) ( &TestCaseName::test, #ClassName, Catch::NameAndDesc( TestName, Desc ), CATCH_INTERNAL_LINEINFO ); \
} \
- void INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ )::test()
+ void TestCaseName::test()
+ #define INTERNAL_CATCH_TEST_CASE_METHOD( ClassName, TestName, Desc )\
+ INTERNAL_CATCH_TEST_CASE_METHOD2( INTERNAL_CATCH_UNIQUE_NAME( ____C_A_T_C_H____T_E_S_T____ ), ClassName, TestName, Desc )
+ ///////////////////////////////////////////////////////////////////////////////
+ #define INTERNAL_CATCH_REGISTER_TESTCASE( Function, Name, Desc ) \
+ Catch::AutoReg( Function, CATCH_INTERNAL_LINEINFO, Catch::NameAndDesc( Name, Desc ) );
#endif
// #included from: internal/catch_capture.hpp
@@ -604,7 +804,9 @@ namespace Catch {
Exception = 0x100 | FailureBit,
ThrewException = Exception | 1,
- DidntThrowException = Exception | 2
+ DidntThrowException = Exception | 2,
+
+ FatalErrorCondition = 0x200 | FailureBit
}; };
@@ -617,11 +819,11 @@ namespace Catch {
// ResultDisposition::Flags enum
struct ResultDisposition { enum Flags {
- Normal = 0x00,
+ Normal = 0x01,
- ContinueOnFailure = 0x01, // Failures fail test, but execution continues
- FalseTest = 0x02, // Prefix expression with !
- SuppressFail = 0x04 // Failures are reported but do not fail the test
+ ContinueOnFailure = 0x02, // Failures fail test, but execution continues
+ FalseTest = 0x04, // Prefix expression with !
+ SuppressFail = 0x08 // Failures are reported but do not fail the test
}; };
inline ResultDisposition::Flags operator | ( ResultDisposition::Flags lhs, ResultDisposition::Flags rhs ) {
@@ -669,7 +871,7 @@ namespace Catch {
AssertionResult();
AssertionResult( AssertionInfo const& info, AssertionResultData const& data );
~AssertionResult();
-# ifdef CATCH_CPP11_OR_GREATER
+# ifdef CATCH_CONFIG_CPP11_GENERATED_METHODS
AssertionResult( AssertionResult const& ) = default;
AssertionResult( AssertionResult && ) = default;
AssertionResult& operator = ( AssertionResult const& ) = default;
@@ -696,6 +898,323 @@ namespace Catch {
} // end namespace Catch
+// #included from: catch_matchers.hpp
+#define TWOBLUECUBES_CATCH_MATCHERS_HPP_INCLUDED
+
+namespace Catch {
+namespace Matchers {
+ namespace Impl {
+
+ namespace Generic {
+ template<typename ExpressionT> class AllOf;
+ template<typename ExpressionT> class AnyOf;
+ template<typename ExpressionT> class Not;
+ }
+
+ template<typename ExpressionT>
+ struct Matcher : SharedImpl<IShared>
+ {
+ typedef ExpressionT ExpressionType;
+
+ virtual ~Matcher() {}
+ virtual Ptr<Matcher> clone() const = 0;
+ virtual bool match( ExpressionT const& expr ) const = 0;
+ virtual std::string toString() const = 0;
+
+ Generic::AllOf<ExpressionT> operator && ( Matcher<ExpressionT> const& other ) const;
+ Generic::AnyOf<ExpressionT> operator || ( Matcher<ExpressionT> const& other ) const;
+ Generic::Not<ExpressionT> operator ! () const;
+ };
+
+ template<typename DerivedT, typename ExpressionT>
+ struct MatcherImpl : Matcher<ExpressionT> {
+
+ virtual Ptr<Matcher<ExpressionT> > clone() const {
+ return Ptr<Matcher<ExpressionT> >( new DerivedT( static_cast<DerivedT const&>( *this ) ) );
+ }
+ };
+
+ namespace Generic {
+ template<typename ExpressionT>
+ class Not : public MatcherImpl<Not<ExpressionT>, ExpressionT> {
+ public:
+ explicit Not( Matcher<ExpressionT> const& matcher ) : m_matcher(matcher.clone()) {}
+ Not( Not const& other ) : m_matcher( other.m_matcher ) {}
+
+ virtual bool match( ExpressionT const& expr ) const CATCH_OVERRIDE {
+ return !m_matcher->match( expr );
+ }
+
+ virtual std::string toString() const CATCH_OVERRIDE {
+ return "not " + m_matcher->toString();
+ }
+ private:
+ Ptr< Matcher<ExpressionT> > m_matcher;
+ };
+
+ template<typename ExpressionT>
+ class AllOf : public MatcherImpl<AllOf<ExpressionT>, ExpressionT> {
+ public:
+
+ AllOf() {}
+ AllOf( AllOf const& other ) : m_matchers( other.m_matchers ) {}
+
+ AllOf& add( Matcher<ExpressionT> const& matcher ) {
+ m_matchers.push_back( matcher.clone() );
+ return *this;
+ }
+ virtual bool match( ExpressionT const& expr ) const
+ {
+ for( std::size_t i = 0; i < m_matchers.size(); ++i )
+ if( !m_matchers[i]->match( expr ) )
+ return false;
+ return true;
+ }
+ virtual std::string toString() const {
+ std::ostringstream oss;
+ oss << "( ";
+ for( std::size_t i = 0; i < m_matchers.size(); ++i ) {
+ if( i != 0 )
+ oss << " and ";
+ oss << m_matchers[i]->toString();
+ }
+ oss << " )";
+ return oss.str();
+ }
+
+ AllOf operator && ( Matcher<ExpressionT> const& other ) const {
+ AllOf allOfExpr( *this );
+ allOfExpr.add( other );
+ return allOfExpr;
+ }
+
+ private:
+ std::vector<Ptr<Matcher<ExpressionT> > > m_matchers;
+ };
+
+ template<typename ExpressionT>
+ class AnyOf : public MatcherImpl<AnyOf<ExpressionT>, ExpressionT> {
+ public:
+
+ AnyOf() {}
+ AnyOf( AnyOf const& other ) : m_matchers( other.m_matchers ) {}
+
+ AnyOf& add( Matcher<ExpressionT> const& matcher ) {
+ m_matchers.push_back( matcher.clone() );
+ return *this;
+ }
+ virtual bool match( ExpressionT const& expr ) const
+ {
+ for( std::size_t i = 0; i < m_matchers.size(); ++i )
+ if( m_matchers[i]->match( expr ) )
+ return true;
+ return false;
+ }
+ virtual std::string toString() const {
+ std::ostringstream oss;
+ oss << "( ";
+ for( std::size_t i = 0; i < m_matchers.size(); ++i ) {
+ if( i != 0 )
+ oss << " or ";
+ oss << m_matchers[i]->toString();
+ }
+ oss << " )";
+ return oss.str();
+ }
+
+ AnyOf operator || ( Matcher<ExpressionT> const& other ) const {
+ AnyOf anyOfExpr( *this );
+ anyOfExpr.add( other );
+ return anyOfExpr;
+ }
+
+ private:
+ std::vector<Ptr<Matcher<ExpressionT> > > m_matchers;
+ };
+
+ } // namespace Generic
+
+ template<typename ExpressionT>
+ Generic::AllOf<ExpressionT> Matcher<ExpressionT>::operator && ( Matcher<ExpressionT> const& other ) const {
+ Generic::AllOf<ExpressionT> allOfExpr;
+ allOfExpr.add( *this );
+ allOfExpr.add( other );
+ return allOfExpr;
+ }
+
+ template<typename ExpressionT>
+ Generic::AnyOf<ExpressionT> Matcher<ExpressionT>::operator || ( Matcher<ExpressionT> const& other ) const {
+ Generic::AnyOf<ExpressionT> anyOfExpr;
+ anyOfExpr.add( *this );
+ anyOfExpr.add( other );
+ return anyOfExpr;
+ }
+
+ template<typename ExpressionT>
+ Generic::Not<ExpressionT> Matcher<ExpressionT>::operator ! () const {
+ return Generic::Not<ExpressionT>( *this );
+ }
+
+ namespace StdString {
+
+ inline std::string makeString( std::string const& str ) { return str; }
+ inline std::string makeString( const char* str ) { return str ? std::string( str ) : std::string(); }
+
+ struct CasedString
+ {
+ CasedString( std::string const& str, CaseSensitive::Choice caseSensitivity )
+ : m_caseSensitivity( caseSensitivity ),
+ m_str( adjustString( str ) )
+ {}
+ std::string adjustString( std::string const& str ) const {
+ return m_caseSensitivity == CaseSensitive::No
+ ? toLower( str )
+ : str;
+
+ }
+ std::string toStringSuffix() const
+ {
+ return m_caseSensitivity == CaseSensitive::No
+ ? " (case insensitive)"
+ : "";
+ }
+ CaseSensitive::Choice m_caseSensitivity;
+ std::string m_str;
+ };
+
+ struct Equals : MatcherImpl<Equals, std::string> {
+ Equals( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes )
+ : m_data( str, caseSensitivity )
+ {}
+ Equals( Equals const& other ) : m_data( other.m_data ){}
+
+ virtual ~Equals();
+
+ virtual bool match( std::string const& expr ) const {
+ return m_data.m_str == m_data.adjustString( expr );;
+ }
+ virtual std::string toString() const {
+ return "equals: \"" + m_data.m_str + "\"" + m_data.toStringSuffix();
+ }
+
+ CasedString m_data;
+ };
+
+ struct Contains : MatcherImpl<Contains, std::string> {
+ Contains( std::string const& substr, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes )
+ : m_data( substr, caseSensitivity ){}
+ Contains( Contains const& other ) : m_data( other.m_data ){}
+
+ virtual ~Contains();
+
+ virtual bool match( std::string const& expr ) const {
+ return m_data.adjustString( expr ).find( m_data.m_str ) != std::string::npos;
+ }
+ virtual std::string toString() const {
+ return "contains: \"" + m_data.m_str + "\"" + m_data.toStringSuffix();
+ }
+
+ CasedString m_data;
+ };
+
+ struct StartsWith : MatcherImpl<StartsWith, std::string> {
+ StartsWith( std::string const& substr, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes )
+ : m_data( substr, caseSensitivity ){}
+
+ StartsWith( StartsWith const& other ) : m_data( other.m_data ){}
+
+ virtual ~StartsWith();
+
+ virtual bool match( std::string const& expr ) const {
+ return startsWith( m_data.adjustString( expr ), m_data.m_str );
+ }
+ virtual std::string toString() const {
+ return "starts with: \"" + m_data.m_str + "\"" + m_data.toStringSuffix();
+ }
+
+ CasedString m_data;
+ };
+
+ struct EndsWith : MatcherImpl<EndsWith, std::string> {
+ EndsWith( std::string const& substr, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes )
+ : m_data( substr, caseSensitivity ){}
+ EndsWith( EndsWith const& other ) : m_data( other.m_data ){}
+
+ virtual ~EndsWith();
+
+ virtual bool match( std::string const& expr ) const {
+ return endsWith( m_data.adjustString( expr ), m_data.m_str );
+ }
+ virtual std::string toString() const {
+ return "ends with: \"" + m_data.m_str + "\"" + m_data.toStringSuffix();
+ }
+
+ CasedString m_data;
+ };
+ } // namespace StdString
+ } // namespace Impl
+
+ // The following functions create the actual matcher objects.
+ // This allows the types to be inferred
+ template<typename ExpressionT>
+ inline Impl::Generic::Not<ExpressionT> Not( Impl::Matcher<ExpressionT> const& m ) {
+ return Impl::Generic::Not<ExpressionT>( m );
+ }
+
+ template<typename ExpressionT>
+ inline Impl::Generic::AllOf<ExpressionT> AllOf( Impl::Matcher<ExpressionT> const& m1,
+ Impl::Matcher<ExpressionT> const& m2 ) {
+ return Impl::Generic::AllOf<ExpressionT>().add( m1 ).add( m2 );
+ }
+ template<typename ExpressionT>
+ inline Impl::Generic::AllOf<ExpressionT> AllOf( Impl::Matcher<ExpressionT> const& m1,
+ Impl::Matcher<ExpressionT> const& m2,
+ Impl::Matcher<ExpressionT> const& m3 ) {
+ return Impl::Generic::AllOf<ExpressionT>().add( m1 ).add( m2 ).add( m3 );
+ }
+ template<typename ExpressionT>
+ inline Impl::Generic::AnyOf<ExpressionT> AnyOf( Impl::Matcher<ExpressionT> const& m1,
+ Impl::Matcher<ExpressionT> const& m2 ) {
+ return Impl::Generic::AnyOf<ExpressionT>().add( m1 ).add( m2 );
+ }
+ template<typename ExpressionT>
+ inline Impl::Generic::AnyOf<ExpressionT> AnyOf( Impl::Matcher<ExpressionT> const& m1,
+ Impl::Matcher<ExpressionT> const& m2,
+ Impl::Matcher<ExpressionT> const& m3 ) {
+ return Impl::Generic::AnyOf<ExpressionT>().add( m1 ).add( m2 ).add( m3 );
+ }
+
+ inline Impl::StdString::Equals Equals( std::string const& str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ) {
+ return Impl::StdString::Equals( str, caseSensitivity );
+ }
+ inline Impl::StdString::Equals Equals( const char* str, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ) {
+ return Impl::StdString::Equals( Impl::StdString::makeString( str ), caseSensitivity );
+ }
+ inline Impl::StdString::Contains Contains( std::string const& substr, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ) {
+ return Impl::StdString::Contains( substr, caseSensitivity );
+ }
+ inline Impl::StdString::Contains Contains( const char* substr, CaseSensitive::Choice caseSensitivity = CaseSensitive::Yes ) {
+ return Impl::StdString::Contains( Impl::StdString::makeString( substr ), caseSensitivity );
+ }
+ inline Impl::StdString::StartsWith StartsWith( std::string const& substr ) {
+ return Impl::StdString::StartsWith( substr );
+ }
+ inline Impl::StdString::StartsWith StartsWith( const char* substr ) {
+ return Impl::StdString::StartsWith( Impl::StdString::makeString( substr ) );
+ }
+ inline Impl::StdString::EndsWith EndsWith( std::string const& substr ) {
+ return Impl::StdString::EndsWith( substr );
+ }
+ inline Impl::StdString::EndsWith EndsWith( const char* substr ) {
+ return Impl::StdString::EndsWith( Impl::StdString::makeString( substr ) );
+ }
+
+} // namespace Matchers
+
+using namespace Matchers;
+
+} // namespace Catch
+
namespace Catch {
struct TestFailureException{};
@@ -722,11 +1241,12 @@ namespace Catch {
ResultBuilder( char const* macroName,
SourceLineInfo const& lineInfo,
char const* capturedExpression,
- ResultDisposition::Flags resultDisposition );
+ ResultDisposition::Flags resultDisposition,
+ char const* secondArg = "" );
template<typename T>
- ExpressionLhs<T const&> operator->* ( T const& operand );
- ExpressionLhs<bool> operator->* ( bool value );
+ ExpressionLhs<T const&> operator <= ( T const& operand );
+ ExpressionLhs<bool> operator <= ( bool value );
template<typename T>
ResultBuilder& operator << ( T const& value ) {
@@ -751,6 +1271,9 @@ namespace Catch {
void useActiveException( ResultDisposition::Flags resultDisposition = ResultDisposition::Normal );
void captureResult( ResultWas::OfType resultType );
void captureExpression();
+ void captureExpectedException( std::string const& expectedMessage );
+ void captureExpectedException( Matchers::Impl::Matcher<std::string> const& matcher );
+ void handleResult( AssertionResult const& result );
void react();
bool shouldDebugBreak() const;
bool allowThrows() const;
@@ -821,37 +1344,37 @@ namespace Internal {
template<typename T1, typename T2>
struct Evaluator<T1, T2, IsEqualTo> {
static bool evaluate( T1 const& lhs, T2 const& rhs) {
- return opCast( lhs ) == opCast( rhs );
+ return bool( opCast( lhs ) == opCast( rhs ) );
}
};
template<typename T1, typename T2>
struct Evaluator<T1, T2, IsNotEqualTo> {
static bool evaluate( T1 const& lhs, T2 const& rhs ) {
- return opCast( lhs ) != opCast( rhs );
+ return bool( opCast( lhs ) != opCast( rhs ) );
}
};
template<typename T1, typename T2>
struct Evaluator<T1, T2, IsLessThan> {
static bool evaluate( T1 const& lhs, T2 const& rhs ) {
- return opCast( lhs ) < opCast( rhs );
+ return bool( opCast( lhs ) < opCast( rhs ) );
}
};
template<typename T1, typename T2>
struct Evaluator<T1, T2, IsGreaterThan> {
static bool evaluate( T1 const& lhs, T2 const& rhs ) {
- return opCast( lhs ) > opCast( rhs );
+ return bool( opCast( lhs ) > opCast( rhs ) );
}
};
template<typename T1, typename T2>
struct Evaluator<T1, T2, IsGreaterThanOrEqualTo> {
static bool evaluate( T1 const& lhs, T2 const& rhs ) {
- return opCast( lhs ) >= opCast( rhs );
+ return bool( opCast( lhs ) >= opCast( rhs ) );
}
};
template<typename T1, typename T2>
struct Evaluator<T1, T2, IsLessThanOrEqualTo> {
static bool evaluate( T1 const& lhs, T2 const& rhs ) {
- return opCast( lhs ) <= opCast( rhs );
+ return bool( opCast( lhs ) <= opCast( rhs ) );
}
};
@@ -929,13 +1452,51 @@ namespace Internal {
return Evaluator<T*, T*, Op>::evaluate( lhs, reinterpret_cast<T*>( rhs ) );
}
+#ifdef CATCH_CONFIG_CPP11_LONG_LONG
+ // long long to unsigned X
+ template<Operator Op> bool compare( long long lhs, unsigned int rhs ) {
+ return applyEvaluator<Op>( static_cast<unsigned long>( lhs ), rhs );
+ }
+ template<Operator Op> bool compare( long long lhs, unsigned long rhs ) {
+ return applyEvaluator<Op>( static_cast<unsigned long>( lhs ), rhs );
+ }
+ template<Operator Op> bool compare( long long lhs, unsigned long long rhs ) {
+ return applyEvaluator<Op>( static_cast<unsigned long>( lhs ), rhs );
+ }
+ template<Operator Op> bool compare( long long lhs, unsigned char rhs ) {
+ return applyEvaluator<Op>( static_cast<unsigned long>( lhs ), rhs );
+ }
+
+ // unsigned long long to X
+ template<Operator Op> bool compare( unsigned long long lhs, int rhs ) {
+ return applyEvaluator<Op>( static_cast<long>( lhs ), rhs );
+ }
+ template<Operator Op> bool compare( unsigned long long lhs, long rhs ) {
+ return applyEvaluator<Op>( static_cast<long>( lhs ), rhs );
+ }
+ template<Operator Op> bool compare( unsigned long long lhs, long long rhs ) {
+ return applyEvaluator<Op>( static_cast<long>( lhs ), rhs );
+ }
+ template<Operator Op> bool compare( unsigned long long lhs, char rhs ) {
+ return applyEvaluator<Op>( static_cast<long>( lhs ), rhs );
+ }
+
+ // pointer to long long (when comparing against NULL)
+ template<Operator Op, typename T> bool compare( long long lhs, T* rhs ) {
+ return Evaluator<T*, T*, Op>::evaluate( reinterpret_cast<T*>( lhs ), rhs );
+ }
+ template<Operator Op, typename T> bool compare( T* lhs, long long rhs ) {
+ return Evaluator<T*, T*, Op>::evaluate( lhs, reinterpret_cast<T*>( rhs ) );
+ }
+#endif // CATCH_CONFIG_CPP11_LONG_LONG
+
#ifdef CATCH_CONFIG_CPP11_NULLPTR
// pointer to nullptr_t (when comparing against nullptr)
template<Operator Op, typename T> bool compare( std::nullptr_t, T* rhs ) {
- return Evaluator<T*, T*, Op>::evaluate( NULL, rhs );
+ return Evaluator<T*, T*, Op>::evaluate( nullptr, rhs );
}
template<Operator Op, typename T> bool compare( T* lhs, std::nullptr_t ) {
- return Evaluator<T*, T*, Op>::evaluate( lhs, NULL );
+ return Evaluator<T*, T*, Op>::evaluate( lhs, nullptr );
}
#endif // CATCH_CONFIG_CPP11_NULLPTR
@@ -949,40 +1510,6 @@ namespace Internal {
// #included from: catch_tostring.h
#define TWOBLUECUBES_CATCH_TOSTRING_H_INCLUDED
-// #included from: catch_sfinae.hpp
-#define TWOBLUECUBES_CATCH_SFINAE_HPP_INCLUDED
-
-// Try to detect if the current compiler supports SFINAE
-
-namespace Catch {
-
- struct TrueType {
- static const bool value = true;
- typedef void Enable;
- char sizer[1];
- };
- struct FalseType {
- static const bool value = false;
- typedef void Disable;
- char sizer[2];
- };
-
-#ifdef CATCH_CONFIG_SFINAE
-
- template<bool> struct NotABooleanExpression;
-
- template<bool c> struct If : NotABooleanExpression<c> {};
- template<> struct If<true> : TrueType {};
- template<> struct If<false> : FalseType {};
-
- template<int size> struct SizedIf;
- template<> struct SizedIf<sizeof(TrueType)> : TrueType {};
- template<> struct SizedIf<sizeof(FalseType)> : FalseType {};
-
-#endif // CATCH_CONFIG_SFINAE
-
-} // end namespace Catch
-
#include <sstream>
#include <iomanip>
#include <limits>
@@ -1035,35 +1562,64 @@ inline id performOptionalSelector( id obj, SEL sel ) {
#endif
+#ifdef CATCH_CONFIG_CPP11_TUPLE
+#include <tuple>
+#endif
+
+#ifdef CATCH_CONFIG_CPP11_IS_ENUM
+#include <type_traits>
+#endif
+
namespace Catch {
-namespace Detail {
-// SFINAE is currently disabled by default for all compilers.
-// If the non SFINAE version of IsStreamInsertable is ambiguous for you
-// and your compiler supports SFINAE, try #defining CATCH_CONFIG_SFINAE
-#ifdef CATCH_CONFIG_SFINAE
+// Why we're here.
+template<typename T>
+std::string toString( T const& value );
- template<typename T>
- class IsStreamInsertableHelper {
- template<int N> struct TrueIfSizeable : TrueType {};
+// Built in overloads
- template<typename T2>
- static TrueIfSizeable<sizeof((*(std::ostream*)0) << *((T2 const*)0))> dummy(T2*);
- static FalseType dummy(...);
+std::string toString( std::string const& value );
+std::string toString( std::wstring const& value );
+std::string toString( const char* const value );
+std::string toString( char* const value );
+std::string toString( const wchar_t* const value );
+std::string toString( wchar_t* const value );
+std::string toString( int value );
+std::string toString( unsigned long value );
+std::string toString( unsigned int value );
+std::string toString( const double value );
+std::string toString( const float value );
+std::string toString( bool value );
+std::string toString( char value );
+std::string toString( signed char value );
+std::string toString( unsigned char value );
- public:
- typedef SizedIf<sizeof(dummy((T*)0))> type;
- };
+#ifdef CATCH_CONFIG_CPP11_LONG_LONG
+std::string toString( long long value );
+std::string toString( unsigned long long value );
+#endif
- template<typename T>
- struct IsStreamInsertable : IsStreamInsertableHelper<T>::type {};
+#ifdef CATCH_CONFIG_CPP11_NULLPTR
+std::string toString( std::nullptr_t );
+#endif
-#else
+#ifdef __OBJC__
+ std::string toString( NSString const * const& nsstring );
+ std::string toString( NSString * CATCH_ARC_STRONG const& nsstring );
+ std::string toString( NSObject* const& nsObject );
+#endif
+
+namespace Detail {
+
+ extern const std::string unprintableString;
struct BorgType {
template<typename T> BorgType( T const& );
};
+ struct TrueType { char sizer[1]; };
+ struct FalseType { char sizer[2]; };
+
TrueType& testStreamable( std::ostream& );
FalseType testStreamable( FalseType );
@@ -1076,12 +1632,38 @@ namespace Detail {
enum { value = sizeof( testStreamable(s << t) ) == sizeof( TrueType ) };
};
-#endif
+#if defined(CATCH_CONFIG_CPP11_IS_ENUM)
+ template<typename T,
+ bool IsEnum = std::is_enum<T>::value
+ >
+ struct EnumStringMaker
+ {
+ static std::string convert( T const& ) { return unprintableString; }
+ };
+ template<typename T>
+ struct EnumStringMaker<T,true>
+ {
+ static std::string convert( T const& v )
+ {
+ return ::Catch::toString(
+ static_cast<typename std::underlying_type<T>::type>(v)
+ );
+ }
+ };
+#endif
template<bool C>
struct StringMakerBase {
+#if defined(CATCH_CONFIG_CPP11_IS_ENUM)
+ template<typename T>
+ static std::string convert( T const& v )
+ {
+ return EnumStringMaker<T>::convert( v );
+ }
+#else
template<typename T>
- static std::string convert( T const& ) { return "{?}"; }
+ static std::string convert( T const& ) { return unprintableString; }
+#endif
};
template<>
@@ -1104,9 +1686,6 @@ namespace Detail {
} // end namespace Detail
template<typename T>
-std::string toString( T const& value );
-
-template<typename T>
struct StringMaker :
Detail::StringMakerBase<Detail::IsStreamInsertable<T>::value> {};
@@ -1115,7 +1694,7 @@ struct StringMaker<T*> {
template<typename U>
static std::string convert( U* p ) {
if( !p )
- return INTERNAL_CATCH_STRINGIFY( NULL );
+ return "NULL";
else
return Detail::rawMemoryToString( p );
}
@@ -1125,7 +1704,7 @@ template<typename R, typename C>
struct StringMaker<R C::*> {
static std::string convert( R C::* p ) {
if( !p )
- return INTERNAL_CATCH_STRINGIFY( NULL );
+ return "NULL";
else
return Detail::rawMemoryToString( p );
}
@@ -1136,12 +1715,59 @@ namespace Detail {
std::string rangeToString( InputIterator first, InputIterator last );
}
+//template<typename T, typename Allocator>
+//struct StringMaker<std::vector<T, Allocator> > {
+// static std::string convert( std::vector<T,Allocator> const& v ) {
+// return Detail::rangeToString( v.begin(), v.end() );
+// }
+//};
+
template<typename T, typename Allocator>
-struct StringMaker<std::vector<T, Allocator> > {
- static std::string convert( std::vector<T,Allocator> const& v ) {
- return Detail::rangeToString( v.begin(), v.end() );
+std::string toString( std::vector<T,Allocator> const& v ) {
+ return Detail::rangeToString( v.begin(), v.end() );
+}
+
+#ifdef CATCH_CONFIG_CPP11_TUPLE
+
+// toString for tuples
+namespace TupleDetail {
+ template<
+ typename Tuple,
+ std::size_t N = 0,
+ bool = (N < std::tuple_size<Tuple>::value)
+ >
+ struct ElementPrinter {
+ static void print( const Tuple& tuple, std::ostream& os )
+ {
+ os << ( N ? ", " : " " )
+ << Catch::toString(std::get<N>(tuple));
+ ElementPrinter<Tuple,N+1>::print(tuple,os);
+ }
+ };
+
+ template<
+ typename Tuple,
+ std::size_t N
+ >
+ struct ElementPrinter<Tuple,N,false> {
+ static void print( const Tuple&, std::ostream& ) {}
+ };
+
+}
+
+template<typename ...Types>
+struct StringMaker<std::tuple<Types...>> {
+
+ static std::string convert( const std::tuple<Types...>& tuple )
+ {
+ std::ostringstream os;
+ os << '{';
+ TupleDetail::ElementPrinter<std::tuple<Types...>>::print( tuple, os );
+ os << " }";
+ return os.str();
}
};
+#endif // CATCH_CONFIG_CPP11_TUPLE
namespace Detail {
template<typename T>
@@ -1162,44 +1788,15 @@ std::string toString( T const& value ) {
return StringMaker<T>::convert( value );
}
-// Built in overloads
-
-std::string toString( std::string const& value );
-std::string toString( std::wstring const& value );
-std::string toString( const char* const value );
-std::string toString( char* const value );
-std::string toString( const wchar_t* const value );
-std::string toString( wchar_t* const value );
-std::string toString( int value );
-std::string toString( unsigned long value );
-std::string toString( unsigned int value );
-std::string toString( const double value );
-std::string toString( const float value );
-std::string toString( bool value );
-std::string toString( char value );
-std::string toString( signed char value );
-std::string toString( unsigned char value );
-
-#ifdef CATCH_CONFIG_CPP11_NULLPTR
-std::string toString( std::nullptr_t );
-#endif
-
-#ifdef __OBJC__
- std::string toString( NSString const * const& nsstring );
- std::string toString( NSString * CATCH_ARC_STRONG const& nsstring );
- std::string toString( NSObject* const& nsObject );
-#endif
-
namespace Detail {
template<typename InputIterator>
std::string rangeToString( InputIterator first, InputIterator last ) {
std::ostringstream oss;
oss << "{ ";
if( first != last ) {
- oss << toString( *first );
- for( ++first ; first != last ; ++first ) {
- oss << ", " << toString( *first );
- }
+ oss << Catch::toString( *first );
+ for( ++first ; first != last ; ++first )
+ oss << ", " << Catch::toString( *first );
}
oss << " }";
return oss.str();
@@ -1215,13 +1812,13 @@ namespace Catch {
template<typename T>
class ExpressionLhs {
ExpressionLhs& operator = ( ExpressionLhs const& );
-# ifdef CATCH_CPP11_OR_GREATER
+# ifdef CATCH_CONFIG_CPP11_GENERATED_METHODS
ExpressionLhs& operator = ( ExpressionLhs && ) = delete;
# endif
public:
ExpressionLhs( ResultBuilder& rb, T lhs ) : m_rb( rb ), m_lhs( lhs ) {}
-# ifdef CATCH_CPP11_OR_GREATER
+# ifdef CATCH_CONFIG_CPP11_GENERATED_METHODS
ExpressionLhs( ExpressionLhs const& ) = default;
ExpressionLhs( ExpressionLhs && ) = default;
# endif
@@ -1302,11 +1899,11 @@ private:
namespace Catch {
template<typename T>
- inline ExpressionLhs<T const&> ResultBuilder::operator->* ( T const& operand ) {
+ inline ExpressionLhs<T const&> ResultBuilder::operator <= ( T const& operand ) {
return ExpressionLhs<T const&>( *this, operand );
}
- inline ExpressionLhs<bool> ResultBuilder::operator->* ( bool value ) {
+ inline ExpressionLhs<bool> ResultBuilder::operator <= ( bool value ) {
return ExpressionLhs<bool>( *this, value );
}
@@ -1379,6 +1976,7 @@ namespace Catch {
class AssertionResult;
struct AssertionInfo;
struct SectionInfo;
+ struct SectionEndInfo;
struct MessageInfo;
class ScopedMessageBuilder;
struct Counts;
@@ -1390,12 +1988,15 @@ namespace Catch {
virtual void assertionEnded( AssertionResult const& result ) = 0;
virtual bool sectionStarted( SectionInfo const& sectionInfo,
Counts& assertions ) = 0;
- virtual void sectionEnded( SectionInfo const& name, Counts const& assertions, double _durationInSeconds ) = 0;
+ virtual void sectionEnded( SectionEndInfo const& endInfo ) = 0;
+ virtual void sectionEndedEarly( SectionEndInfo const& endInfo ) = 0;
virtual void pushScopedMessage( MessageInfo const& message ) = 0;
virtual void popScopedMessage( MessageInfo const& message ) = 0;
virtual std::string getCurrentTestName() const = 0;
virtual const AssertionResult* getLastResult() const = 0;
+
+ virtual void handleFatalErrorCondition( std::string const& message ) = 0;
};
IResultCapture& getResultCapture();
@@ -1476,13 +2077,14 @@ namespace Catch {
do { \
Catch::ResultBuilder __catchResult( macroName, CATCH_INTERNAL_LINEINFO, #expr, resultDisposition ); \
try { \
- ( __catchResult->*expr ).endExpression(); \
+ CATCH_INTERNAL_SUPPRESS_PARENTHESES_WARNINGS \
+ ( __catchResult <= expr ).endExpression(); \
} \
catch( ... ) { \
__catchResult.useActiveException( Catch::ResultDisposition::Normal ); \
} \
INTERNAL_CATCH_REACT( __catchResult ) \
- } while( Catch::isTrue( false && (expr) ) ) // expr here is never evaluated at runtime but it forces the compiler to give it a look
+ } while( Catch::isTrue( false && !!(expr) ) ) // expr here is never evaluated at runtime but it forces the compiler to give it a look
///////////////////////////////////////////////////////////////////////////////
#define INTERNAL_CATCH_IF( expr, resultDisposition, macroName ) \
@@ -1509,16 +2111,16 @@ namespace Catch {
} while( Catch::alwaysFalse() )
///////////////////////////////////////////////////////////////////////////////
-#define INTERNAL_CATCH_THROWS( expr, resultDisposition, macroName ) \
+#define INTERNAL_CATCH_THROWS( expr, resultDisposition, matcher, macroName ) \
do { \
- Catch::ResultBuilder __catchResult( macroName, CATCH_INTERNAL_LINEINFO, #expr, resultDisposition ); \
+ Catch::ResultBuilder __catchResult( macroName, CATCH_INTERNAL_LINEINFO, #expr, resultDisposition, #matcher ); \
if( __catchResult.allowThrows() ) \
try { \
expr; \
__catchResult.captureResult( Catch::ResultWas::DidntThrowException ); \
} \
catch( ... ) { \
- __catchResult.captureResult( Catch::ResultWas::Ok ); \
+ __catchResult.captureExpectedException( matcher ); \
} \
else \
__catchResult.captureResult( Catch::ResultWas::Ok ); \
@@ -1571,14 +2173,14 @@ namespace Catch {
///////////////////////////////////////////////////////////////////////////////
#define INTERNAL_CHECK_THAT( arg, matcher, resultDisposition, macroName ) \
do { \
- Catch::ResultBuilder __catchResult( macroName, CATCH_INTERNAL_LINEINFO, #arg " " #matcher, resultDisposition ); \
+ Catch::ResultBuilder __catchResult( macroName, CATCH_INTERNAL_LINEINFO, #arg ", " #matcher, resultDisposition ); \
try { \
- std::string matcherAsString = ::Catch::Matchers::matcher.toString(); \
+ std::string matcherAsString = (matcher).toString(); \
__catchResult \
.setLhs( Catch::toString( arg ) ) \
- .setRhs( matcherAsString == "{?}" ? #matcher : matcherAsString ) \
+ .setRhs( matcherAsString == Catch::Detail::unprintableString ? #matcher : matcherAsString ) \
.setOp( "matches" ) \
- .setResultType( ::Catch::Matchers::matcher.match( arg ) ); \
+ .setResultType( (matcher).match( arg ) ); \
__catchResult.captureExpression(); \
} catch( ... ) { \
__catchResult.useActiveException( resultDisposition | Catch::ResultDisposition::ContinueOnFailure ); \
@@ -1592,21 +2194,6 @@ namespace Catch {
// #included from: catch_section_info.h
#define TWOBLUECUBES_CATCH_SECTION_INFO_H_INCLUDED
-namespace Catch {
-
- struct SectionInfo {
- SectionInfo
- ( SourceLineInfo const& _lineInfo,
- std::string const& _name,
- std::string const& _description = std::string() );
-
- std::string name;
- std::string description;
- SourceLineInfo lineInfo;
- };
-
-} // end namespace Catch
-
// #included from: catch_totals.hpp
#define TWOBLUECUBES_CATCH_TOTALS_HPP_INCLUDED
@@ -1637,6 +2224,9 @@ namespace Catch {
bool allPassed() const {
return failed == 0 && failedButOk == 0;
}
+ bool allOk() const {
+ return failed == 0;
+ }
std::size_t passed;
std::size_t failed;
@@ -1674,6 +2264,31 @@ namespace Catch {
};
}
+namespace Catch {
+
+ struct SectionInfo {
+ SectionInfo
+ ( SourceLineInfo const& _lineInfo,
+ std::string const& _name,
+ std::string const& _description = std::string() );
+
+ std::string name;
+ std::string description;
+ SourceLineInfo lineInfo;
+ };
+
+ struct SectionEndInfo {
+ SectionEndInfo( SectionInfo const& _sectionInfo, Counts const& _prevAssertions, double _durationInSeconds )
+ : sectionInfo( _sectionInfo ), prevAssertions( _prevAssertions ), durationInSeconds( _durationInSeconds )
+ {}
+
+ SectionInfo sectionInfo;
+ Counts prevAssertions;
+ double durationInSeconds;
+ };
+
+} // end namespace Catch
+
// #included from: catch_timer.h
#define TWOBLUECUBES_CATCH_TIMER_H_INCLUDED
@@ -1689,7 +2304,7 @@ namespace Catch {
public:
Timer() : m_ticks( 0 ) {}
void start();
- unsigned int getElapsedNanoseconds() const;
+ unsigned int getElapsedMicroseconds() const;
unsigned int getElapsedMilliseconds() const;
double getElapsedSeconds() const;
@@ -1703,7 +2318,7 @@ namespace Catch {
namespace Catch {
- class Section {
+ class Section : NonCopyable {
public:
Section( SectionInfo const& info );
~Section();
@@ -1712,15 +2327,6 @@ namespace Catch {
operator bool() const;
private:
-#ifdef CATCH_CPP11_OR_GREATER
- Section( Section const& ) = delete;
- Section( Section && ) = delete;
- Section& operator = ( Section const& ) = delete;
- Section& operator = ( Section && ) = delete;
-#else
- Section( Section const& info );
- Section& operator = ( Section const& );
-#endif
SectionInfo m_info;
std::string m_name;
@@ -1923,6 +2529,8 @@ using namespace Generators;
#define TWOBLUECUBES_CATCH_INTERFACES_EXCEPTION_H_INCLUDED
#include <string>
+#include <vector>
+
// #included from: catch_interfaces_registry_hub.h
#define TWOBLUECUBES_CATCH_INTERFACES_REGISTRY_HUB_H_INCLUDED
@@ -1947,7 +2555,8 @@ namespace Catch {
struct IMutableRegistryHub {
virtual ~IMutableRegistryHub();
- virtual void registerReporter( std::string const& name, IReporterFactory* factory ) = 0;
+ virtual void registerReporter( std::string const& name, Ptr<IReporterFactory> const& factory ) = 0;
+ virtual void registerListener( Ptr<IReporterFactory> const& factory ) = 0;
virtual void registerTest( TestCase const& testInfo ) = 0;
virtual void registerTranslator( const IExceptionTranslator* translator ) = 0;
};
@@ -1959,14 +2568,16 @@ namespace Catch {
}
-
namespace Catch {
typedef std::string(*exceptionTranslateFunction)();
+ struct IExceptionTranslator;
+ typedef std::vector<const IExceptionTranslator*> ExceptionTranslators;
+
struct IExceptionTranslator {
virtual ~IExceptionTranslator();
- virtual std::string translate() const = 0;
+ virtual std::string translate( ExceptionTranslators::const_iterator it, ExceptionTranslators::const_iterator itEnd ) const = 0;
};
struct IExceptionTranslatorRegistry {
@@ -1984,9 +2595,12 @@ namespace Catch {
: m_translateFunction( translateFunction )
{}
- virtual std::string translate() const {
+ virtual std::string translate( ExceptionTranslators::const_iterator it, ExceptionTranslators::const_iterator itEnd ) const CATCH_OVERRIDE {
try {
- throw;
+ if( it == itEnd )
+ throw;
+ else
+ return (*it)->translate( it+1, itEnd );
}
catch( T& ex ) {
return m_translateFunction( ex );
@@ -2007,10 +2621,12 @@ namespace Catch {
}
///////////////////////////////////////////////////////////////////////////////
-#define INTERNAL_CATCH_TRANSLATE_EXCEPTION( signature ) \
- static std::string INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionTranslator )( signature ); \
- namespace{ Catch::ExceptionTranslatorRegistrar INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionRegistrar )( &INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionTranslator ) ); }\
- static std::string INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionTranslator )( signature )
+#define INTERNAL_CATCH_TRANSLATE_EXCEPTION2( translatorName, signature ) \
+ static std::string translatorName( signature ); \
+ namespace{ Catch::ExceptionTranslatorRegistrar INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionRegistrar )( &translatorName ); }\
+ static std::string translatorName( signature )
+
+#define INTERNAL_CATCH_TRANSLATE_EXCEPTION( signature ) INTERNAL_CATCH_TRANSLATE_EXCEPTION2( INTERNAL_CATCH_UNIQUE_NAME( catch_internal_ExceptionTranslator ), signature )
// #included from: internal/catch_approx.hpp
#define TWOBLUECUBES_CATCH_APPROX_HPP_INCLUDED
@@ -2060,263 +2676,58 @@ namespace Detail {
}
friend bool operator != ( Approx const& lhs, double rhs ) {
- return !operator==( rhs, lhs );
- }
-
- Approx& epsilon( double newEpsilon ) {
- m_epsilon = newEpsilon;
- return *this;
- }
-
- Approx& scale( double newScale ) {
- m_scale = newScale;
- return *this;
- }
-
- std::string toString() const {
- std::ostringstream oss;
- oss << "Approx( " << Catch::toString( m_value ) << " )";
- return oss.str();
- }
-
- private:
- double m_epsilon;
- double m_scale;
- double m_value;
- };
-}
-
-template<>
-inline std::string toString<Detail::Approx>( Detail::Approx const& value ) {
- return value.toString();
-}
-
-} // end namespace Catch
-
-// #included from: internal/catch_matchers.hpp
-#define TWOBLUECUBES_CATCH_MATCHERS_HPP_INCLUDED
-
-namespace Catch {
-namespace Matchers {
- namespace Impl {
-
- template<typename ExpressionT>
- struct Matcher : SharedImpl<IShared>
- {
- typedef ExpressionT ExpressionType;
-
- virtual ~Matcher() {}
- virtual Ptr<Matcher> clone() const = 0;
- virtual bool match( ExpressionT const& expr ) const = 0;
- virtual std::string toString() const = 0;
- };
-
- template<typename DerivedT, typename ExpressionT>
- struct MatcherImpl : Matcher<ExpressionT> {
-
- virtual Ptr<Matcher<ExpressionT> > clone() const {
- return Ptr<Matcher<ExpressionT> >( new DerivedT( static_cast<DerivedT const&>( *this ) ) );
- }
- };
-
- namespace Generic {
-
- template<typename ExpressionT>
- class AllOf : public MatcherImpl<AllOf<ExpressionT>, ExpressionT> {
- public:
-
- AllOf() {}
- AllOf( AllOf const& other ) : m_matchers( other.m_matchers ) {}
-
- AllOf& add( Matcher<ExpressionT> const& matcher ) {
- m_matchers.push_back( matcher.clone() );
- return *this;
- }
- virtual bool match( ExpressionT const& expr ) const
- {
- for( std::size_t i = 0; i < m_matchers.size(); ++i )
- if( !m_matchers[i]->match( expr ) )
- return false;
- return true;
- }
- virtual std::string toString() const {
- std::ostringstream oss;
- oss << "( ";
- for( std::size_t i = 0; i < m_matchers.size(); ++i ) {
- if( i != 0 )
- oss << " and ";
- oss << m_matchers[i]->toString();
- }
- oss << " )";
- return oss.str();
- }
-
- private:
- std::vector<Ptr<Matcher<ExpressionT> > > m_matchers;
- };
-
- template<typename ExpressionT>
- class AnyOf : public MatcherImpl<AnyOf<ExpressionT>, ExpressionT> {
- public:
-
- AnyOf() {}
- AnyOf( AnyOf const& other ) : m_matchers( other.m_matchers ) {}
-
- AnyOf& add( Matcher<ExpressionT> const& matcher ) {
- m_matchers.push_back( matcher.clone() );
- return *this;
- }
- virtual bool match( ExpressionT const& expr ) const
- {
- for( std::size_t i = 0; i < m_matchers.size(); ++i )
- if( m_matchers[i]->match( expr ) )
- return true;
- return false;
- }
- virtual std::string toString() const {
- std::ostringstream oss;
- oss << "( ";
- for( std::size_t i = 0; i < m_matchers.size(); ++i ) {
- if( i != 0 )
- oss << " or ";
- oss << m_matchers[i]->toString();
- }
- oss << " )";
- return oss.str();
- }
-
- private:
- std::vector<Ptr<Matcher<ExpressionT> > > m_matchers;
- };
-
- }
-
- namespace StdString {
-
- inline std::string makeString( std::string const& str ) { return str; }
- inline std::string makeString( const char* str ) { return str ? std::string( str ) : std::string(); }
-
- struct Equals : MatcherImpl<Equals, std::string> {
- Equals( std::string const& str ) : m_str( str ){}
- Equals( Equals const& other ) : m_str( other.m_str ){}
-
- virtual ~Equals();
-
- virtual bool match( std::string const& expr ) const {
- return m_str == expr;
- }
- virtual std::string toString() const {
- return "equals: \"" + m_str + "\"";
- }
-
- std::string m_str;
- };
-
- struct Contains : MatcherImpl<Contains, std::string> {
- Contains( std::string const& substr ) : m_substr( substr ){}
- Contains( Contains const& other ) : m_substr( other.m_substr ){}
-
- virtual ~Contains();
-
- virtual bool match( std::string const& expr ) const {
- return expr.find( m_substr ) != std::string::npos;
- }
- virtual std::string toString() const {
- return "contains: \"" + m_substr + "\"";
- }
-
- std::string m_substr;
- };
-
- struct StartsWith : MatcherImpl<StartsWith, std::string> {
- StartsWith( std::string const& substr ) : m_substr( substr ){}
- StartsWith( StartsWith const& other ) : m_substr( other.m_substr ){}
-
- virtual ~StartsWith();
-
- virtual bool match( std::string const& expr ) const {
- return expr.find( m_substr ) == 0;
- }
- virtual std::string toString() const {
- return "starts with: \"" + m_substr + "\"";
- }
+ return !operator==( rhs, lhs );
+ }
- std::string m_substr;
- };
+ friend bool operator <= ( double lhs, Approx const& rhs )
+ {
+ return lhs < rhs.m_value || lhs == rhs;
+ }
- struct EndsWith : MatcherImpl<EndsWith, std::string> {
- EndsWith( std::string const& substr ) : m_substr( substr ){}
- EndsWith( EndsWith const& other ) : m_substr( other.m_substr ){}
+ friend bool operator <= ( Approx const& lhs, double rhs )
+ {
+ return lhs.m_value < rhs || lhs == rhs;
+ }
- virtual ~EndsWith();
+ friend bool operator >= ( double lhs, Approx const& rhs )
+ {
+ return lhs > rhs.m_value || lhs == rhs;
+ }
- virtual bool match( std::string const& expr ) const {
- return expr.find( m_substr ) == expr.size() - m_substr.size();
- }
- virtual std::string toString() const {
- return "ends with: \"" + m_substr + "\"";
- }
+ friend bool operator >= ( Approx const& lhs, double rhs )
+ {
+ return lhs.m_value > rhs || lhs == rhs;
+ }
- std::string m_substr;
- };
- } // namespace StdString
- } // namespace Impl
+ Approx& epsilon( double newEpsilon ) {
+ m_epsilon = newEpsilon;
+ return *this;
+ }
- // The following functions create the actual matcher objects.
- // This allows the types to be inferred
- template<typename ExpressionT>
- inline Impl::Generic::AllOf<ExpressionT> AllOf( Impl::Matcher<ExpressionT> const& m1,
- Impl::Matcher<ExpressionT> const& m2 ) {
- return Impl::Generic::AllOf<ExpressionT>().add( m1 ).add( m2 );
- }
- template<typename ExpressionT>
- inline Impl::Generic::AllOf<ExpressionT> AllOf( Impl::Matcher<ExpressionT> const& m1,
- Impl::Matcher<ExpressionT> const& m2,
- Impl::Matcher<ExpressionT> const& m3 ) {
- return Impl::Generic::AllOf<ExpressionT>().add( m1 ).add( m2 ).add( m3 );
- }
- template<typename ExpressionT>
- inline Impl::Generic::AnyOf<ExpressionT> AnyOf( Impl::Matcher<ExpressionT> const& m1,
- Impl::Matcher<ExpressionT> const& m2 ) {
- return Impl::Generic::AnyOf<ExpressionT>().add( m1 ).add( m2 );
- }
- template<typename ExpressionT>
- inline Impl::Generic::AnyOf<ExpressionT> AnyOf( Impl::Matcher<ExpressionT> const& m1,
- Impl::Matcher<ExpressionT> const& m2,
- Impl::Matcher<ExpressionT> const& m3 ) {
- return Impl::Generic::AnyOf<ExpressionT>().add( m1 ).add( m2 ).add( m3 );
- }
+ Approx& scale( double newScale ) {
+ m_scale = newScale;
+ return *this;
+ }
- inline Impl::StdString::Equals Equals( std::string const& str ) {
- return Impl::StdString::Equals( str );
- }
- inline Impl::StdString::Equals Equals( const char* str ) {
- return Impl::StdString::Equals( Impl::StdString::makeString( str ) );
- }
- inline Impl::StdString::Contains Contains( std::string const& substr ) {
- return Impl::StdString::Contains( substr );
- }
- inline Impl::StdString::Contains Contains( const char* substr ) {
- return Impl::StdString::Contains( Impl::StdString::makeString( substr ) );
- }
- inline Impl::StdString::StartsWith StartsWith( std::string const& substr ) {
- return Impl::StdString::StartsWith( substr );
- }
- inline Impl::StdString::StartsWith StartsWith( const char* substr ) {
- return Impl::StdString::StartsWith( Impl::StdString::makeString( substr ) );
- }
- inline Impl::StdString::EndsWith EndsWith( std::string const& substr ) {
- return Impl::StdString::EndsWith( substr );
- }
- inline Impl::StdString::EndsWith EndsWith( const char* substr ) {
- return Impl::StdString::EndsWith( Impl::StdString::makeString( substr ) );
- }
+ std::string toString() const {
+ std::ostringstream oss;
+ oss << "Approx( " << Catch::toString( m_value ) << " )";
+ return oss.str();
+ }
-} // namespace Matchers
+ private:
+ double m_epsilon;
+ double m_scale;
+ double m_value;
+ };
+}
-using namespace Matchers;
+template<>
+inline std::string toString<Detail::Approx>( Detail::Approx const& value ) {
+ return value.toString();
+}
-} // namespace Catch
+} // end namespace Catch
// #included from: internal/catch_interfaces_tag_alias_registry.h
#define TWOBLUECUBES_CATCH_INTERFACES_TAG_ALIAS_REGISTRY_H_INCLUDED
@@ -2351,12 +2762,12 @@ namespace Catch {
template<typename T>
class Option {
public:
- Option() : nullableValue( NULL ) {}
+ Option() : nullableValue( CATCH_NULL ) {}
Option( T const& _value )
: nullableValue( new( storage ) T( _value ) )
{}
Option( Option const& _other )
- : nullableValue( _other ? new( storage ) T( *_other ) : NULL )
+ : nullableValue( _other ? new( storage ) T( *_other ) : CATCH_NULL )
{}
~Option() {
@@ -2380,7 +2791,7 @@ namespace Catch {
void reset() {
if( nullableValue )
nullableValue->~T();
- nullableValue = NULL;
+ nullableValue = CATCH_NULL;
}
T& operator*() { return *nullableValue; }
@@ -2392,10 +2803,10 @@ namespace Catch {
return nullableValue ? *nullableValue : defaultValue;
}
- bool some() const { return nullableValue != NULL; }
- bool none() const { return nullableValue == NULL; }
+ bool some() const { return nullableValue != CATCH_NULL; }
+ bool none() const { return nullableValue == CATCH_NULL; }
- bool operator !() const { return nullableValue == NULL; }
+ bool operator !() const { return nullableValue == CATCH_NULL; }
operator SafeBool::type() const {
return SafeBool::makeSafe( some() );
}
@@ -2453,6 +2864,8 @@ namespace Catch {
TestCaseInfo( TestCaseInfo const& other );
+ friend void setTags( TestCaseInfo& testCaseInfo, std::set<std::string> const& tags );
+
bool isHidden() const;
bool throws() const;
bool okToFail() const;
@@ -2565,7 +2978,7 @@ namespace Catch {
inline size_t registerTestMethods() {
size_t noTestMethods = 0;
- int noClasses = objc_getClassList( NULL, 0 );
+ int noClasses = objc_getClassList( CATCH_NULL, 0 );
Class* classes = (CATCH_UNSAFE_UNRETAINED Class *)malloc( sizeof(Class) * noClasses);
objc_getClassList( classes, noClasses );
@@ -2695,7 +3108,7 @@ return @ desc; \
#endif
-#ifdef CATCH_CONFIG_RUNNER
+#ifdef CATCH_IMPL
// #included from: internal/catch_impl.hpp
#define TWOBLUECUBES_CATCH_IMPL_HPP_INCLUDED
@@ -2707,7 +3120,7 @@ return @ desc; \
#pragma clang diagnostic ignored "-Wweak-vtables"
#endif
-// #included from: catch_runner.hpp
+// #included from: ../catch_session.hpp
#define TWOBLUECUBES_CATCH_RUNNER_HPP_INCLUDED
// #included from: internal/catch_commandline.hpp
@@ -2732,6 +3145,67 @@ return @ desc; \
#pragma clang diagnostic ignored "-Wpadded"
#endif
+// #included from: catch_wildcard_pattern.hpp
+#define TWOBLUECUBES_CATCH_WILDCARD_PATTERN_HPP_INCLUDED
+
+namespace Catch
+{
+ class WildcardPattern {
+ enum WildcardPosition {
+ NoWildcard = 0,
+ WildcardAtStart = 1,
+ WildcardAtEnd = 2,
+ WildcardAtBothEnds = WildcardAtStart | WildcardAtEnd
+ };
+
+ public:
+
+ WildcardPattern( std::string const& pattern, CaseSensitive::Choice caseSensitivity )
+ : m_caseSensitivity( caseSensitivity ),
+ m_wildcard( NoWildcard ),
+ m_pattern( adjustCase( pattern ) )
+ {
+ if( startsWith( m_pattern, "*" ) ) {
+ m_pattern = m_pattern.substr( 1 );
+ m_wildcard = WildcardAtStart;
+ }
+ if( endsWith( m_pattern, "*" ) ) {
+ m_pattern = m_pattern.substr( 0, m_pattern.size()-1 );
+ m_wildcard = static_cast<WildcardPosition>( m_wildcard | WildcardAtEnd );
+ }
+ }
+ virtual ~WildcardPattern();
+ virtual bool matches( std::string const& str ) const {
+ switch( m_wildcard ) {
+ case NoWildcard:
+ return m_pattern == adjustCase( str );
+ case WildcardAtStart:
+ return endsWith( adjustCase( str ), m_pattern );
+ case WildcardAtEnd:
+ return startsWith( adjustCase( str ), m_pattern );
+ case WildcardAtBothEnds:
+ return contains( adjustCase( str ), m_pattern );
+ }
+
+#ifdef __clang__
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunreachable-code"
+#endif
+ throw std::logic_error( "Unknown enum" );
+#ifdef __clang__
+#pragma clang diagnostic pop
+#endif
+ }
+ private:
+ std::string adjustCase( std::string const& str ) const {
+ return m_caseSensitivity == CaseSensitive::No ? toLower( str ) : str;
+ }
+ CaseSensitive::Choice m_caseSensitivity;
+ WildcardPosition m_wildcard;
+ std::string m_pattern;
+ };
+}
+
#include <string>
#include <vector>
@@ -2743,50 +3217,18 @@ namespace Catch {
virtual bool matches( TestCaseInfo const& testCase ) const = 0;
};
class NamePattern : public Pattern {
- enum WildcardPosition {
- NoWildcard = 0,
- WildcardAtStart = 1,
- WildcardAtEnd = 2,
- WildcardAtBothEnds = WildcardAtStart | WildcardAtEnd
- };
-
public:
- NamePattern( std::string const& name ) : m_name( toLower( name ) ), m_wildcard( NoWildcard ) {
- if( startsWith( m_name, "*" ) ) {
- m_name = m_name.substr( 1 );
- m_wildcard = WildcardAtStart;
- }
- if( endsWith( m_name, "*" ) ) {
- m_name = m_name.substr( 0, m_name.size()-1 );
- m_wildcard = static_cast<WildcardPosition>( m_wildcard | WildcardAtEnd );
- }
- }
+ NamePattern( std::string const& name )
+ : m_wildcardPattern( toLower( name ), CaseSensitive::No )
+ {}
virtual ~NamePattern();
virtual bool matches( TestCaseInfo const& testCase ) const {
- switch( m_wildcard ) {
- case NoWildcard:
- return m_name == toLower( testCase.name );
- case WildcardAtStart:
- return endsWith( toLower( testCase.name ), m_name );
- case WildcardAtEnd:
- return startsWith( toLower( testCase.name ), m_name );
- case WildcardAtBothEnds:
- return contains( toLower( testCase.name ), m_name );
- }
-
-#ifdef __clang__
-#pragma clang diagnostic push
-#pragma clang diagnostic ignored "-Wunreachable-code"
-#endif
- throw std::logic_error( "Unknown enum" );
-#ifdef __clang__
-#pragma clang diagnostic pop
-#endif
+ return m_wildcardPattern.matches( toLower( testCase.name ) );
}
private:
- std::string m_name;
- WildcardPosition m_wildcard;
+ WildcardPattern m_wildcardPattern;
};
+
class TagPattern : public Pattern {
public:
TagPattern( std::string const& tag ) : m_tag( toLower( tag ) ) {}
@@ -2797,6 +3239,7 @@ namespace Catch {
private:
std::string m_tag;
};
+
class ExcludedPattern : public Pattern {
public:
ExcludedPattern( Ptr<Pattern> const& underlyingPattern ) : m_underlyingPattern( underlyingPattern ) {}
@@ -2811,10 +3254,11 @@ namespace Catch {
bool matches( TestCaseInfo const& testCase ) const {
// All patterns in a filter must match for the filter to be a match
- for( std::vector<Ptr<Pattern> >::const_iterator it = m_patterns.begin(), itEnd = m_patterns.end(); it != itEnd; ++it )
+ for( std::vector<Ptr<Pattern> >::const_iterator it = m_patterns.begin(), itEnd = m_patterns.end(); it != itEnd; ++it ) {
if( !(*it)->matches( testCase ) )
return false;
- return true;
+ }
+ return true;
}
};
@@ -2844,11 +3288,12 @@ namespace Catch {
namespace Catch {
class TestSpecParser {
- enum Mode{ None, Name, QuotedName, Tag };
+ enum Mode{ None, Name, QuotedName, Tag, EscapedName };
Mode m_mode;
bool m_exclusion;
std::size_t m_start, m_pos;
std::string m_arg;
+ std::vector<std::size_t> m_escapeChars;
TestSpec::Filter m_currentFilter;
TestSpec m_testSpec;
ITagAliasRegistry const* m_tagAliases;
@@ -2861,6 +3306,7 @@ namespace Catch {
m_exclusion = false;
m_start = std::string::npos;
m_arg = m_tagAliases->expandAliases( arg );
+ m_escapeChars.clear();
for( m_pos = 0; m_pos < m_arg.size(); ++m_pos )
visitChar( m_arg[m_pos] );
if( m_mode == Name )
@@ -2879,6 +3325,7 @@ namespace Catch {
case '~': m_exclusion = true; return;
case '[': return startNewMode( Tag, ++m_pos );
case '"': return startNewMode( QuotedName, ++m_pos );
+ case '\\': return escape();
default: startNewMode( Name, m_pos ); break;
}
}
@@ -2894,7 +3341,11 @@ namespace Catch {
addPattern<TestSpec::NamePattern>();
startNewMode( Tag, ++m_pos );
}
+ else if( c == '\\' )
+ escape();
}
+ else if( m_mode == EscapedName )
+ m_mode = Name;
else if( m_mode == QuotedName && c == '"' )
addPattern<TestSpec::NamePattern>();
else if( m_mode == Tag && c == ']' )
@@ -2904,10 +3355,17 @@ namespace Catch {
m_mode = mode;
m_start = start;
}
+ void escape() {
+ m_mode = EscapedName;
+ m_escapeChars.push_back( m_pos );
+ }
std::string subString() const { return m_arg.substr( m_start, m_pos - m_start ); }
template<typename T>
void addPattern() {
std::string token = subString();
+ for( size_t i = 0; i < m_escapeChars.size(); ++i )
+ token = token.substr( 0, m_escapeChars[i] ) + token.substr( m_escapeChars[i]+1 );
+ m_escapeChars.clear();
if( startsWith( token, "exclude:" ) ) {
m_exclusion = true;
token = token.substr( 8 );
@@ -2963,6 +3421,16 @@ namespace Catch {
Always,
Never
}; };
+ struct RunTests { enum InWhatOrder {
+ InDeclarationOrder,
+ InLexicographicalOrder,
+ InRandomOrder
+ }; };
+ struct UseColour { enum YesOrNo {
+ Auto,
+ Yes,
+ No
+ }; };
class TestSpec;
@@ -2980,30 +3448,71 @@ namespace Catch {
virtual bool showInvisibles() const = 0;
virtual ShowDurations::OrNot showDurations() const = 0;
virtual TestSpec const& testSpec() const = 0;
+ virtual RunTests::InWhatOrder runOrder() const = 0;
+ virtual unsigned int rngSeed() const = 0;
+ virtual UseColour::YesOrNo useColour() const = 0;
};
}
// #included from: catch_stream.h
#define TWOBLUECUBES_CATCH_STREAM_H_INCLUDED
+// #included from: catch_streambuf.h
+#define TWOBLUECUBES_CATCH_STREAMBUF_H_INCLUDED
+
#include <streambuf>
-#ifdef __clang__
-#pragma clang diagnostic ignored "-Wpadded"
-#endif
+namespace Catch {
+
+ class StreamBufBase : public std::streambuf {
+ public:
+ virtual ~StreamBufBase() CATCH_NOEXCEPT;
+ };
+}
+
+#include <streambuf>
+#include <ostream>
+#include <fstream>
+#include <memory>
namespace Catch {
- class Stream {
+ std::ostream& cout();
+ std::ostream& cerr();
+
+ struct IStream {
+ virtual ~IStream() CATCH_NOEXCEPT;
+ virtual std::ostream& stream() const = 0;
+ };
+
+ class FileStream : public IStream {
+ mutable std::ofstream m_ofs;
public:
- Stream();
- Stream( std::streambuf* _streamBuf, bool _isOwned );
- void release();
+ FileStream( std::string const& filename );
+ virtual ~FileStream() CATCH_NOEXCEPT;
+ public: // IStream
+ virtual std::ostream& stream() const CATCH_OVERRIDE;
+ };
- std::streambuf* streamBuf;
+ class CoutStream : public IStream {
+ mutable std::ostream m_os;
+ public:
+ CoutStream();
+ virtual ~CoutStream() CATCH_NOEXCEPT;
- private:
- bool isOwned;
+ public: // IStream
+ virtual std::ostream& stream() const CATCH_OVERRIDE;
+ };
+
+ class DebugOutStream : public IStream {
+ CATCH_AUTO_PTR( StreamBufBase ) m_streamBuf;
+ mutable std::ostream m_os;
+ public:
+ DebugOutStream();
+ virtual ~DebugOutStream() CATCH_NOEXCEPT;
+
+ public: // IStream
+ virtual std::ostream& stream() const CATCH_OVERRIDE;
};
}
@@ -3011,6 +3520,7 @@ namespace Catch {
#include <vector>
#include <string>
#include <iostream>
+#include <ctime>
#ifndef CATCH_CONFIG_CONSOLE_WIDTH
#define CATCH_CONFIG_CONSOLE_WIDTH 80
@@ -3030,10 +3540,14 @@ namespace Catch {
noThrow( false ),
showHelp( false ),
showInvisibles( false ),
+ filenamesAsTags( false ),
abortAfter( -1 ),
+ rngSeed( 0 ),
verbosity( Verbosity::Normal ),
warnings( WarnAbout::Nothing ),
- showDurations( ShowDurations::DefaultForReporter )
+ showDurations( ShowDurations::DefaultForReporter ),
+ runOrder( RunTests::InDeclarationOrder ),
+ useColour( UseColour::Auto )
{}
bool listTests;
@@ -3046,18 +3560,22 @@ namespace Catch {
bool noThrow;
bool showHelp;
bool showInvisibles;
+ bool filenamesAsTags;
int abortAfter;
+ unsigned int rngSeed;
Verbosity::Level verbosity;
WarnAbout::What warnings;
ShowDurations::OrNot showDurations;
+ RunTests::InWhatOrder runOrder;
+ UseColour::YesOrNo useColour;
- std::string reporterName;
std::string outputFilename;
std::string name;
std::string processName;
+ std::vector<std::string> reporterNames;
std::vector<std::string> testsOrTags;
};
@@ -3069,12 +3587,11 @@ namespace Catch {
public:
Config()
- : m_os( std::cout.rdbuf() )
{}
Config( ConfigData const& data )
: m_data( data ),
- m_os( std::cout.rdbuf() )
+ m_stream( openStream() )
{
if( !data.testsOrTags.empty() ) {
TestSpecParser parser( ITagAliasRegistry::get() );
@@ -3085,12 +3602,6 @@ namespace Catch {
}
virtual ~Config() {
- m_os.rdbuf( std::cout.rdbuf() );
- m_stream.release();
- }
-
- void setFilename( std::string const& filename ) {
- m_data.outputFilename = filename;
}
std::string const& getFilename() const {
@@ -3106,18 +3617,7 @@ namespace Catch {
bool shouldDebugBreak() const { return m_data.shouldDebugBreak; }
- void setStreamBuf( std::streambuf* buf ) {
- m_os.rdbuf( buf ? buf : std::cout.rdbuf() );
- }
-
- void useStream( std::string const& streamName ) {
- Stream stream = createStream( streamName );
- setStreamBuf( stream.streamBuf );
- m_stream.release();
- m_stream = stream;
- }
-
- std::string getReporterName() const { return m_data.reporterName; }
+ std::vector<std::string> getReporterNames() const { return m_data.reporterNames; }
int abortAfter() const { return m_data.abortAfter; }
@@ -3128,17 +3628,32 @@ namespace Catch {
// IConfig interface
virtual bool allowThrows() const { return !m_data.noThrow; }
- virtual std::ostream& stream() const { return m_os; }
+ virtual std::ostream& stream() const { return m_stream->stream(); }
virtual std::string name() const { return m_data.name.empty() ? m_data.processName : m_data.name; }
virtual bool includeSuccessfulResults() const { return m_data.showSuccessfulTests; }
virtual bool warnAboutMissingAssertions() const { return m_data.warnings & WarnAbout::NoAssertions; }
virtual ShowDurations::OrNot showDurations() const { return m_data.showDurations; }
+ virtual RunTests::InWhatOrder runOrder() const { return m_data.runOrder; }
+ virtual unsigned int rngSeed() const { return m_data.rngSeed; }
+ virtual UseColour::YesOrNo useColour() const { return m_data.useColour; }
private:
+
+ IStream const* openStream() {
+ if( m_data.outputFilename.empty() )
+ return new CoutStream();
+ else if( m_data.outputFilename[0] == '%' ) {
+ if( m_data.outputFilename == "%debug" )
+ return new DebugOutStream();
+ else
+ throw std::domain_error( "Unrecognised stream: " + m_data.outputFilename );
+ }
+ else
+ return new FileStream( m_data.outputFilename );
+ }
ConfigData m_data;
- Stream m_stream;
- mutable std::ostream m_os;
+ CATCH_AUTO_PTR( IStream const ) m_stream;
TestSpec m_testSpec;
};
@@ -3158,6 +3673,8 @@ namespace Catch {
#define STITCH_CLARA_OPEN_NAMESPACE namespace Catch {
// #included from: ../external/clara.h
+// Version 0.0.2.4
+
// Only use header guard if we are not using an outer namespace
#if !defined(TWOBLUECUBES_CLARA_H_INCLUDED) || defined(STITCH_CLARA_OPEN_NAMESPACE)
@@ -3182,6 +3699,7 @@ namespace Catch {
#include <string>
#include <vector>
#include <sstream>
+#include <algorithm>
// Use optional outer namespace
#ifdef STITCH_TBC_TEXT_FORMAT_OUTER_NAMESPACE
@@ -3309,22 +3827,172 @@ namespace Tbc {
} // end namespace Tbc
-#ifdef STITCH_TBC_TEXT_FORMAT_OUTER_NAMESPACE
-} // end outer namespace
+#ifdef STITCH_TBC_TEXT_FORMAT_OUTER_NAMESPACE
+} // end outer namespace
+#endif
+
+#endif // TBC_TEXT_FORMAT_H_INCLUDED
+
+// ----------- end of #include from tbc_text_format.h -----------
+// ........... back in clara.h
+
+#undef STITCH_TBC_TEXT_FORMAT_OPEN_NAMESPACE
+
+// ----------- #included from clara_compilers.h -----------
+
+#ifndef TWOBLUECUBES_CLARA_COMPILERS_H_INCLUDED
+#define TWOBLUECUBES_CLARA_COMPILERS_H_INCLUDED
+
+// Detect a number of compiler features - mostly C++11/14 conformance - by compiler
+// The following features are defined:
+//
+// CLARA_CONFIG_CPP11_NULLPTR : is nullptr supported?
+// CLARA_CONFIG_CPP11_NOEXCEPT : is noexcept supported?
+// CLARA_CONFIG_CPP11_GENERATED_METHODS : The delete and default keywords for compiler generated methods
+// CLARA_CONFIG_CPP11_OVERRIDE : is override supported?
+// CLARA_CONFIG_CPP11_UNIQUE_PTR : is unique_ptr supported (otherwise use auto_ptr)
+
+// CLARA_CONFIG_CPP11_OR_GREATER : Is C++11 supported?
+
+// CLARA_CONFIG_VARIADIC_MACROS : are variadic macros supported?
+
+// In general each macro has a _NO_<feature name> form
+// (e.g. CLARA_CONFIG_CPP11_NO_NULLPTR) which disables the feature.
+// Many features, at point of detection, define an _INTERNAL_ macro, so they
+// can be combined, en-mass, with the _NO_ forms later.
+
+// All the C++11 features can be disabled with CLARA_CONFIG_NO_CPP11
+
+#ifdef __clang__
+
+#if __has_feature(cxx_nullptr)
+#define CLARA_INTERNAL_CONFIG_CPP11_NULLPTR
+#endif
+
+#if __has_feature(cxx_noexcept)
+#define CLARA_INTERNAL_CONFIG_CPP11_NOEXCEPT
+#endif
+
+#endif // __clang__
+
+////////////////////////////////////////////////////////////////////////////////
+// GCC
+#ifdef __GNUC__
+
+#if __GNUC__ == 4 && __GNUC_MINOR__ >= 6 && defined(__GXX_EXPERIMENTAL_CXX0X__)
+#define CLARA_INTERNAL_CONFIG_CPP11_NULLPTR
+#endif
+
+// - otherwise more recent versions define __cplusplus >= 201103L
+// and will get picked up below
+
+#endif // __GNUC__
+
+////////////////////////////////////////////////////////////////////////////////
+// Visual C++
+#ifdef _MSC_VER
+
+#if (_MSC_VER >= 1600)
+#define CLARA_INTERNAL_CONFIG_CPP11_NULLPTR
+#define CLARA_INTERNAL_CONFIG_CPP11_UNIQUE_PTR
+#endif
+
+#if (_MSC_VER >= 1900 ) // (VC++ 13 (VS2015))
+#define CLARA_INTERNAL_CONFIG_CPP11_NOEXCEPT
+#define CLARA_INTERNAL_CONFIG_CPP11_GENERATED_METHODS
+#endif
+
+#endif // _MSC_VER
+
+////////////////////////////////////////////////////////////////////////////////
+// C++ language feature support
+
+// catch all support for C++11
+#if defined(__cplusplus) && __cplusplus >= 201103L
+
+#define CLARA_CPP11_OR_GREATER
+
+#if !defined(CLARA_INTERNAL_CONFIG_CPP11_NULLPTR)
+#define CLARA_INTERNAL_CONFIG_CPP11_NULLPTR
+#endif
+
+#ifndef CLARA_INTERNAL_CONFIG_CPP11_NOEXCEPT
+#define CLARA_INTERNAL_CONFIG_CPP11_NOEXCEPT
+#endif
+
+#ifndef CLARA_INTERNAL_CONFIG_CPP11_GENERATED_METHODS
+#define CLARA_INTERNAL_CONFIG_CPP11_GENERATED_METHODS
+#endif
+
+#if !defined(CLARA_INTERNAL_CONFIG_CPP11_OVERRIDE)
+#define CLARA_INTERNAL_CONFIG_CPP11_OVERRIDE
+#endif
+#if !defined(CLARA_INTERNAL_CONFIG_CPP11_UNIQUE_PTR)
+#define CLARA_INTERNAL_CONFIG_CPP11_UNIQUE_PTR
+#endif
+
+#endif // __cplusplus >= 201103L
+
+// Now set the actual defines based on the above + anything the user has configured
+#if defined(CLARA_INTERNAL_CONFIG_CPP11_NULLPTR) && !defined(CLARA_CONFIG_CPP11_NO_NULLPTR) && !defined(CLARA_CONFIG_CPP11_NULLPTR) && !defined(CLARA_CONFIG_NO_CPP11)
+#define CLARA_CONFIG_CPP11_NULLPTR
+#endif
+#if defined(CLARA_INTERNAL_CONFIG_CPP11_NOEXCEPT) && !defined(CLARA_CONFIG_CPP11_NO_NOEXCEPT) && !defined(CLARA_CONFIG_CPP11_NOEXCEPT) && !defined(CLARA_CONFIG_NO_CPP11)
+#define CLARA_CONFIG_CPP11_NOEXCEPT
+#endif
+#if defined(CLARA_INTERNAL_CONFIG_CPP11_GENERATED_METHODS) && !defined(CLARA_CONFIG_CPP11_NO_GENERATED_METHODS) && !defined(CLARA_CONFIG_CPP11_GENERATED_METHODS) && !defined(CLARA_CONFIG_NO_CPP11)
+#define CLARA_CONFIG_CPP11_GENERATED_METHODS
+#endif
+#if defined(CLARA_INTERNAL_CONFIG_CPP11_OVERRIDE) && !defined(CLARA_CONFIG_NO_OVERRIDE) && !defined(CLARA_CONFIG_CPP11_OVERRIDE) && !defined(CLARA_CONFIG_NO_CPP11)
+#define CLARA_CONFIG_CPP11_OVERRIDE
+#endif
+#if defined(CLARA_INTERNAL_CONFIG_CPP11_UNIQUE_PTR) && !defined(CLARA_CONFIG_NO_UNIQUE_PTR) && !defined(CLARA_CONFIG_CPP11_UNIQUE_PTR) && !defined(CLARA_CONFIG_NO_CPP11)
+#define CLARA_CONFIG_CPP11_UNIQUE_PTR
+#endif
+
+// noexcept support:
+#if defined(CLARA_CONFIG_CPP11_NOEXCEPT) && !defined(CLARA_NOEXCEPT)
+#define CLARA_NOEXCEPT noexcept
+# define CLARA_NOEXCEPT_IS(x) noexcept(x)
+#else
+#define CLARA_NOEXCEPT throw()
+# define CLARA_NOEXCEPT_IS(x)
+#endif
+
+// nullptr support
+#ifdef CLARA_CONFIG_CPP11_NULLPTR
+#define CLARA_NULL nullptr
+#else
+#define CLARA_NULL NULL
+#endif
+
+// override support
+#ifdef CLARA_CONFIG_CPP11_OVERRIDE
+#define CLARA_OVERRIDE override
+#else
+#define CLARA_OVERRIDE
#endif
-#endif // TBC_TEXT_FORMAT_H_INCLUDED
+// unique_ptr support
+#ifdef CLARA_CONFIG_CPP11_UNIQUE_PTR
+# define CLARA_AUTO_PTR( T ) std::unique_ptr<T>
+#else
+# define CLARA_AUTO_PTR( T ) std::auto_ptr<T>
+#endif
-// ----------- end of #include from tbc_text_format.h -----------
-// ........... back in /Users/philnash/Dev/OSS/Clara/srcs/clara.h
+#endif // TWOBLUECUBES_CLARA_COMPILERS_H_INCLUDED
-#undef STITCH_TBC_TEXT_FORMAT_OPEN_NAMESPACE
+// ----------- end of #include from clara_compilers.h -----------
+// ........... back in clara.h
#include <map>
-#include <algorithm>
#include <stdexcept>
#include <memory>
+#if defined(WIN32) || defined(__WIN32__) || defined(_WIN32) || defined(_MSC_VER)
+#define CLARA_PLATFORM_WINDOWS
+#endif
+
// Use optional outer namespace
#ifdef STITCH_CLARA_OPEN_NAMESPACE
STITCH_CLARA_OPEN_NAMESPACE
@@ -3373,9 +4041,12 @@ namespace Clara {
inline void convertInto( std::string const& _source, std::string& _dest ) {
_dest = _source;
}
+ char toLowerCh(char c) {
+ return static_cast<char>( ::tolower( c ) );
+ }
inline void convertInto( std::string const& _source, bool& _dest ) {
std::string sourceLC = _source;
- std::transform( sourceLC.begin(), sourceLC.end(), sourceLC.begin(), ::tolower );
+ std::transform( sourceLC.begin(), sourceLC.end(), sourceLC.begin(), toLowerCh );
if( sourceLC == "y" || sourceLC == "1" || sourceLC == "true" || sourceLC == "yes" || sourceLC == "on" )
_dest = true;
else if( sourceLC == "n" || sourceLC == "0" || sourceLC == "false" || sourceLC == "no" || sourceLC == "off" )
@@ -3383,23 +4054,15 @@ namespace Clara {
else
throw std::runtime_error( "Expected a boolean value but did not recognise:\n '" + _source + "'" );
}
- inline void convertInto( bool _source, bool& _dest ) {
- _dest = _source;
- }
- template<typename T>
- inline void convertInto( bool, T& ) {
- throw std::runtime_error( "Invalid conversion" );
- }
template<typename ConfigT>
struct IArgFunction {
virtual ~IArgFunction() {}
-# ifdef CATCH_CPP11_OR_GREATER
+#ifdef CLARA_CONFIG_CPP11_GENERATED_METHODS
IArgFunction() = default;
IArgFunction( IArgFunction const& ) = default;
-# endif
+#endif
virtual void set( ConfigT& config, std::string const& value ) const = 0;
- virtual void setFlag( ConfigT& config ) const = 0;
virtual bool takesArg() const = 0;
virtual IArgFunction* clone() const = 0;
};
@@ -3407,11 +4070,11 @@ namespace Clara {
template<typename ConfigT>
class BoundArgFunction {
public:
- BoundArgFunction() : functionObj( NULL ) {}
+ BoundArgFunction() : functionObj( CLARA_NULL ) {}
BoundArgFunction( IArgFunction<ConfigT>* _functionObj ) : functionObj( _functionObj ) {}
- BoundArgFunction( BoundArgFunction const& other ) : functionObj( other.functionObj ? other.functionObj->clone() : NULL ) {}
+ BoundArgFunction( BoundArgFunction const& other ) : functionObj( other.functionObj ? other.functionObj->clone() : CLARA_NULL ) {}
BoundArgFunction& operator = ( BoundArgFunction const& other ) {
- IArgFunction<ConfigT>* newFunctionObj = other.functionObj ? other.functionObj->clone() : NULL;
+ IArgFunction<ConfigT>* newFunctionObj = other.functionObj ? other.functionObj->clone() : CLARA_NULL;
delete functionObj;
functionObj = newFunctionObj;
return *this;
@@ -3421,13 +4084,10 @@ namespace Clara {
void set( ConfigT& config, std::string const& value ) const {
functionObj->set( config, value );
}
- void setFlag( ConfigT& config ) const {
- functionObj->setFlag( config );
- }
bool takesArg() const { return functionObj->takesArg(); }
bool isSet() const {
- return functionObj != NULL;
+ return functionObj != CLARA_NULL;
}
private:
IArgFunction<ConfigT>* functionObj;
@@ -3436,7 +4096,6 @@ namespace Clara {
template<typename C>
struct NullBinder : IArgFunction<C>{
virtual void set( C&, std::string const& ) const {}
- virtual void setFlag( C& ) const {}
virtual bool takesArg() const { return true; }
virtual IArgFunction<C>* clone() const { return new NullBinder( *this ); }
};
@@ -3447,9 +4106,6 @@ namespace Clara {
virtual void set( C& p, std::string const& stringValue ) const {
convertInto( stringValue, p.*member );
}
- virtual void setFlag( C& p ) const {
- convertInto( true, p.*member );
- }
virtual bool takesArg() const { return !IsBool<M>::value; }
virtual IArgFunction<C>* clone() const { return new BoundDataMember( *this ); }
M C::* member;
@@ -3462,11 +4118,6 @@ namespace Clara {
convertInto( stringValue, value );
(p.*member)( value );
}
- virtual void setFlag( C& p ) const {
- typename RemoveConstRef<M>::type value;
- convertInto( true, value );
- (p.*member)( value );
- }
virtual bool takesArg() const { return !IsBool<M>::value; }
virtual IArgFunction<C>* clone() const { return new BoundUnaryMethod( *this ); }
void (C::*member)( M );
@@ -3480,9 +4131,6 @@ namespace Clara {
if( value )
(p.*member)();
}
- virtual void setFlag( C& p ) const {
- (p.*member)();
- }
virtual bool takesArg() const { return false; }
virtual IArgFunction<C>* clone() const { return new BoundNullaryMethod( *this ); }
void (C::*member)();
@@ -3497,9 +4145,6 @@ namespace Clara {
if( value )
function( obj );
}
- virtual void setFlag( C& p ) const {
- function( p );
- }
virtual bool takesArg() const { return false; }
virtual IArgFunction<C>* clone() const { return new BoundUnaryFunction( *this ); }
void (*function)( C& );
@@ -3513,11 +4158,6 @@ namespace Clara {
convertInto( stringValue, value );
function( obj, value );
}
- virtual void setFlag( C& obj ) const {
- typename RemoveConstRef<T>::type value;
- convertInto( true, value );
- function( obj, value );
- }
virtual bool takesArg() const { return !IsBool<T>::value; }
virtual IArgFunction<C>* clone() const { return new BoundBinaryFunction( *this ); }
void (*function)( C&, T );
@@ -3525,8 +4165,20 @@ namespace Clara {
} // namespace Detail
- struct Parser {
- Parser() : separators( " \t=:" ) {}
+ inline std::vector<std::string> argsToVector( int argc, char const* const* const argv ) {
+ std::vector<std::string> args( static_cast<std::size_t>( argc ) );
+ for( std::size_t i = 0; i < static_cast<std::size_t>( argc ); ++i )
+ args[i] = argv[i];
+
+ return args;
+ }
+
+ class Parser {
+ enum Mode { None, MaybeShortOpt, SlashOpt, ShortOpt, LongOpt, Positional };
+ Mode mode;
+ std::size_t from;
+ bool inQuotes;
+ public:
struct Token {
enum Type { Positional, ShortOpt, LongOpt };
@@ -3535,38 +4187,75 @@ namespace Clara {
std::string data;
};
- void parseIntoTokens( int argc, char const * const * argv, std::vector<Parser::Token>& tokens ) const {
+ Parser() : mode( None ), from( 0 ), inQuotes( false ){}
+
+ void parseIntoTokens( std::vector<std::string> const& args, std::vector<Token>& tokens ) {
const std::string doubleDash = "--";
- for( int i = 1; i < argc && argv[i] != doubleDash; ++i )
- parseIntoTokens( argv[i] , tokens);
- }
- void parseIntoTokens( std::string arg, std::vector<Parser::Token>& tokens ) const {
- while( !arg.empty() ) {
- Parser::Token token( Parser::Token::Positional, arg );
- arg = "";
- if( token.data[0] == '-' ) {
- if( token.data.size() > 1 && token.data[1] == '-' ) {
- token = Parser::Token( Parser::Token::LongOpt, token.data.substr( 2 ) );
- }
- else {
- token = Parser::Token( Parser::Token::ShortOpt, token.data.substr( 1 ) );
- if( token.data.size() > 1 && separators.find( token.data[1] ) == std::string::npos ) {
- arg = "-" + token.data.substr( 1 );
- token.data = token.data.substr( 0, 1 );
- }
- }
- }
- if( token.type != Parser::Token::Positional ) {
- std::size_t pos = token.data.find_first_of( separators );
- if( pos != std::string::npos ) {
- arg = token.data.substr( pos+1 );
- token.data = token.data.substr( 0, pos );
- }
- }
- tokens.push_back( token );
+ for( std::size_t i = 1; i < args.size() && args[i] != doubleDash; ++i )
+ parseIntoTokens( args[i], tokens);
+ }
+
+ void parseIntoTokens( std::string const& arg, std::vector<Token>& tokens ) {
+ for( std::size_t i = 0; i <= arg.size(); ++i ) {
+ char c = arg[i];
+ if( c == '"' )
+ inQuotes = !inQuotes;
+ mode = handleMode( i, c, arg, tokens );
+ }
+ }
+ Mode handleMode( std::size_t i, char c, std::string const& arg, std::vector<Token>& tokens ) {
+ switch( mode ) {
+ case None: return handleNone( i, c );
+ case MaybeShortOpt: return handleMaybeShortOpt( i, c );
+ case ShortOpt:
+ case LongOpt:
+ case SlashOpt: return handleOpt( i, c, arg, tokens );
+ case Positional: return handlePositional( i, c, arg, tokens );
+ default: throw std::logic_error( "Unknown mode" );
+ }
+ }
+
+ Mode handleNone( std::size_t i, char c ) {
+ if( inQuotes ) {
+ from = i;
+ return Positional;
+ }
+ switch( c ) {
+ case '-': return MaybeShortOpt;
+#ifdef CLARA_PLATFORM_WINDOWS
+ case '/': from = i+1; return SlashOpt;
+#endif
+ default: from = i; return Positional;
+ }
+ }
+ Mode handleMaybeShortOpt( std::size_t i, char c ) {
+ switch( c ) {
+ case '-': from = i+1; return LongOpt;
+ default: from = i; return ShortOpt;
}
}
- std::string separators;
+ Mode handleOpt( std::size_t i, char c, std::string const& arg, std::vector<Token>& tokens ) {
+ if( std::string( ":=\0", 3 ).find( c ) == std::string::npos )
+ return mode;
+
+ std::string optName = arg.substr( from, i-from );
+ if( mode == ShortOpt )
+ for( std::size_t j = 0; j < optName.size(); ++j )
+ tokens.push_back( Token( Token::ShortOpt, optName.substr( j, 1 ) ) );
+ else if( mode == SlashOpt && optName.size() == 1 )
+ tokens.push_back( Token( Token::ShortOpt, optName ) );
+ else
+ tokens.push_back( Token( Token::LongOpt, optName ) );
+ return None;
+ }
+ Mode handlePositional( std::size_t i, char c, std::string const& arg, std::vector<Token>& tokens ) {
+ if( inQuotes || std::string( "\0", 1 ).find( c ) == std::string::npos )
+ return mode;
+
+ std::string data = arg.substr( from, i-from );
+ tokens.push_back( Token( Token::Positional, data ) );
+ return None;
+ }
};
template<typename ConfigT>
@@ -3645,12 +4334,7 @@ namespace Clara {
}
};
- // NOTE: std::auto_ptr is deprecated in c++11/c++0x
-#if defined(__cplusplus) && __cplusplus > 199711L
- typedef std::unique_ptr<Arg> ArgAutoPtr;
-#else
- typedef std::auto_ptr<Arg> ArgAutoPtr;
-#endif
+ typedef CLARA_AUTO_PTR( Arg ) ArgAutoPtr;
friend void addOptName( Arg& arg, std::string const& optName )
{
@@ -3761,7 +4445,7 @@ namespace Clara {
m_throwOnUnrecognisedTokens( other.m_throwOnUnrecognisedTokens )
{
if( other.m_floatingArg.get() )
- m_floatingArg = ArgAutoPtr( new Arg( *other.m_floatingArg ) );
+ m_floatingArg.reset( new Arg( *other.m_floatingArg ) );
}
CommandLine& setThrowOnUnrecognisedTokens( bool shouldThrow = true ) {
@@ -3789,7 +4473,7 @@ namespace Clara {
ArgBuilder operator[]( UnpositionalTag ) {
if( m_floatingArg.get() )
throw std::logic_error( "Only one unpositional argument can be added" );
- m_floatingArg = ArgAutoPtr( new Arg() );
+ m_floatingArg.reset( new Arg() );
ArgBuilder builder( m_floatingArg.get() );
return builder;
}
@@ -3874,21 +4558,21 @@ namespace Clara {
return oss.str();
}
- ConfigT parse( int argc, char const * const * argv ) const {
+ ConfigT parse( std::vector<std::string> const& args ) const {
ConfigT config;
- parseInto( argc, argv, config );
+ parseInto( args, config );
return config;
}
- std::vector<Parser::Token> parseInto( int argc, char const * const * argv, ConfigT& config ) const {
- std::string processName = argv[0];
+ std::vector<Parser::Token> parseInto( std::vector<std::string> const& args, ConfigT& config ) const {
+ std::string processName = args[0];
std::size_t lastSlash = processName.find_last_of( "/\\" );
if( lastSlash != std::string::npos )
processName = processName.substr( lastSlash+1 );
m_boundProcessName.set( config, processName );
std::vector<Parser::Token> tokens;
Parser parser;
- parser.parseIntoTokens( argc, argv, tokens );
+ parser.parseIntoTokens( args, tokens );
return populate( tokens, config );
}
@@ -3919,7 +4603,7 @@ namespace Clara {
arg.boundField.set( config, tokens[++i].data );
}
else {
- arg.boundField.setFlag( config );
+ arg.boundField.set( config, "true" );
}
break;
}
@@ -3931,7 +4615,7 @@ namespace Clara {
if( it == itEnd ) {
if( token.type == Parser::Token::Positional || !m_throwOnUnrecognisedTokens )
unusedTokens.push_back( token );
- else if( m_throwOnUnrecognisedTokens )
+ else if( errors.empty() && m_throwOnUnrecognisedTokens )
errors.push_back( "unrecognised option: " + token.data );
}
}
@@ -4023,13 +4707,35 @@ namespace Catch {
config.abortAfter = x;
}
inline void addTestOrTags( ConfigData& config, std::string const& _testSpec ) { config.testsOrTags.push_back( _testSpec ); }
+ inline void addReporterName( ConfigData& config, std::string const& _reporterName ) { config.reporterNames.push_back( _reporterName ); }
inline void addWarning( ConfigData& config, std::string const& _warning ) {
if( _warning == "NoAssertions" )
config.warnings = static_cast<WarnAbout::What>( config.warnings | WarnAbout::NoAssertions );
else
throw std::runtime_error( "Unrecognised warning: '" + _warning + "'" );
-
+ }
+ inline void setOrder( ConfigData& config, std::string const& order ) {
+ if( startsWith( "declared", order ) )
+ config.runOrder = RunTests::InDeclarationOrder;
+ else if( startsWith( "lexical", order ) )
+ config.runOrder = RunTests::InLexicographicalOrder;
+ else if( startsWith( "random", order ) )
+ config.runOrder = RunTests::InRandomOrder;
+ else
+ throw std::runtime_error( "Unrecognised ordering: '" + order + "'" );
+ }
+ inline void setRngSeed( ConfigData& config, std::string const& seed ) {
+ if( seed == "time" ) {
+ config.rngSeed = static_cast<unsigned int>( std::time(0) );
+ }
+ else {
+ std::stringstream ss;
+ ss << seed;
+ ss >> config.rngSeed;
+ if( ss.fail() )
+ throw std::runtime_error( "Argment to --rng-seed should be the word 'time' or a number" );
+ }
}
inline void setVerbosity( ConfigData& config, int level ) {
// !TBD: accept strings?
@@ -4040,6 +4746,21 @@ namespace Catch {
? ShowDurations::Always
: ShowDurations::Never;
}
+ inline void setUseColour( ConfigData& config, std::string const& value ) {
+ std::string mode = toLower( value );
+
+ if( mode == "yes" )
+ config.useColour = UseColour::Yes;
+ else if( mode == "no" )
+ config.useColour = UseColour::No;
+ else if( mode == "auto" )
+ config.useColour = UseColour::Auto;
+ else
+ throw std::runtime_error( "colour mode must be one of: auto, yes or no" );
+ }
+ inline void forceColour( ConfigData& config ) {
+ config.useColour = UseColour::Yes;
+ }
inline void loadTestNamesFromFile( ConfigData& config, std::string const& _filename ) {
std::ifstream f( _filename.c_str() );
if( !f.is_open() )
@@ -4048,8 +4769,11 @@ namespace Catch {
std::string line;
while( std::getline( f, line ) ) {
line = trim(line);
- if( !line.empty() && !startsWith( line, "#" ) )
- addTestOrTags( config, "\"" + line + "\"," );
+ if( !line.empty() && !startsWith( line, "#" ) ) {
+ if( !startsWith( line, "\"" ) )
+ line = "\"" + line + "\"";
+ addTestOrTags( config, line + "," );
+ }
}
}
@@ -4095,7 +4819,7 @@ namespace Catch {
cli["-r"]["--reporter"]
// .placeholder( "name[:filename]" )
.describe( "reporter to use (defaults to console)" )
- .bind( &ConfigData::reporterName, "name" );
+ .bind( &addReporterName, "name" );
cli["-n"]["--name"]
.describe( "suite name" )
@@ -4126,12 +4850,16 @@ namespace Catch {
cli["-d"]["--durations"]
.describe( "show test durations" )
- .bind( &setShowDurations, "yes/no" );
+ .bind( &setShowDurations, "yes|no" );
cli["-f"]["--input-file"]
.describe( "load test names to run from a file" )
.bind( &loadTestNamesFromFile, "filename" );
+ cli["-#"]["--filenames-as-tags"]
+ .describe( "adds a tag for the filename" )
+ .bind( &ConfigData::filenamesAsTags );
+
// Less common commands which don't have a short form
cli["--list-test-names-only"]
.describe( "list all/matching test cases names only" )
@@ -4141,6 +4869,22 @@ namespace Catch {
.describe( "list all reporters" )
.bind( &ConfigData::listReporters );
+ cli["--order"]
+ .describe( "test case order (defaults to decl)" )
+ .bind( &setOrder, "decl|lex|rand" );
+
+ cli["--rng-seed"]
+ .describe( "set a specific seed for random numbers" )
+ .bind( &setRngSeed, "'time'|number" );
+
+ cli["--force-colour"]
+ .describe( "force colourised output (deprecated)" )
+ .bind( &forceColour );
+
+ cli["--use-colour"]
+ .describe( "should output be colourised" )
+ .bind( &setUseColour, "yes|no" );
+
return cli;
}
@@ -4314,10 +5058,6 @@ namespace Catch {
namespace Catch {
- namespace Detail {
- struct IColourImpl;
- }
-
struct Colour {
enum Code {
None = 0,
@@ -4363,7 +5103,6 @@ namespace Catch {
static void use( Code _colourCode );
private:
- static Detail::IColourImpl* impl();
bool m_moved;
};
@@ -4382,18 +5121,18 @@ namespace Catch {
namespace Catch
{
struct ReporterConfig {
- explicit ReporterConfig( Ptr<IConfig> const& _fullConfig )
+ explicit ReporterConfig( Ptr<IConfig const> const& _fullConfig )
: m_stream( &_fullConfig->stream() ), m_fullConfig( _fullConfig ) {}
- ReporterConfig( Ptr<IConfig> const& _fullConfig, std::ostream& _stream )
+ ReporterConfig( Ptr<IConfig const> const& _fullConfig, std::ostream& _stream )
: m_stream( &_stream ), m_fullConfig( _fullConfig ) {}
std::ostream& stream() const { return *m_stream; }
- Ptr<IConfig> fullConfig() const { return m_fullConfig; }
+ Ptr<IConfig const> fullConfig() const { return m_fullConfig; }
private:
std::ostream* m_stream;
- Ptr<IConfig> m_fullConfig;
+ Ptr<IConfig const> m_fullConfig;
};
struct ReporterPreferences {
@@ -4457,7 +5196,7 @@ namespace Catch
}
virtual ~AssertionStats();
-# ifdef CATCH_CPP11_OR_GREATER
+# ifdef CATCH_CONFIG_CPP11_GENERATED_METHODS
AssertionStats( AssertionStats const& ) = default;
AssertionStats( AssertionStats && ) = default;
AssertionStats& operator = ( AssertionStats const& ) = default;
@@ -4480,7 +5219,7 @@ namespace Catch
missingAssertions( _missingAssertions )
{}
virtual ~SectionStats();
-# ifdef CATCH_CPP11_OR_GREATER
+# ifdef CATCH_CONFIG_CPP11_GENERATED_METHODS
SectionStats( SectionStats const& ) = default;
SectionStats( SectionStats && ) = default;
SectionStats& operator = ( SectionStats const& ) = default;
@@ -4507,7 +5246,7 @@ namespace Catch
{}
virtual ~TestCaseStats();
-# ifdef CATCH_CPP11_OR_GREATER
+# ifdef CATCH_CONFIG_CPP11_GENERATED_METHODS
TestCaseStats( TestCaseStats const& ) = default;
TestCaseStats( TestCaseStats && ) = default;
TestCaseStats& operator = ( TestCaseStats const& ) = default;
@@ -4535,7 +5274,7 @@ namespace Catch
{}
virtual ~TestGroupStats();
-# ifdef CATCH_CPP11_OR_GREATER
+# ifdef CATCH_CONFIG_CPP11_GENERATED_METHODS
TestGroupStats( TestGroupStats const& ) = default;
TestGroupStats( TestGroupStats && ) = default;
TestGroupStats& operator = ( TestGroupStats const& ) = default;
@@ -4557,7 +5296,7 @@ namespace Catch
{}
virtual ~TestRunStats();
-# ifndef CATCH_CPP11_OR_GREATER
+# ifndef CATCH_CONFIG_CPP11_GENERATED_METHODS
TestRunStats( TestRunStats const& _other )
: runInfo( _other.runInfo ),
totals( _other.totals ),
@@ -4575,6 +5314,8 @@ namespace Catch
bool aborting;
};
+ class MultipleReporters;
+
struct IStreamingReporter : IShared {
virtual ~IStreamingReporter();
@@ -4593,27 +5334,37 @@ namespace Catch
virtual void assertionStarting( AssertionInfo const& assertionInfo ) = 0;
+ // The return value indicates if the messages buffer should be cleared:
virtual bool assertionEnded( AssertionStats const& assertionStats ) = 0;
+
virtual void sectionEnded( SectionStats const& sectionStats ) = 0;
virtual void testCaseEnded( TestCaseStats const& testCaseStats ) = 0;
virtual void testGroupEnded( TestGroupStats const& testGroupStats ) = 0;
virtual void testRunEnded( TestRunStats const& testRunStats ) = 0;
+
+ virtual void skipTest( TestCaseInfo const& testInfo ) = 0;
+
+ virtual MultipleReporters* tryAsMulti() { return CATCH_NULL; }
};
- struct IReporterFactory {
+ struct IReporterFactory : IShared {
virtual ~IReporterFactory();
virtual IStreamingReporter* create( ReporterConfig const& config ) const = 0;
virtual std::string getDescription() const = 0;
};
struct IReporterRegistry {
- typedef std::map<std::string, IReporterFactory*> FactoryMap;
+ typedef std::map<std::string, Ptr<IReporterFactory> > FactoryMap;
+ typedef std::vector<Ptr<IReporterFactory> > Listeners;
virtual ~IReporterRegistry();
- virtual IStreamingReporter* create( std::string const& name, Ptr<IConfig> const& config ) const = 0;
+ virtual IStreamingReporter* create( std::string const& name, Ptr<IConfig const> const& config ) const = 0;
virtual FactoryMap const& getFactories() const = 0;
+ virtual Listeners const& getListeners() const = 0;
};
+ Ptr<IStreamingReporter> addReporter( Ptr<IStreamingReporter> const& existingReporter, Ptr<IStreamingReporter> const& additionalReporter );
+
}
#include <limits>
@@ -4625,9 +5376,9 @@ namespace Catch {
TestSpec testSpec = config.testSpec();
if( config.testSpec().hasFilters() )
- std::cout << "Matching test cases:\n";
+ Catch::cout() << "Matching test cases:\n";
else {
- std::cout << "All available test cases:\n";
+ Catch::cout() << "All available test cases:\n";
testSpec = TestSpecParser( ITagAliasRegistry::get() ).parse( "*" ).testSpec();
}
@@ -4636,8 +5387,7 @@ namespace Catch {
nameAttr.setInitialIndent( 2 ).setIndent( 4 );
tagsAttr.setIndent( 6 );
- std::vector<TestCase> matchedTestCases;
- getRegistryHub().getTestCaseRegistry().getFilteredTests( testSpec, config, matchedTestCases );
+ std::vector<TestCase> matchedTestCases = filterTests( getAllTestCasesSorted( config ), testSpec, config );
for( std::vector<TestCase>::const_iterator it = matchedTestCases.begin(), itEnd = matchedTestCases.end();
it != itEnd;
++it ) {
@@ -4648,15 +5398,15 @@ namespace Catch {
: Colour::None;
Colour colourGuard( colour );
- std::cout << Text( testCaseInfo.name, nameAttr ) << std::endl;
+ Catch::cout() << Text( testCaseInfo.name, nameAttr ) << std::endl;
if( !testCaseInfo.tags.empty() )
- std::cout << Text( testCaseInfo.tagsAsString, tagsAttr ) << std::endl;
+ Catch::cout() << Text( testCaseInfo.tagsAsString, tagsAttr ) << std::endl;
}
if( !config.testSpec().hasFilters() )
- std::cout << pluralise( matchedTests, "test case" ) << "\n" << std::endl;
+ Catch::cout() << pluralise( matchedTests, "test case" ) << "\n" << std::endl;
else
- std::cout << pluralise( matchedTests, "matching test case" ) << "\n" << std::endl;
+ Catch::cout() << pluralise( matchedTests, "matching test case" ) << "\n" << std::endl;
return matchedTests;
}
@@ -4665,14 +5415,16 @@ namespace Catch {
if( !config.testSpec().hasFilters() )
testSpec = TestSpecParser( ITagAliasRegistry::get() ).parse( "*" ).testSpec();
std::size_t matchedTests = 0;
- std::vector<TestCase> matchedTestCases;
- getRegistryHub().getTestCaseRegistry().getFilteredTests( testSpec, config, matchedTestCases );
+ std::vector<TestCase> matchedTestCases = filterTests( getAllTestCasesSorted( config ), testSpec, config );
for( std::vector<TestCase>::const_iterator it = matchedTestCases.begin(), itEnd = matchedTestCases.end();
it != itEnd;
++it ) {
matchedTests++;
TestCaseInfo const& testCaseInfo = it->getTestCaseInfo();
- std::cout << testCaseInfo.name << std::endl;
+ if( startsWith( testCaseInfo.name, "#" ) )
+ Catch::cout() << "\"" << testCaseInfo.name << "\"" << std::endl;
+ else
+ Catch::cout() << testCaseInfo.name << std::endl;
}
return matchedTests;
}
@@ -4698,16 +5450,15 @@ namespace Catch {
inline std::size_t listTags( Config const& config ) {
TestSpec testSpec = config.testSpec();
if( config.testSpec().hasFilters() )
- std::cout << "Tags for matching test cases:\n";
+ Catch::cout() << "Tags for matching test cases:\n";
else {
- std::cout << "All available tags:\n";
+ Catch::cout() << "All available tags:\n";
testSpec = TestSpecParser( ITagAliasRegistry::get() ).parse( "*" ).testSpec();
}
std::map<std::string, TagInfo> tagCounts;
- std::vector<TestCase> matchedTestCases;
- getRegistryHub().getTestCaseRegistry().getFilteredTests( testSpec, config, matchedTestCases );
+ std::vector<TestCase> matchedTestCases = filterTests( getAllTestCasesSorted( config ), testSpec, config );
for( std::vector<TestCase>::const_iterator it = matchedTestCases.begin(), itEnd = matchedTestCases.end();
it != itEnd;
++it ) {
@@ -4734,14 +5485,14 @@ namespace Catch {
.setInitialIndent( 0 )
.setIndent( oss.str().size() )
.setWidth( CATCH_CONFIG_CONSOLE_WIDTH-10 ) );
- std::cout << oss.str() << wrapper << "\n";
+ Catch::cout() << oss.str() << wrapper << "\n";
}
- std::cout << pluralise( tagCounts.size(), "tag" ) << "\n" << std::endl;
+ Catch::cout() << pluralise( tagCounts.size(), "tag" ) << "\n" << std::endl;
return tagCounts.size();
}
inline std::size_t listReporters( Config const& /*config*/ ) {
- std::cout << "Available reports:\n";
+ Catch::cout() << "Available reporters:\n";
IReporterRegistry::FactoryMap const& factories = getRegistryHub().getReporterRegistry().getFactories();
IReporterRegistry::FactoryMap::const_iterator itBegin = factories.begin(), itEnd = factories.end(), it;
std::size_t maxNameLen = 0;
@@ -4753,13 +5504,13 @@ namespace Catch {
.setInitialIndent( 0 )
.setIndent( 7+maxNameLen )
.setWidth( CATCH_CONFIG_CONSOLE_WIDTH - maxNameLen-8 ) );
- std::cout << " "
+ Catch::cout() << " "
<< it->first
<< ":"
<< std::string( maxNameLen - it->first.size() + 2, ' ' )
<< wrapper << "\n";
}
- std::cout << std::endl;
+ Catch::cout() << std::endl;
return factories.size();
}
@@ -4778,7 +5529,7 @@ namespace Catch {
} // end namespace Catch
-// #included from: internal/catch_runner_impl.hpp
+// #included from: internal/catch_run_context.hpp
#define TWOBLUECUBES_CATCH_RUNNER_IMPL_HPP_INCLUDED
// #included from: catch_test_case_tracker.hpp
@@ -4787,135 +5538,392 @@ namespace Catch {
#include <map>
#include <string>
#include <assert.h>
+#include <vector>
namespace Catch {
-namespace SectionTracking {
+namespace TestCaseTracking {
+
+ struct ITracker : SharedImpl<> {
+ virtual ~ITracker();
- class TrackedSection {
+ // static queries
+ virtual std::string name() const = 0;
- typedef std::map<std::string, TrackedSection> TrackedSections;
+ // dynamic queries
+ virtual bool isComplete() const = 0; // Successfully completed or failed
+ virtual bool isSuccessfullyCompleted() const = 0;
+ virtual bool isOpen() const = 0; // Started but not complete
+ virtual bool hasChildren() const = 0;
+
+ virtual ITracker& parent() = 0;
+
+ // actions
+ virtual void close() = 0; // Successfully complete
+ virtual void fail() = 0;
+ virtual void markAsNeedingAnotherRun() = 0;
+
+ virtual void addChild( Ptr<ITracker> const& child ) = 0;
+ virtual ITracker* findChild( std::string const& name ) = 0;
+ virtual void openChild() = 0;
+
+ // Debug/ checking
+ virtual bool isSectionTracker() const = 0;
+ virtual bool isIndexTracker() const = 0;
+ };
+
+ class TrackerContext {
- public:
enum RunState {
NotStarted,
Executing,
- ExecutingChildren,
- Completed
+ CompletedCycle
};
- TrackedSection( std::string const& name, TrackedSection* parent )
- : m_name( name ), m_runState( NotStarted ), m_parent( parent )
+ Ptr<ITracker> m_rootTracker;
+ ITracker* m_currentTracker;
+ RunState m_runState;
+
+ public:
+
+ static TrackerContext& instance() {
+ static TrackerContext s_instance;
+ return s_instance;
+ }
+
+ TrackerContext()
+ : m_currentTracker( CATCH_NULL ),
+ m_runState( NotStarted )
{}
- RunState runState() const { return m_runState; }
+ ITracker& startRun();
- TrackedSection* findChild( std::string const& childName ) {
- TrackedSections::iterator it = m_children.find( childName );
- return it != m_children.end()
- ? &it->second
- : NULL;
+ void endRun() {
+ m_rootTracker.reset();
+ m_currentTracker = CATCH_NULL;
+ m_runState = NotStarted;
}
- TrackedSection* acquireChild( std::string const& childName ) {
- if( TrackedSection* child = findChild( childName ) )
- return child;
- m_children.insert( std::make_pair( childName, TrackedSection( childName, this ) ) );
- return findChild( childName );
+
+ void startCycle() {
+ m_currentTracker = m_rootTracker.get();
+ m_runState = Executing;
}
- void enter() {
- if( m_runState == NotStarted )
- m_runState = Executing;
+ void completeCycle() {
+ m_runState = CompletedCycle;
}
- void leave() {
- for( TrackedSections::const_iterator it = m_children.begin(), itEnd = m_children.end();
- it != itEnd;
- ++it )
- if( it->second.runState() != Completed ) {
- m_runState = ExecutingChildren;
- return;
- }
- m_runState = Completed;
+
+ bool completedCycle() const {
+ return m_runState == CompletedCycle;
}
- TrackedSection* getParent() {
- return m_parent;
+ ITracker& currentTracker() {
+ return *m_currentTracker;
}
- bool hasChildren() const {
- return !m_children.empty();
+ void setCurrentTracker( ITracker* tracker ) {
+ m_currentTracker = tracker;
}
-
- private:
- std::string m_name;
- RunState m_runState;
- TrackedSections m_children;
- TrackedSection* m_parent;
-
};
- class TestCaseTracker {
+ class TrackerBase : public ITracker {
+ protected:
+ enum CycleState {
+ NotStarted,
+ Executing,
+ ExecutingChildren,
+ NeedsAnotherRun,
+ CompletedSuccessfully,
+ Failed
+ };
+ class TrackerHasName {
+ std::string m_name;
+ public:
+ TrackerHasName( std::string const& name ) : m_name( name ) {}
+ bool operator ()( Ptr<ITracker> const& tracker ) {
+ return tracker->name() == m_name;
+ }
+ };
+ typedef std::vector<Ptr<ITracker> > Children;
+ std::string m_name;
+ TrackerContext& m_ctx;
+ ITracker* m_parent;
+ Children m_children;
+ CycleState m_runState;
public:
- TestCaseTracker( std::string const& testCaseName )
- : m_testCase( testCaseName, NULL ),
- m_currentSection( &m_testCase ),
- m_completedASectionThisRun( false )
+ TrackerBase( std::string const& name, TrackerContext& ctx, ITracker* parent )
+ : m_name( name ),
+ m_ctx( ctx ),
+ m_parent( parent ),
+ m_runState( NotStarted )
{}
+ virtual ~TrackerBase();
- bool enterSection( std::string const& name ) {
- TrackedSection* child = m_currentSection->acquireChild( name );
- if( m_completedASectionThisRun || child->runState() == TrackedSection::Completed )
- return false;
+ virtual std::string name() const CATCH_OVERRIDE {
+ return m_name;
+ }
+ virtual bool isComplete() const CATCH_OVERRIDE {
+ return m_runState == CompletedSuccessfully || m_runState == Failed;
+ }
+ virtual bool isSuccessfullyCompleted() const CATCH_OVERRIDE {
+ return m_runState == CompletedSuccessfully;
+ }
+ virtual bool isOpen() const CATCH_OVERRIDE {
+ return m_runState != NotStarted && !isComplete();
+ }
+ virtual bool hasChildren() const CATCH_OVERRIDE {
+ return !m_children.empty();
+ }
- m_currentSection = child;
- m_currentSection->enter();
- return true;
+ virtual void addChild( Ptr<ITracker> const& child ) CATCH_OVERRIDE {
+ m_children.push_back( child );
+ }
+
+ virtual ITracker* findChild( std::string const& name ) CATCH_OVERRIDE {
+ Children::const_iterator it = std::find_if( m_children.begin(), m_children.end(), TrackerHasName( name ) );
+ return( it != m_children.end() )
+ ? it->get()
+ : CATCH_NULL;
}
- void leaveSection() {
- m_currentSection->leave();
- m_currentSection = m_currentSection->getParent();
- assert( m_currentSection != NULL );
- m_completedASectionThisRun = true;
+ virtual ITracker& parent() CATCH_OVERRIDE {
+ assert( m_parent ); // Should always be non-null except for root
+ return *m_parent;
}
- bool currentSectionHasChildren() const {
- return m_currentSection->hasChildren();
+ virtual void openChild() CATCH_OVERRIDE {
+ if( m_runState != ExecutingChildren ) {
+ m_runState = ExecutingChildren;
+ if( m_parent )
+ m_parent->openChild();
+ }
}
- bool isCompleted() const {
- return m_testCase.runState() == TrackedSection::Completed;
+
+ virtual bool isSectionTracker() const CATCH_OVERRIDE { return false; }
+ virtual bool isIndexTracker() const CATCH_OVERRIDE { return false; }
+
+ void open() {
+ m_runState = Executing;
+ moveToThis();
+ if( m_parent )
+ m_parent->openChild();
}
- class Guard {
- public:
- Guard( TestCaseTracker& tracker ) : m_tracker( tracker ) {
- m_tracker.enterTestCase();
+ virtual void close() CATCH_OVERRIDE {
+
+ // Close any still open children (e.g. generators)
+ while( &m_ctx.currentTracker() != this )
+ m_ctx.currentTracker().close();
+
+ switch( m_runState ) {
+ case NotStarted:
+ case CompletedSuccessfully:
+ case Failed:
+ throw std::logic_error( "Illogical state" );
+
+ case NeedsAnotherRun:
+ break;;
+
+ case Executing:
+ m_runState = CompletedSuccessfully;
+ break;
+ case ExecutingChildren:
+ if( m_children.empty() || m_children.back()->isComplete() )
+ m_runState = CompletedSuccessfully;
+ break;
+
+ default:
+ throw std::logic_error( "Unexpected state" );
+ }
+ moveToParent();
+ m_ctx.completeCycle();
+ }
+ virtual void fail() CATCH_OVERRIDE {
+ m_runState = Failed;
+ if( m_parent )
+ m_parent->markAsNeedingAnotherRun();
+ moveToParent();
+ m_ctx.completeCycle();
+ }
+ virtual void markAsNeedingAnotherRun() CATCH_OVERRIDE {
+ m_runState = NeedsAnotherRun;
+ }
+ private:
+ void moveToParent() {
+ assert( m_parent );
+ m_ctx.setCurrentTracker( m_parent );
+ }
+ void moveToThis() {
+ m_ctx.setCurrentTracker( this );
+ }
+ };
+
+ class SectionTracker : public TrackerBase {
+ public:
+ SectionTracker( std::string const& name, TrackerContext& ctx, ITracker* parent )
+ : TrackerBase( name, ctx, parent )
+ {}
+ virtual ~SectionTracker();
+
+ virtual bool isSectionTracker() const CATCH_OVERRIDE { return true; }
+
+ static SectionTracker& acquire( TrackerContext& ctx, std::string const& name ) {
+ SectionTracker* section = CATCH_NULL;
+
+ ITracker& currentTracker = ctx.currentTracker();
+ if( ITracker* childTracker = currentTracker.findChild( name ) ) {
+ assert( childTracker );
+ assert( childTracker->isSectionTracker() );
+ section = static_cast<SectionTracker*>( childTracker );
}
- ~Guard() {
- m_tracker.leaveTestCase();
+ else {
+ section = new SectionTracker( name, ctx, ¤tTracker );
+ currentTracker.addChild( section );
}
- private:
- Guard( Guard const& );
- void operator = ( Guard const& );
- TestCaseTracker& m_tracker;
- };
+ if( !ctx.completedCycle() && !section->isComplete() ) {
- private:
- void enterTestCase() {
- m_currentSection = &m_testCase;
- m_completedASectionThisRun = false;
- m_testCase.enter();
+ section->open();
+ }
+ return *section;
+ }
+ };
+
+ class IndexTracker : public TrackerBase {
+ int m_size;
+ int m_index;
+ public:
+ IndexTracker( std::string const& name, TrackerContext& ctx, ITracker* parent, int size )
+ : TrackerBase( name, ctx, parent ),
+ m_size( size ),
+ m_index( -1 )
+ {}
+ virtual ~IndexTracker();
+
+ virtual bool isIndexTracker() const CATCH_OVERRIDE { return true; }
+
+ static IndexTracker& acquire( TrackerContext& ctx, std::string const& name, int size ) {
+ IndexTracker* tracker = CATCH_NULL;
+
+ ITracker& currentTracker = ctx.currentTracker();
+ if( ITracker* childTracker = currentTracker.findChild( name ) ) {
+ assert( childTracker );
+ assert( childTracker->isIndexTracker() );
+ tracker = static_cast<IndexTracker*>( childTracker );
+ }
+ else {
+ tracker = new IndexTracker( name, ctx, ¤tTracker, size );
+ currentTracker.addChild( tracker );
+ }
+
+ if( !ctx.completedCycle() && !tracker->isComplete() ) {
+ if( tracker->m_runState != ExecutingChildren && tracker->m_runState != NeedsAnotherRun )
+ tracker->moveNext();
+ tracker->open();
+ }
+
+ return *tracker;
}
- void leaveTestCase() {
- m_testCase.leave();
+
+ int index() const { return m_index; }
+
+ void moveNext() {
+ m_index++;
+ m_children.clear();
}
- TrackedSection m_testCase;
- TrackedSection* m_currentSection;
- bool m_completedASectionThisRun;
+ virtual void close() CATCH_OVERRIDE {
+ TrackerBase::close();
+ if( m_runState == CompletedSuccessfully && m_index < m_size-1 )
+ m_runState = Executing;
+ }
};
-} // namespace SectionTracking
+ inline ITracker& TrackerContext::startRun() {
+ m_rootTracker = new SectionTracker( "{root}", *this, CATCH_NULL );
+ m_currentTracker = CATCH_NULL;
+ m_runState = Executing;
+ return *m_rootTracker;
+ }
+
+} // namespace TestCaseTracking
+
+using TestCaseTracking::ITracker;
+using TestCaseTracking::TrackerContext;
+using TestCaseTracking::SectionTracker;
+using TestCaseTracking::IndexTracker;
+
+} // namespace Catch
+
+// #included from: catch_fatal_condition.hpp
+#define TWOBLUECUBES_CATCH_FATAL_CONDITION_H_INCLUDED
+
+namespace Catch {
+
+ // Report the error condition then exit the process
+ inline void fatal( std::string const& message, int exitCode ) {
+ IContext& context = Catch::getCurrentContext();
+ IResultCapture* resultCapture = context.getResultCapture();
+ resultCapture->handleFatalErrorCondition( message );
+
+ if( Catch::alwaysTrue() ) // avoids "no return" warnings
+ exit( exitCode );
+ }
+
+} // namespace Catch
+
+#if defined ( CATCH_PLATFORM_WINDOWS ) /////////////////////////////////////////
+
+namespace Catch {
+
+ struct FatalConditionHandler {
+ void reset() {}
+ };
+
+} // namespace Catch
+
+#else // Not Windows - assumed to be POSIX compatible //////////////////////////
+
+#include <signal.h>
+
+namespace Catch {
+
+ struct SignalDefs { int id; const char* name; };
+ extern SignalDefs signalDefs[];
+ SignalDefs signalDefs[] = {
+ { SIGINT, "SIGINT - Terminal interrupt signal" },
+ { SIGILL, "SIGILL - Illegal instruction signal" },
+ { SIGFPE, "SIGFPE - Floating point error signal" },
+ { SIGSEGV, "SIGSEGV - Segmentation violation signal" },
+ { SIGTERM, "SIGTERM - Termination request signal" },
+ { SIGABRT, "SIGABRT - Abort (abnormal termination) signal" }
+ };
+
+ struct FatalConditionHandler {
+
+ static void handleSignal( int sig ) {
+ for( std::size_t i = 0; i < sizeof(signalDefs)/sizeof(SignalDefs); ++i )
+ if( sig == signalDefs[i].id )
+ fatal( signalDefs[i].name, -sig );
+ fatal( "<unknown signal>", -sig );
+ }
+
+ FatalConditionHandler() : m_isSet( true ) {
+ for( std::size_t i = 0; i < sizeof(signalDefs)/sizeof(SignalDefs); ++i )
+ signal( signalDefs[i].id, handleSignal );
+ }
+ ~FatalConditionHandler() {
+ reset();
+ }
+ void reset() {
+ if( m_isSet ) {
+ for( std::size_t i = 0; i < sizeof(signalDefs)/sizeof(SignalDefs); ++i )
+ signal( signalDefs[i].id, SIG_DFL );
+ m_isSet = false;
+ }
+ }
-using SectionTracking::TestCaseTracker;
+ bool m_isSet;
+ };
} // namespace Catch
+#endif // not Windows
+
#include <set>
#include <string>
@@ -4953,15 +5961,12 @@ namespace Catch {
public:
- explicit RunContext( Ptr<IConfig const> const& config, Ptr<IStreamingReporter> const& reporter )
- : m_runInfo( config->name() ),
+ explicit RunContext( Ptr<IConfig const> const& _config, Ptr<IStreamingReporter> const& reporter )
+ : m_runInfo( _config->name() ),
m_context( getCurrentMutableContext() ),
- m_activeTestCase( NULL ),
- m_config( config ),
- m_reporter( reporter ),
- m_prevRunner( m_context.getRunner() ),
- m_prevResultCapture( m_context.getResultCapture() ),
- m_prevConfig( m_context.getConfig() )
+ m_activeTestCase( CATCH_NULL ),
+ m_config( _config ),
+ m_reporter( reporter )
{
m_context.setRunner( this );
m_context.setConfig( m_config );
@@ -4971,10 +5976,6 @@ namespace Catch {
virtual ~RunContext() {
m_reporter->testRunEnded( TestRunStats( m_runInfo, m_totals, aborting() ) );
- m_context.setRunner( m_prevRunner );
- m_context.setConfig( NULL );
- m_context.setResultCapture( m_prevResultCapture );
- m_context.setConfig( m_prevConfig );
}
void testGroupStarting( std::string const& testSpec, std::size_t groupIndex, std::size_t groupsCount ) {
@@ -4995,17 +5996,25 @@ namespace Catch {
m_reporter->testCaseStarting( testInfo );
m_activeTestCase = &testCase;
- m_testCaseTracker = TestCaseTracker( testInfo.name );
do {
+ m_trackerContext.startRun();
do {
+ m_trackerContext.startCycle();
+ m_testCaseTracker = &SectionTracker::acquire( m_trackerContext, testInfo.name );
runCurrentTest( redirectedCout, redirectedCerr );
}
- while( !m_testCaseTracker->isCompleted() && !aborting() );
+ while( !m_testCaseTracker->isSuccessfullyCompleted() && !aborting() );
}
+ // !TBD: deprecated - this will be replaced by indexed trackers
while( getCurrentContext().advanceGeneratorsForCurrentTest() && !aborting() );
Totals deltaTotals = m_totals.delta( prevTotals );
+ if( testInfo.expectedToFail() && deltaTotals.testCases.passed > 0 ) {
+ deltaTotals.assertions.failed++;
+ deltaTotals.testCases.passed--;
+ deltaTotals.testCases.failed++;
+ }
m_totals.testCases += deltaTotals.testCases;
m_reporter->testCaseEnded( TestCaseStats( testInfo,
deltaTotals,
@@ -5013,8 +6022,8 @@ namespace Catch {
redirectedCerr,
aborting() ) );
- m_activeTestCase = NULL;
- m_testCaseTracker.reset();
+ m_activeTestCase = CATCH_NULL;
+ m_testCaseTracker = CATCH_NULL;
return deltaTotals;
}
@@ -5049,8 +6058,10 @@ namespace Catch {
std::ostringstream oss;
oss << sectionInfo.name << "@" << sectionInfo.lineInfo;
- if( !m_testCaseTracker->enterSection( oss.str() ) )
+ ITracker& sectionTracker = SectionTracker::acquire( m_trackerContext, oss.str() );
+ if( !sectionTracker.isOpen() )
return false;
+ m_activeSections.push_back( §ionTracker );
m_lastAssertionInfo.lineInfo = sectionInfo.lineInfo;
@@ -5061,30 +6072,40 @@ namespace Catch {
return true;
}
bool testForMissingAssertions( Counts& assertions ) {
- if( assertions.total() != 0 ||
- !m_config->warnAboutMissingAssertions() ||
- m_testCaseTracker->currentSectionHasChildren() )
+ if( assertions.total() != 0 )
+ return false;
+ if( !m_config->warnAboutMissingAssertions() )
+ return false;
+ if( m_trackerContext.currentTracker().hasChildren() )
return false;
m_totals.assertions.failed++;
assertions.failed++;
return true;
}
- virtual void sectionEnded( SectionInfo const& info, Counts const& prevAssertions, double _durationInSeconds ) {
- if( std::uncaught_exception() ) {
- m_unfinishedSections.push_back( UnfinishedSections( info, prevAssertions, _durationInSeconds ) );
- return;
- }
-
- Counts assertions = m_totals.assertions - prevAssertions;
+ virtual void sectionEnded( SectionEndInfo const& endInfo ) {
+ Counts assertions = m_totals.assertions - endInfo.prevAssertions;
bool missingAssertions = testForMissingAssertions( assertions );
- m_testCaseTracker->leaveSection();
+ if( !m_activeSections.empty() ) {
+ m_activeSections.back()->close();
+ m_activeSections.pop_back();
+ }
- m_reporter->sectionEnded( SectionStats( info, assertions, _durationInSeconds, missingAssertions ) );
+ m_reporter->sectionEnded( SectionStats( endInfo.sectionInfo, assertions, endInfo.durationInSeconds, missingAssertions ) );
m_messages.clear();
}
+ virtual void sectionEndedEarly( SectionEndInfo const& endInfo ) {
+ if( m_unfinishedSections.empty() )
+ m_activeSections.back()->fail();
+ else
+ m_activeSections.back()->close();
+ m_activeSections.pop_back();
+
+ m_unfinishedSections.push_back( endInfo );
+ }
+
virtual void pushScopedMessage( MessageInfo const& message ) {
m_messages.push_back( message );
}
@@ -5103,6 +6124,37 @@ namespace Catch {
return &m_lastResult;
}
+ virtual void handleFatalErrorCondition( std::string const& message ) {
+ ResultBuilder resultBuilder = makeUnexpectedResultBuilder();
+ resultBuilder.setResultType( ResultWas::FatalErrorCondition );
+ resultBuilder << message;
+ resultBuilder.captureExpression();
+
+ handleUnfinishedSections();
+
+ // Recreate section for test case (as we will lose the one that was in scope)
+ TestCaseInfo const& testCaseInfo = m_activeTestCase->getTestCaseInfo();
+ SectionInfo testCaseSection( testCaseInfo.lineInfo, testCaseInfo.name, testCaseInfo.description );
+
+ Counts assertions;
+ assertions.failed = 1;
+ SectionStats testCaseSectionStats( testCaseSection, assertions, 0, false );
+ m_reporter->sectionEnded( testCaseSectionStats );
+
+ TestCaseInfo testInfo = m_activeTestCase->getTestCaseInfo();
+
+ Totals deltaTotals;
+ deltaTotals.testCases.failed = 1;
+ m_reporter->testCaseEnded( TestCaseStats( testInfo,
+ deltaTotals,
+ "",
+ "",
+ false ) );
+ m_totals.testCases.failed++;
+ testGroupEnded( "", m_totals, 1, 1 );
+ m_reporter->testRunEnded( TestRunStats( m_runInfo, m_totals, false ) );
+ }
+
public:
// !TBD We need to do this another way!
bool aborting() const {
@@ -5119,17 +6171,18 @@ namespace Catch {
double duration = 0;
try {
m_lastAssertionInfo = AssertionInfo( "TEST_CASE", testCaseInfo.lineInfo, "", ResultDisposition::Normal );
- TestCaseTracker::Guard guard( *m_testCaseTracker );
+
+ seedRng( *m_config );
Timer timer;
timer.start();
if( m_reporter->getPreferences().shouldRedirectStdOut ) {
- StreamRedirect coutRedir( std::cout, redirectedCout );
- StreamRedirect cerrRedir( std::cerr, redirectedCerr );
- m_activeTestCase->invoke();
+ StreamRedirect coutRedir( Catch::cout(), redirectedCout );
+ StreamRedirect cerrRedir( Catch::cerr(), redirectedCerr );
+ invokeActiveTestCase();
}
else {
- m_activeTestCase->invoke();
+ invokeActiveTestCase();
}
duration = timer.getElapsedSeconds();
}
@@ -5137,20 +6190,10 @@ namespace Catch {
// This just means the test was aborted due to failure
}
catch(...) {
- ResultBuilder exResult( m_lastAssertionInfo.macroName.c_str(),
- m_lastAssertionInfo.lineInfo,
- m_lastAssertionInfo.capturedExpression.c_str(),
- m_lastAssertionInfo.resultDisposition );
- exResult.useActiveException();
+ makeUnexpectedResultBuilder().useActiveException();
}
- // If sections ended prematurely due to an exception we stored their
- // infos here so we can tear them down outside the unwind process.
- for( std::vector<UnfinishedSections>::const_reverse_iterator it = m_unfinishedSections.rbegin(),
- itEnd = m_unfinishedSections.rend();
- it != itEnd;
- ++it )
- sectionEnded( it->info, it->prevAssertions, it->durationInSeconds );
- m_unfinishedSections.clear();
+ m_testCaseTracker->close();
+ handleUnfinishedSections();
m_messages.clear();
Counts assertions = m_totals.assertions - prevAssertions;
@@ -5166,32 +6209,47 @@ namespace Catch {
m_reporter->sectionEnded( testCaseSectionStats );
}
+ void invokeActiveTestCase() {
+ FatalConditionHandler fatalConditionHandler; // Handle signals
+ m_activeTestCase->invoke();
+ fatalConditionHandler.reset();
+ }
+
private:
- struct UnfinishedSections {
- UnfinishedSections( SectionInfo const& _info, Counts const& _prevAssertions, double _durationInSeconds )
- : info( _info ), prevAssertions( _prevAssertions ), durationInSeconds( _durationInSeconds )
- {}
- SectionInfo info;
- Counts prevAssertions;
- double durationInSeconds;
- };
+ ResultBuilder makeUnexpectedResultBuilder() const {
+ return ResultBuilder( m_lastAssertionInfo.macroName.c_str(),
+ m_lastAssertionInfo.lineInfo,
+ m_lastAssertionInfo.capturedExpression.c_str(),
+ m_lastAssertionInfo.resultDisposition );
+ }
+
+ void handleUnfinishedSections() {
+ // If sections ended prematurely due to an exception we stored their
+ // infos here so we can tear them down outside the unwind process.
+ for( std::vector<SectionEndInfo>::const_reverse_iterator it = m_unfinishedSections.rbegin(),
+ itEnd = m_unfinishedSections.rend();
+ it != itEnd;
+ ++it )
+ sectionEnded( *it );
+ m_unfinishedSections.clear();
+ }
TestRunInfo m_runInfo;
IMutableContext& m_context;
TestCase const* m_activeTestCase;
- Option<TestCaseTracker> m_testCaseTracker;
+ ITracker* m_testCaseTracker;
+ ITracker* m_currentSectionTracker;
AssertionResult m_lastResult;
Ptr<IConfig const> m_config;
Totals m_totals;
Ptr<IStreamingReporter> m_reporter;
std::vector<MessageInfo> m_messages;
- IRunner* m_prevRunner;
- IResultCapture* m_prevResultCapture;
- Ptr<IConfig const> m_prevConfig;
AssertionInfo m_lastAssertionInfo;
- std::vector<UnfinishedSections> m_unfinishedSections;
+ std::vector<SectionEndInfo> m_unfinishedSections;
+ std::vector<ITracker*> m_activeSections;
+ TrackerContext m_trackerContext;
};
IResultCapture& getResultCapture() {
@@ -5212,18 +6270,19 @@ namespace Catch {
struct Version {
Version( unsigned int _majorVersion,
unsigned int _minorVersion,
- unsigned int _buildNumber,
- char const* const _branchName )
- : majorVersion( _majorVersion ),
- minorVersion( _minorVersion ),
- buildNumber( _buildNumber ),
- branchName( _branchName )
- {}
+ unsigned int _patchNumber,
+ std::string const& _branchName,
+ unsigned int _buildNumber );
unsigned int const majorVersion;
unsigned int const minorVersion;
+ unsigned int const patchNumber;
+
+ // buildNumber is only used if branchName is not null
+ std::string const branchName;
unsigned int const buildNumber;
- char const* const branchName;
+
+ friend std::ostream& operator << ( std::ostream& os, Version const& version );
private:
void operator=( Version const& );
@@ -5238,83 +6297,89 @@ namespace Catch {
namespace Catch {
- class Runner {
-
- public:
- Runner( Ptr<Config> const& config )
- : m_config( config )
- {
- openStream();
- makeReporter();
+ Ptr<IStreamingReporter> createReporter( std::string const& reporterName, Ptr<Config> const& config ) {
+ Ptr<IStreamingReporter> reporter = getRegistryHub().getReporterRegistry().create( reporterName, config.get() );
+ if( !reporter ) {
+ std::ostringstream oss;
+ oss << "No reporter registered with name: '" << reporterName << "'";
+ throw std::domain_error( oss.str() );
}
+ return reporter;
+ }
- Totals runTests() {
+ Ptr<IStreamingReporter> makeReporter( Ptr<Config> const& config ) {
+ std::vector<std::string> reporters = config->getReporterNames();
+ if( reporters.empty() )
+ reporters.push_back( "console" );
- RunContext context( m_config.get(), m_reporter );
+ Ptr<IStreamingReporter> reporter;
+ for( std::vector<std::string>::const_iterator it = reporters.begin(), itEnd = reporters.end();
+ it != itEnd;
+ ++it )
+ reporter = addReporter( reporter, createReporter( *it, config ) );
+ return reporter;
+ }
+ Ptr<IStreamingReporter> addListeners( Ptr<IConfig const> const& config, Ptr<IStreamingReporter> reporters ) {
+ IReporterRegistry::Listeners listeners = getRegistryHub().getReporterRegistry().getListeners();
+ for( IReporterRegistry::Listeners::const_iterator it = listeners.begin(), itEnd = listeners.end();
+ it != itEnd;
+ ++it )
+ reporters = addReporter(reporters, (*it)->create( ReporterConfig( config ) ) );
+ return reporters;
+ }
- Totals totals;
+ Totals runTests( Ptr<Config> const& config ) {
- context.testGroupStarting( "", 1, 1 ); // deprecated?
+ Ptr<IConfig const> iconfig = config.get();
- TestSpec testSpec = m_config->testSpec();
- if( !testSpec.hasFilters() )
- testSpec = TestSpecParser( ITagAliasRegistry::get() ).parse( "~[.]" ).testSpec(); // All not hidden tests
+ Ptr<IStreamingReporter> reporter = makeReporter( config );
+ reporter = addListeners( iconfig, reporter );
- std::vector<TestCase> testCases;
- getRegistryHub().getTestCaseRegistry().getFilteredTests( testSpec, *m_config, testCases );
+ RunContext context( iconfig, reporter );
- int testsRunForGroup = 0;
- for( std::vector<TestCase>::const_iterator it = testCases.begin(), itEnd = testCases.end();
- it != itEnd;
- ++it ) {
- testsRunForGroup++;
- if( m_testsAlreadyRun.find( *it ) == m_testsAlreadyRun.end() ) {
+ Totals totals;
- if( context.aborting() )
- break;
+ context.testGroupStarting( config->name(), 1, 1 );
- totals += context.runTest( *it );
- m_testsAlreadyRun.insert( *it );
- }
- }
- context.testGroupEnded( "", totals, 1, 1 );
- return totals;
- }
+ TestSpec testSpec = config->testSpec();
+ if( !testSpec.hasFilters() )
+ testSpec = TestSpecParser( ITagAliasRegistry::get() ).parse( "~[.]" ).testSpec(); // All not hidden tests
- private:
- void openStream() {
- // Open output file, if specified
- if( !m_config->getFilename().empty() ) {
- m_ofs.open( m_config->getFilename().c_str() );
- if( m_ofs.fail() ) {
- std::ostringstream oss;
- oss << "Unable to open file: '" << m_config->getFilename() << "'";
- throw std::domain_error( oss.str() );
- }
- m_config->setStreamBuf( m_ofs.rdbuf() );
- }
+ std::vector<TestCase> const& allTestCases = getAllTestCasesSorted( *iconfig );
+ for( std::vector<TestCase>::const_iterator it = allTestCases.begin(), itEnd = allTestCases.end();
+ it != itEnd;
+ ++it ) {
+ if( !context.aborting() && matchTest( *it, testSpec, *iconfig ) )
+ totals += context.runTest( *it );
+ else
+ reporter->skipTest( *it );
}
- void makeReporter() {
- std::string reporterName = m_config->getReporterName().empty()
- ? "console"
- : m_config->getReporterName();
- m_reporter = getRegistryHub().getReporterRegistry().create( reporterName, m_config.get() );
- if( !m_reporter ) {
- std::ostringstream oss;
- oss << "No reporter registered with name: '" << reporterName << "'";
- throw std::domain_error( oss.str() );
- }
- }
+ context.testGroupEnded( iconfig->name(), totals, 1, 1 );
+ return totals;
+ }
- private:
- Ptr<Config> m_config;
- std::ofstream m_ofs;
- Ptr<IStreamingReporter> m_reporter;
- std::set<TestCase> m_testsAlreadyRun;
- };
+ void applyFilenamesAsTags( IConfig const& config ) {
+ std::vector<TestCase> const& tests = getAllTestCasesSorted( config );
+ for(std::size_t i = 0; i < tests.size(); ++i ) {
+ TestCase& test = const_cast<TestCase&>( tests[i] );
+ std::set<std::string> tags = test.tags;
+
+ std::string filename = test.lineInfo.file;
+ std::string::size_type lastSlash = filename.find_last_of( "\\/" );
+ if( lastSlash != std::string::npos )
+ filename = filename.substr( lastSlash+1 );
+
+ std::string::size_type lastDot = filename.find_last_of( "." );
+ if( lastDot != std::string::npos )
+ filename = filename.substr( 0, lastDot );
- class Session {
+ tags.insert( "#" + filename );
+ setTags( test, tags );
+ }
+ }
+
+ class Session : NonCopyable {
static bool alreadyInstantiated;
public:
@@ -5325,7 +6390,7 @@ namespace Catch {
: m_cli( makeCommandLineParser() ) {
if( alreadyInstantiated ) {
std::string msg = "Only one instance of Catch::Session can ever be used";
- std::cerr << msg << std::endl;
+ Catch::cerr() << msg << std::endl;
throw std::logic_error( msg );
}
alreadyInstantiated = true;
@@ -5335,21 +6400,16 @@ namespace Catch {
}
void showHelp( std::string const& processName ) {
- std::cout << "\nCatch v" << libraryVersion.majorVersion << "."
- << libraryVersion.minorVersion << " build "
- << libraryVersion.buildNumber;
- if( libraryVersion.branchName != std::string( "master" ) )
- std::cout << " (" << libraryVersion.branchName << " branch)";
- std::cout << "\n";
+ Catch::cout() << "\nCatch v" << libraryVersion << "\n";
- m_cli.usage( std::cout, processName );
- std::cout << "For more detail usage please see the project docs\n" << std::endl;
+ m_cli.usage( Catch::cout(), processName );
+ Catch::cout() << "For more detail usage please see the project docs\n" << std::endl;
}
- int applyCommandLine( int argc, char* const argv[], OnUnusedOptions::DoWhat unusedOptionBehaviour = OnUnusedOptions::Fail ) {
+ int applyCommandLine( int argc, char const* const* const argv, OnUnusedOptions::DoWhat unusedOptionBehaviour = OnUnusedOptions::Fail ) {
try {
m_cli.setThrowOnUnrecognisedTokens( unusedOptionBehaviour == OnUnusedOptions::Fail );
- m_unusedTokens = m_cli.parseInto( argc, argv, m_configData );
+ m_unusedTokens = m_cli.parseInto( Clara::argsToVector( argc, argv ), m_configData );
if( m_configData.showHelp )
showHelp( m_configData.processName );
m_config.reset();
@@ -5357,11 +6417,12 @@ namespace Catch {
catch( std::exception& ex ) {
{
Colour colourGuard( Colour::Red );
- std::cerr << "\nError(s) in input:\n"
- << Text( ex.what(), TextAttributes().setIndent(2) )
- << "\n\n";
+ Catch::cerr()
+ << "\nError(s) in input:\n"
+ << Text( ex.what(), TextAttributes().setIndent(2) )
+ << "\n\n";
}
- m_cli.usage( std::cout, m_configData.processName );
+ m_cli.usage( Catch::cout(), m_configData.processName );
return (std::numeric_limits<int>::max)();
}
return 0;
@@ -5372,7 +6433,7 @@ namespace Catch {
m_config.reset();
}
- int run( int argc, char* const argv[] ) {
+ int run( int argc, char const* const* const argv ) {
int returnCode = applyCommandLine( argc, argv );
if( returnCode == 0 )
@@ -5387,16 +6448,20 @@ namespace Catch {
try
{
config(); // Force config to be constructed
- Runner runner( m_config );
+
+ seedRng( *m_config );
+
+ if( m_configData.filenamesAsTags )
+ applyFilenamesAsTags( *m_config );
// Handle list request
if( Option<std::size_t> listed = list( config() ) )
return static_cast<int>( *listed );
- return static_cast<int>( runner.runTests().assertions.failed );
+ return static_cast<int>( runTests( m_config ).assertions.failed );
}
catch( std::exception& ex ) {
- std::cerr << ex.what() << std::endl;
+ Catch::cerr() << ex.what() << std::endl;
return (std::numeric_limits<int>::max)();
}
}
@@ -5415,7 +6480,6 @@ namespace Catch {
m_config = new Config( m_configData );
return *m_config;
}
-
private:
Clara::CommandLine<ConfigData> m_cli;
std::vector<Clara::Parser::Token> m_unusedTokens;
@@ -5437,12 +6501,94 @@ namespace Catch {
#include <set>
#include <sstream>
#include <iostream>
+#include <algorithm>
namespace Catch {
+ struct RandomNumberGenerator {
+ typedef std::ptrdiff_t result_type;
+
+ result_type operator()( result_type n ) const { return std::rand() % n; }
+
+#ifdef CATCH_CONFIG_CPP11_SHUFFLE
+ static constexpr result_type min() { return 0; }
+ static constexpr result_type max() { return 1000000; }
+ result_type operator()() const { return std::rand() % max(); }
+#endif
+ template<typename V>
+ static void shuffle( V& vector ) {
+ RandomNumberGenerator rng;
+#ifdef CATCH_CONFIG_CPP11_SHUFFLE
+ std::shuffle( vector.begin(), vector.end(), rng );
+#else
+ std::random_shuffle( vector.begin(), vector.end(), rng );
+#endif
+ }
+ };
+
+ inline std::vector<TestCase> sortTests( IConfig const& config, std::vector<TestCase> const& unsortedTestCases ) {
+
+ std::vector<TestCase> sorted = unsortedTestCases;
+
+ switch( config.runOrder() ) {
+ case RunTests::InLexicographicalOrder:
+ std::sort( sorted.begin(), sorted.end() );
+ break;
+ case RunTests::InRandomOrder:
+ {
+ seedRng( config );
+ RandomNumberGenerator::shuffle( sorted );
+ }
+ break;
+ case RunTests::InDeclarationOrder:
+ // already in declaration order
+ break;
+ }
+ return sorted;
+ }
+ bool matchTest( TestCase const& testCase, TestSpec const& testSpec, IConfig const& config ) {
+ return testSpec.matches( testCase ) && ( config.allowThrows() || !testCase.throws() );
+ }
+
+ void enforceNoDuplicateTestCases( std::vector<TestCase> const& functions ) {
+ std::set<TestCase> seenFunctions;
+ for( std::vector<TestCase>::const_iterator it = functions.begin(), itEnd = functions.end();
+ it != itEnd;
+ ++it ) {
+ std::pair<std::set<TestCase>::const_iterator, bool> prev = seenFunctions.insert( *it );
+ if( !prev.second ) {
+ std::ostringstream ss;
+
+ ss << Colour( Colour::Red )
+ << "error: TEST_CASE( \"" << it->name << "\" ) already defined.\n"
+ << "\tFirst seen at " << prev.first->getTestCaseInfo().lineInfo << "\n"
+ << "\tRedefined at " << it->getTestCaseInfo().lineInfo << std::endl;
+
+ throw std::runtime_error(ss.str());
+ }
+ }
+ }
+
+ std::vector<TestCase> filterTests( std::vector<TestCase> const& testCases, TestSpec const& testSpec, IConfig const& config ) {
+ std::vector<TestCase> filtered;
+ filtered.reserve( testCases.size() );
+ for( std::vector<TestCase>::const_iterator it = testCases.begin(), itEnd = testCases.end();
+ it != itEnd;
+ ++it )
+ if( matchTest( *it, testSpec, config ) )
+ filtered.push_back( *it );
+ return filtered;
+ }
+ std::vector<TestCase> const& getAllTestCasesSorted( IConfig const& config ) {
+ return getRegistryHub().getTestCaseRegistry().getAllTestsSorted( config );
+ }
+
class TestRegistry : public ITestCaseRegistry {
public:
- TestRegistry() : m_unnamedCount( 0 ) {}
+ TestRegistry()
+ : m_currentSortOrder( RunTests::InDeclarationOrder ),
+ m_unnamedCount( 0 )
+ {}
virtual ~TestRegistry();
virtual void registerTest( TestCase const& testCase ) {
@@ -5452,49 +6598,29 @@ namespace Catch {
oss << "Anonymous test case " << ++m_unnamedCount;
return registerTest( testCase.withName( oss.str() ) );
}
-
- if( m_functions.find( testCase ) == m_functions.end() ) {
- m_functions.insert( testCase );
- m_functionsInOrder.push_back( testCase );
- if( !testCase.isHidden() )
- m_nonHiddenFunctions.push_back( testCase );
- }
- else {
- TestCase const& prev = *m_functions.find( testCase );
- {
- Colour colourGuard( Colour::Red );
- std::cerr << "error: TEST_CASE( \"" << name << "\" ) already defined.\n"
- << "\tFirst seen at " << prev.getTestCaseInfo().lineInfo << "\n"
- << "\tRedefined at " << testCase.getTestCaseInfo().lineInfo << std::endl;
- }
- exit(1);
- }
+ m_functions.push_back( testCase );
}
virtual std::vector<TestCase> const& getAllTests() const {
- return m_functionsInOrder;
- }
-
- virtual std::vector<TestCase> const& getAllNonHiddenTests() const {
- return m_nonHiddenFunctions;
+ return m_functions;
}
+ virtual std::vector<TestCase> const& getAllTestsSorted( IConfig const& config ) const {
+ if( m_sortedFunctions.empty() )
+ enforceNoDuplicateTestCases( m_functions );
- virtual void getFilteredTests( TestSpec const& testSpec, IConfig const& config, std::vector<TestCase>& matchingTestCases ) const {
- for( std::vector<TestCase>::const_iterator it = m_functionsInOrder.begin(),
- itEnd = m_functionsInOrder.end();
- it != itEnd;
- ++it ) {
- if( testSpec.matches( *it ) && ( config.allowThrows() || !it->throws() ) )
- matchingTestCases.push_back( *it );
+ if( m_currentSortOrder != config.runOrder() || m_sortedFunctions.empty() ) {
+ m_sortedFunctions = sortTests( config, m_functions );
+ m_currentSortOrder = config.runOrder();
}
+ return m_sortedFunctions;
}
private:
-
- std::set<TestCase> m_functions;
- std::vector<TestCase> m_functionsInOrder;
- std::vector<TestCase> m_nonHiddenFunctions;
+ std::vector<TestCase> m_functions;
+ mutable RunTests::InWhatOrder m_currentSortOrder;
+ mutable std::vector<TestCase> m_sortedFunctions;
size_t m_unnamedCount;
+ std::ios_base::Init m_ostreamInit; // Forces cout/ cerr to be initialised
};
///////////////////////////////////////////////////////////////////////////
@@ -5527,29 +6653,38 @@ namespace Catch {
return className;
}
- ///////////////////////////////////////////////////////////////////////////
+ void registerTestCase
+ ( ITestCase* testCase,
+ char const* classOrQualifiedMethodName,
+ NameAndDesc const& nameAndDesc,
+ SourceLineInfo const& lineInfo ) {
- AutoReg::AutoReg( TestFunction function,
- SourceLineInfo const& lineInfo,
- NameAndDesc const& nameAndDesc ) {
+ getMutableRegistryHub().registerTest
+ ( makeTestCase
+ ( testCase,
+ extractClassName( classOrQualifiedMethodName ),
+ nameAndDesc.name,
+ nameAndDesc.description,
+ lineInfo ) );
+ }
+ void registerTestCaseFunction
+ ( TestFunction function,
+ SourceLineInfo const& lineInfo,
+ NameAndDesc const& nameAndDesc ) {
registerTestCase( new FreeFunctionTestCase( function ), "", nameAndDesc, lineInfo );
}
- AutoReg::~AutoReg() {}
-
- void AutoReg::registerTestCase( ITestCase* testCase,
- char const* classOrQualifiedMethodName,
- NameAndDesc const& nameAndDesc,
- SourceLineInfo const& lineInfo ) {
+ ///////////////////////////////////////////////////////////////////////////
- getMutableRegistryHub().registerTest
- ( makeTestCase( testCase,
- extractClassName( classOrQualifiedMethodName ),
- nameAndDesc.name,
- nameAndDesc.description,
- lineInfo ) );
+ AutoReg::AutoReg
+ ( TestFunction function,
+ SourceLineInfo const& lineInfo,
+ NameAndDesc const& nameAndDesc ) {
+ registerTestCaseFunction( function, lineInfo, nameAndDesc );
}
+ AutoReg::~AutoReg() {}
+
} // end namespace Catch
// #included from: catch_reporter_registry.hpp
@@ -5563,27 +6698,32 @@ namespace Catch {
public:
- virtual ~ReporterRegistry() {
- deleteAllValues( m_factories );
- }
+ virtual ~ReporterRegistry() CATCH_OVERRIDE {}
- virtual IStreamingReporter* create( std::string const& name, Ptr<IConfig> const& config ) const {
+ virtual IStreamingReporter* create( std::string const& name, Ptr<IConfig const> const& config ) const CATCH_OVERRIDE {
FactoryMap::const_iterator it = m_factories.find( name );
if( it == m_factories.end() )
- return NULL;
+ return CATCH_NULL;
return it->second->create( ReporterConfig( config ) );
}
- void registerReporter( std::string const& name, IReporterFactory* factory ) {
+ void registerReporter( std::string const& name, Ptr<IReporterFactory> const& factory ) {
m_factories.insert( std::make_pair( name, factory ) );
}
+ void registerListener( Ptr<IReporterFactory> const& factory ) {
+ m_listeners.push_back( factory );
+ }
- FactoryMap const& getFactories() const {
+ virtual FactoryMap const& getFactories() const CATCH_OVERRIDE {
return m_factories;
}
+ virtual Listeners const& getListeners() const CATCH_OVERRIDE {
+ return m_listeners;
+ }
private:
FactoryMap m_factories;
+ Listeners m_listeners;
};
}
@@ -5611,13 +6751,13 @@ namespace Catch {
#ifdef __OBJC__
// In Objective-C try objective-c exceptions first
@try {
- throw;
+ return tryTranslators();
}
@catch (NSException *exception) {
- return toString( [exception description] );
+ return Catch::toString( [exception description] );
}
#else
- throw;
+ return tryTranslators();
#endif
}
catch( TestFailureException& ) {
@@ -5633,20 +6773,15 @@ namespace Catch {
return msg;
}
catch(...) {
- return tryTranslators( m_translators.begin() );
+ return "Unknown exception";
}
}
- std::string tryTranslators( std::vector<const IExceptionTranslator*>::const_iterator it ) const {
- if( it == m_translators.end() )
- return "Unknown exception";
-
- try {
- return (*it)->translate();
- }
- catch(...) {
- return tryTranslators( it+1 );
- }
+ std::string tryTranslators() const {
+ if( m_translators.empty() )
+ throw;
+ else
+ return m_translators[0]->translate( m_translators.begin()+1, m_translators.end() );
}
private:
@@ -5666,24 +6801,27 @@ namespace Catch {
public: // IRegistryHub
RegistryHub() {
}
- virtual IReporterRegistry const& getReporterRegistry() const {
+ virtual IReporterRegistry const& getReporterRegistry() const CATCH_OVERRIDE {
return m_reporterRegistry;
}
- virtual ITestCaseRegistry const& getTestCaseRegistry() const {
+ virtual ITestCaseRegistry const& getTestCaseRegistry() const CATCH_OVERRIDE {
return m_testCaseRegistry;
}
- virtual IExceptionTranslatorRegistry& getExceptionTranslatorRegistry() {
+ virtual IExceptionTranslatorRegistry& getExceptionTranslatorRegistry() CATCH_OVERRIDE {
return m_exceptionTranslatorRegistry;
}
public: // IMutableRegistryHub
- virtual void registerReporter( std::string const& name, IReporterFactory* factory ) {
+ virtual void registerReporter( std::string const& name, Ptr<IReporterFactory> const& factory ) CATCH_OVERRIDE {
m_reporterRegistry.registerReporter( name, factory );
}
- virtual void registerTest( TestCase const& testInfo ) {
+ virtual void registerListener( Ptr<IReporterFactory> const& factory ) CATCH_OVERRIDE {
+ m_reporterRegistry.registerListener( factory );
+ }
+ virtual void registerTest( TestCase const& testInfo ) CATCH_OVERRIDE {
m_testCaseRegistry.registerTest( testInfo );
}
- virtual void registerTranslator( const IExceptionTranslator* translator ) {
+ virtual void registerTranslator( const IExceptionTranslator* translator ) CATCH_OVERRIDE {
m_exceptionTranslatorRegistry.registerTranslator( translator );
}
@@ -5695,7 +6833,7 @@ namespace Catch {
// Single, global, instance
inline RegistryHub*& getTheRegistryHub() {
- static RegistryHub* theRegistryHub = NULL;
+ static RegistryHub* theRegistryHub = CATCH_NULL;
if( !theRegistryHub )
theRegistryHub = new RegistryHub();
return theRegistryHub;
@@ -5710,7 +6848,7 @@ namespace Catch {
}
void cleanUp() {
delete getTheRegistryHub();
- getTheRegistryHub() = NULL;
+ getTheRegistryHub() = CATCH_NULL;
cleanUpContext();
}
std::string translateActiveException() {
@@ -5746,21 +6884,9 @@ namespace Catch {
// #included from: catch_stream.hpp
#define TWOBLUECUBES_CATCH_STREAM_HPP_INCLUDED
-// #included from: catch_streambuf.h
-#define TWOBLUECUBES_CATCH_STREAMBUF_H_INCLUDED
-
-#include <streambuf>
-
-namespace Catch {
-
- class StreamBufBase : public std::streambuf {
- public:
- virtual ~StreamBufBase() CATCH_NOEXCEPT;
- };
-}
-
#include <stdexcept>
#include <cstdio>
+#include <iostream>
namespace Catch {
@@ -5802,6 +6928,19 @@ namespace Catch {
///////////////////////////////////////////////////////////////////////////
+ FileStream::FileStream( std::string const& filename ) {
+ m_ofs.open( filename.c_str() );
+ if( m_ofs.fail() ) {
+ std::ostringstream oss;
+ oss << "Unable to open file: '" << filename << "'";
+ throw std::domain_error( oss.str() );
+ }
+ }
+
+ std::ostream& FileStream::stream() const {
+ return m_ofs;
+ }
+
struct OutputDebugWriter {
void operator()( std::string const&str ) {
@@ -5809,28 +6948,40 @@ namespace Catch {
}
};
- Stream::Stream()
- : streamBuf( NULL ), isOwned( false )
+ DebugOutStream::DebugOutStream()
+ : m_streamBuf( new StreamBufImpl<OutputDebugWriter>() ),
+ m_os( m_streamBuf.get() )
{}
- Stream::Stream( std::streambuf* _streamBuf, bool _isOwned )
- : streamBuf( _streamBuf ), isOwned( _isOwned )
+ std::ostream& DebugOutStream::stream() const {
+ return m_os;
+ }
+
+ // Store the streambuf from cout up-front because
+ // cout may get redirected when running tests
+ CoutStream::CoutStream()
+ : m_os( Catch::cout().rdbuf() )
{}
- void Stream::release() {
- if( isOwned ) {
- delete streamBuf;
- streamBuf = NULL;
- isOwned = false;
- }
+ std::ostream& CoutStream::stream() const {
+ return m_os;
}
+
+#ifndef CATCH_CONFIG_NOSTDOUT // If you #define this you must implement these functions
+ std::ostream& cout() {
+ return std::cout;
+ }
+ std::ostream& cerr() {
+ return std::cerr;
+ }
+#endif
}
namespace Catch {
class Context : public IMutableContext {
- Context() : m_config( NULL ), m_runner( NULL ), m_resultCapture( NULL ) {}
+ Context() : m_config( CATCH_NULL ), m_runner( CATCH_NULL ), m_resultCapture( CATCH_NULL ) {}
Context( Context const& );
void operator=( Context const& );
@@ -5873,10 +7024,10 @@ namespace Catch {
std::string testName = getResultCapture()->getCurrentTestName();
std::map<std::string, IGeneratorsForTest*>::const_iterator it =
- m_generatorsByTestName.find( testName );
+ m_generatorsByTestName.find( testName );
return it != m_generatorsByTestName.end()
? it->second
- : NULL;
+ : CATCH_NULL;
}
IGeneratorsForTest& getGeneratorsForCurrentTest() {
@@ -5897,7 +7048,7 @@ namespace Catch {
};
namespace {
- Context* currentContext = NULL;
+ Context* currentContext = CATCH_NULL;
}
IMutableContext& getCurrentMutableContext() {
if( !currentContext )
@@ -5908,31 +7059,44 @@ namespace Catch {
return getCurrentMutableContext();
}
- Stream createStream( std::string const& streamName ) {
- if( streamName == "stdout" ) return Stream( std::cout.rdbuf(), false );
- if( streamName == "stderr" ) return Stream( std::cerr.rdbuf(), false );
- if( streamName == "debug" ) return Stream( new StreamBufImpl<OutputDebugWriter>, true );
-
- throw std::domain_error( "Unknown stream: " + streamName );
- }
-
void cleanUpContext() {
delete currentContext;
- currentContext = NULL;
+ currentContext = CATCH_NULL;
}
}
// #included from: catch_console_colour_impl.hpp
#define TWOBLUECUBES_CATCH_CONSOLE_COLOUR_IMPL_HPP_INCLUDED
-namespace Catch { namespace Detail {
- struct IColourImpl {
- virtual ~IColourImpl() {}
- virtual void use( Colour::Code _colourCode ) = 0;
- };
-}}
+namespace Catch {
+ namespace {
-#if defined ( CATCH_PLATFORM_WINDOWS ) /////////////////////////////////////////
+ struct IColourImpl {
+ virtual ~IColourImpl() {}
+ virtual void use( Colour::Code _colourCode ) = 0;
+ };
+
+ struct NoColourImpl : IColourImpl {
+ void use( Colour::Code ) {}
+
+ static IColourImpl* instance() {
+ static NoColourImpl s_instance;
+ return &s_instance;
+ }
+ };
+
+ } // anon namespace
+} // namespace Catch
+
+#if !defined( CATCH_CONFIG_COLOUR_NONE ) && !defined( CATCH_CONFIG_COLOUR_WINDOWS ) && !defined( CATCH_CONFIG_COLOUR_ANSI )
+# ifdef CATCH_PLATFORM_WINDOWS
+# define CATCH_CONFIG_COLOUR_WINDOWS
+# else
+# define CATCH_CONFIG_COLOUR_ANSI
+# endif
+#endif
+
+#if defined ( CATCH_CONFIG_COLOUR_WINDOWS ) /////////////////////////////////////////
#ifndef NOMINMAX
#define NOMINMAX
@@ -5947,18 +7111,19 @@ namespace Catch { namespace Detail {
namespace Catch {
namespace {
- class Win32ColourImpl : public Detail::IColourImpl {
+ class Win32ColourImpl : public IColourImpl {
public:
Win32ColourImpl() : stdoutHandle( GetStdHandle(STD_OUTPUT_HANDLE) )
{
CONSOLE_SCREEN_BUFFER_INFO csbiInfo;
GetConsoleScreenBufferInfo( stdoutHandle, &csbiInfo );
- originalAttributes = csbiInfo.wAttributes;
+ originalForegroundAttributes = csbiInfo.wAttributes & ~( BACKGROUND_GREEN | BACKGROUND_RED | BACKGROUND_BLUE | BACKGROUND_INTENSITY );
+ originalBackgroundAttributes = csbiInfo.wAttributes & ~( FOREGROUND_GREEN | FOREGROUND_RED | FOREGROUND_BLUE | FOREGROUND_INTENSITY );
}
virtual void use( Colour::Code _colourCode ) {
switch( _colourCode ) {
- case Colour::None: return setTextAttribute( originalAttributes );
+ case Colour::None: return setTextAttribute( originalForegroundAttributes );
case Colour::White: return setTextAttribute( FOREGROUND_GREEN | FOREGROUND_RED | FOREGROUND_BLUE );
case Colour::Red: return setTextAttribute( FOREGROUND_RED );
case Colour::Green: return setTextAttribute( FOREGROUND_GREEN );
@@ -5978,25 +7143,33 @@ namespace {
private:
void setTextAttribute( WORD _textAttribute ) {
- SetConsoleTextAttribute( stdoutHandle, _textAttribute );
+ SetConsoleTextAttribute( stdoutHandle, _textAttribute | originalBackgroundAttributes );
}
HANDLE stdoutHandle;
- WORD originalAttributes;
+ WORD originalForegroundAttributes;
+ WORD originalBackgroundAttributes;
};
- inline bool shouldUseColourForPlatform() {
- return true;
- }
-
- static Detail::IColourImpl* platformColourInstance() {
+ IColourImpl* platformColourInstance() {
static Win32ColourImpl s_instance;
- return &s_instance;
+
+ Ptr<IConfig const> config = getCurrentContext().getConfig();
+ UseColour::YesOrNo colourMode = config
+ ? config->useColour()
+ : UseColour::Auto;
+ if( colourMode == UseColour::Auto )
+ colourMode = !isDebuggerActive()
+ ? UseColour::Yes
+ : UseColour::No;
+ return colourMode == UseColour::Yes
+ ? &s_instance
+ : NoColourImpl::instance();
}
} // end anon namespace
} // end namespace Catch
-#else // Not Windows - assumed to be POSIX compatible //////////////////////////
+#elif defined( CATCH_CONFIG_COLOUR_ANSI ) //////////////////////////////////////
#include <unistd.h>
@@ -6007,7 +7180,7 @@ namespace {
// Thanks to Adam Strzelecki for original contribution
// (http://github.com/nanoant)
// https://github.com/philsquared/Catch/pull/131
- class PosixColourImpl : public Detail::IColourImpl {
+ class PosixColourImpl : public IColourImpl {
public:
virtual void use( Colour::Code _colourCode ) {
switch( _colourCode ) {
@@ -6015,7 +7188,7 @@ namespace {
case Colour::White: return setColour( "[0m" );
case Colour::Red: return setColour( "[0;31m" );
case Colour::Green: return setColour( "[0;32m" );
- case Colour::Blue: return setColour( "[0:34m" );
+ case Colour::Blue: return setColour( "[0;34m" );
case Colour::Cyan: return setColour( "[0;36m" );
case Colour::Yellow: return setColour( "[0;33m" );
case Colour::Grey: return setColour( "[1;30m" );
@@ -6028,53 +7201,53 @@ namespace {
case Colour::Bright: throw std::logic_error( "not a colour" );
}
}
+ static IColourImpl* instance() {
+ static PosixColourImpl s_instance;
+ return &s_instance;
+ }
+
private:
void setColour( const char* _escapeCode ) {
- std::cout << '\033' << _escapeCode;
+ Catch::cout() << '\033' << _escapeCode;
}
};
- inline bool shouldUseColourForPlatform() {
- return isatty(STDOUT_FILENO);
- }
-
- static Detail::IColourImpl* platformColourInstance() {
- static PosixColourImpl s_instance;
- return &s_instance;
+ IColourImpl* platformColourInstance() {
+ Ptr<IConfig const> config = getCurrentContext().getConfig();
+ UseColour::YesOrNo colourMode = config
+ ? config->useColour()
+ : UseColour::Auto;
+ if( colourMode == UseColour::Auto )
+ colourMode = (!isDebuggerActive() && isatty(STDOUT_FILENO) )
+ ? UseColour::Yes
+ : UseColour::No;
+ return colourMode == UseColour::Yes
+ ? PosixColourImpl::instance()
+ : NoColourImpl::instance();
}
} // end anon namespace
} // end namespace Catch
-#endif // not Windows
+#else // not Windows or ANSI ///////////////////////////////////////////////
namespace Catch {
- namespace {
- struct NoColourImpl : Detail::IColourImpl {
- void use( Colour::Code ) {}
+ static IColourImpl* platformColourInstance() { return NoColourImpl::instance(); }
- static IColourImpl* instance() {
- static NoColourImpl s_instance;
- return &s_instance;
- }
- };
- static bool shouldUseColour() {
- return shouldUseColourForPlatform() && !isDebuggerActive();
- }
- }
+} // end namespace Catch
+
+#endif // Windows/ ANSI/ None
+
+namespace Catch {
Colour::Colour( Code _colourCode ) : m_moved( false ) { use( _colourCode ); }
Colour::Colour( Colour const& _other ) : m_moved( false ) { const_cast<Colour&>( _other ).m_moved = true; }
Colour::~Colour(){ if( !m_moved ) use( None ); }
- void Colour::use( Code _colourCode ) {
- impl()->use( _colourCode );
- }
- Detail::IColourImpl* Colour::impl() {
- return shouldUseColour()
- ? platformColourInstance()
- : NoColourImpl::instance();
+ void Colour::use( Code _colourCode ) {
+ static IColourImpl* impl = platformColourInstance();
+ impl->use( _colourCode );
}
} // end namespace Catch
@@ -6239,7 +7412,7 @@ namespace Catch {
namespace Catch {
inline TestCaseInfo::SpecialProperties parseSpecialTag( std::string const& tag ) {
- if( tag == "." ||
+ if( startsWith( tag, "." ) ||
tag == "hide" ||
tag == "!hide" )
return TestCaseInfo::IsHidden;
@@ -6259,13 +7432,13 @@ namespace Catch {
if( isReservedTag( tag ) ) {
{
Colour colourGuard( Colour::Red );
- std::cerr
+ Catch::cerr()
<< "Tag name [" << tag << "] not allowed.\n"
<< "Tag names starting with non alpha-numeric characters are reserved\n";
}
{
Colour colourGuard( Colour::FileName );
- std::cerr << _lineInfo << std::endl;
+ Catch::cerr() << _lineInfo << std::endl;
}
exit(1);
}
@@ -6293,14 +7466,15 @@ namespace Catch {
}
else {
if( c == ']' ) {
- enforceNotReservedTag( tag, _lineInfo );
-
- inTag = false;
- if( tag == "hide" || tag == "." )
+ TestCaseInfo::SpecialProperties prop = parseSpecialTag( tag );
+ if( prop == TestCaseInfo::IsHidden )
isHidden = true;
- else
- tags.insert( tag );
+ else if( prop == TestCaseInfo::None )
+ enforceNotReservedTag( tag, _lineInfo );
+
+ tags.insert( tag );
tag.clear();
+ inTag = false;
}
else
tag += c;
@@ -6315,6 +7489,21 @@ namespace Catch {
return TestCase( _testCase, info );
}
+ void setTags( TestCaseInfo& testCaseInfo, std::set<std::string> const& tags )
+ {
+ testCaseInfo.tags = tags;
+ testCaseInfo.lcaseTags.clear();
+
+ std::ostringstream oss;
+ for( std::set<std::string>::const_iterator it = tags.begin(), itEnd = tags.end(); it != itEnd; ++it ) {
+ oss << "[" << *it << "]";
+ std::string lcaseTag = toLower( *it );
+ testCaseInfo.properties = static_cast<TestCaseInfo::SpecialProperties>( testCaseInfo.properties | parseSpecialTag( lcaseTag ) );
+ testCaseInfo.lcaseTags.insert( lcaseTag );
+ }
+ testCaseInfo.tagsAsString = oss.str();
+ }
+
TestCaseInfo::TestCaseInfo( std::string const& _name,
std::string const& _className,
std::string const& _description,
@@ -6323,18 +7512,10 @@ namespace Catch {
: name( _name ),
className( _className ),
description( _description ),
- tags( _tags ),
lineInfo( _lineInfo ),
properties( None )
{
- std::ostringstream oss;
- for( std::set<std::string>::const_iterator it = _tags.begin(), itEnd = _tags.end(); it != itEnd; ++it ) {
- oss << "[" << *it << "]";
- std::string lcaseTag = toLower( *it );
- properties = static_cast<SpecialProperties>( properties | parseSpecialTag( lcaseTag ) );
- lcaseTags.insert( lcaseTag );
- }
- tagsAsString = oss.str();
+ setTags( *this, _tags );
}
TestCaseInfo::TestCaseInfo( TestCaseInfo const& other )
@@ -6417,8 +7598,33 @@ namespace Catch {
namespace Catch {
- // These numbers are maintained by a script
- Version libraryVersion( 1, 0, 53, "master" );
+ Version::Version
+ ( unsigned int _majorVersion,
+ unsigned int _minorVersion,
+ unsigned int _patchNumber,
+ std::string const& _branchName,
+ unsigned int _buildNumber )
+ : majorVersion( _majorVersion ),
+ minorVersion( _minorVersion ),
+ patchNumber( _patchNumber ),
+ branchName( _branchName ),
+ buildNumber( _buildNumber )
+ {}
+
+ std::ostream& operator << ( std::ostream& os, Version const& version ) {
+ os << version.majorVersion << "."
+ << version.minorVersion << "."
+ << version.patchNumber;
+
+ if( !version.branchName.empty() ) {
+ os << "-" << version.branchName
+ << "." << version.buildNumber;
+ }
+ return os;
+ }
+
+ Version libraryVersion( 1, 6, 0, "", 0 );
+
}
// #included from: catch_message.hpp
@@ -6502,6 +7708,7 @@ namespace Catch
virtual void testCaseEnded( TestCaseStats const& testCaseStats );
virtual void testGroupEnded( TestGroupStats const& testGroupStats );
virtual void testRunEnded( TestRunStats const& testRunStats );
+ virtual void skipTest( TestCaseInfo const& );
private:
Ptr<IReporter> m_legacyReporter;
@@ -6575,6 +7782,8 @@ namespace Catch
void LegacyReporterAdapter::testRunEnded( TestRunStats const& testRunStats ) {
m_legacyReporter->EndTesting( testRunStats.totals );
}
+ void LegacyReporterAdapter::skipTest( TestCaseInfo const& ) {
+ }
}
// #included from: catch_timer.hpp
@@ -6597,17 +7806,17 @@ namespace Catch {
uint64_t getCurrentTicks() {
static uint64_t hz=0, hzo=0;
if (!hz) {
- QueryPerformanceFrequency((LARGE_INTEGER*)&hz);
- QueryPerformanceCounter((LARGE_INTEGER*)&hzo);
+ QueryPerformanceFrequency( reinterpret_cast<LARGE_INTEGER*>( &hz ) );
+ QueryPerformanceCounter( reinterpret_cast<LARGE_INTEGER*>( &hzo ) );
}
uint64_t t;
- QueryPerformanceCounter((LARGE_INTEGER*)&t);
+ QueryPerformanceCounter( reinterpret_cast<LARGE_INTEGER*>( &t ) );
return ((t-hzo)*1000000)/hz;
}
#else
uint64_t getCurrentTicks() {
timeval t;
- gettimeofday(&t,NULL);
+ gettimeofday(&t,CATCH_NULL);
return static_cast<uint64_t>( t.tv_sec ) * 1000000ull + static_cast<uint64_t>( t.tv_usec );
}
#endif
@@ -6616,14 +7825,14 @@ namespace Catch {
void Timer::start() {
m_ticks = getCurrentTicks();
}
- unsigned int Timer::getElapsedNanoseconds() const {
+ unsigned int Timer::getElapsedMicroseconds() const {
return static_cast<unsigned int>(getCurrentTicks() - m_ticks);
}
unsigned int Timer::getElapsedMilliseconds() const {
- return static_cast<unsigned int>((getCurrentTicks() - m_ticks)/1000);
+ return static_cast<unsigned int>(getElapsedMicroseconds()/1000);
}
double Timer::getElapsedSeconds() const {
- return (getCurrentTicks() - m_ticks)/1000000.0;
+ return getElapsedMicroseconds()/1000000.0;
}
} // namespace Catch
@@ -6645,8 +7854,11 @@ namespace Catch {
bool contains( std::string const& s, std::string const& infix ) {
return s.find( infix ) != std::string::npos;
}
+ char toLowerCh(char c) {
+ return static_cast<char>( ::tolower( c ) );
+ }
void toLowerInPlace( std::string& s ) {
- std::transform( s.begin(), s.end(), s.begin(), ::tolower );
+ std::transform( s.begin(), s.end(), s.begin(), toLowerCh );
}
std::string toLower( std::string const& s ) {
std::string lc = s;
@@ -6661,6 +7873,20 @@ namespace Catch {
return start != std::string::npos ? str.substr( start, 1+end-start ) : "";
}
+ bool replaceInPlace( std::string& str, std::string const& replaceThis, std::string const& withThis ) {
+ bool replaced = false;
+ std::size_t i = str.find( replaceThis );
+ while( i != std::string::npos ) {
+ replaced = true;
+ str = str.substr( 0, i ) + withThis + str.substr( i+replaceThis.size() );
+ if( i < str.size()-withThis.size() )
+ i = str.find( replaceThis, i+withThis.size() );
+ else
+ i = std::string::npos;
+ }
+ return replaced;
+ }
+
pluralise::pluralise( std::size_t count, std::string const& label )
: m_count( count ),
m_label( label )
@@ -6688,6 +7914,17 @@ namespace Catch {
bool SourceLineInfo::operator == ( SourceLineInfo const& other ) const {
return line == other.line && file == other.file;
}
+ bool SourceLineInfo::operator < ( SourceLineInfo const& other ) const {
+ return line < other.line || ( line == other.line && file < other.file );
+ }
+
+ void seedRng( IConfig const& config ) {
+ if( config.rngSeed() != 0 )
+ std::srand( config.rngSeed() );
+ }
+ unsigned int rngSeed() {
+ return getCurrentContext().getConfig()->rngSeed();
+ }
std::ostream& operator << ( std::ostream& os, SourceLineInfo const& info ) {
#ifndef __GNUG__
@@ -6728,8 +7965,13 @@ namespace Catch {
}
Section::~Section() {
- if( m_sectionIncluded )
- getResultCapture().sectionEnded( m_info, m_assertions, m_timer.getElapsedSeconds() );
+ if( m_sectionIncluded ) {
+ SectionEndInfo endInfo( m_info, m_assertions, m_timer.getElapsedSeconds() );
+ if( std::uncaught_exception() )
+ getResultCapture().sectionEndedEarly( endInfo );
+ else
+ getResultCapture().sectionEnded( endInfo );
+ }
}
// This indicates whether the section should be executed or not
@@ -6781,8 +8023,8 @@ namespace Catch {
// Call sysctl.
size = sizeof(info);
- if( sysctl(mib, sizeof(mib) / sizeof(*mib), &info, &size, NULL, 0) != 0 ) {
- std::cerr << "\n** Call to sysctl failed - unable to determine if debugger is active **\n" << std::endl;
+ if( sysctl(mib, sizeof(mib) / sizeof(*mib), &info, &size, CATCH_NULL, 0) != 0 ) {
+ Catch::cerr() << "\n** Call to sysctl failed - unable to determine if debugger is active **\n" << std::endl;
return false;
}
@@ -6823,7 +8065,7 @@ namespace Catch {
namespace Catch {
void writeToDebugConsole( std::string const& text ) {
// !TBD: Need a version for Mac/ XCode and other IDEs
- std::cout << text;
+ Catch::cout() << text;
}
}
#endif // Platform
@@ -6835,7 +8077,11 @@ namespace Catch {
namespace Detail {
+ const std::string unprintableString = "{?}";
+
namespace {
+ const int hexThreshold = 255;
+
struct Endianness {
enum Arch { Big, Little };
@@ -6893,7 +8139,7 @@ std::string toString( std::wstring const& value ) {
s.reserve( value.size() );
for(size_t i = 0; i < value.size(); ++i )
s += value[i] <= 0xff ? static_cast<char>( value[i] ) : '?';
- return toString( s );
+ return Catch::toString( s );
}
std::string toString( const char* const value ) {
@@ -6917,20 +8163,21 @@ std::string toString( wchar_t* const value )
std::string toString( int value ) {
std::ostringstream oss;
oss << value;
+ if( value > Detail::hexThreshold )
+ oss << " (0x" << std::hex << value << ")";
return oss.str();
}
std::string toString( unsigned long value ) {
std::ostringstream oss;
- if( value > 8192 )
- oss << "0x" << std::hex << value;
- else
- oss << value;
+ oss << value;
+ if( value > Detail::hexThreshold )
+ oss << " (0x" << std::hex << value << ")";
return oss.str();
}
std::string toString( unsigned int value ) {
- return toString( static_cast<unsigned long>( value ) );
+ return Catch::toString( static_cast<unsigned long>( value ) );
}
template<typename T>
@@ -6974,6 +8221,23 @@ std::string toString( unsigned char value ) {
return toString( static_cast<char>( value ) );
}
+#ifdef CATCH_CONFIG_CPP11_LONG_LONG
+std::string toString( long long value ) {
+ std::ostringstream oss;
+ oss << value;
+ if( value > Detail::hexThreshold )
+ oss << " (0x" << std::hex << value << ")";
+ return oss.str();
+}
+std::string toString( unsigned long long value ) {
+ std::ostringstream oss;
+ oss << value;
+ if( value > Detail::hexThreshold )
+ oss << " (0x" << std::hex << value << ")";
+ return oss.str();
+}
+#endif
+
#ifdef CATCH_CONFIG_CPP11_NULLPTR
std::string toString( std::nullptr_t ) {
return "nullptr";
@@ -7003,11 +8267,17 @@ std::string toString( std::nullptr_t ) {
namespace Catch {
+ std::string capturedExpressionWithSecondArgument( std::string const& capturedExpression, std::string const& secondArg ) {
+ return secondArg.empty() || secondArg == "\"\""
+ ? capturedExpression
+ : capturedExpression + ", " + secondArg;
+ }
ResultBuilder::ResultBuilder( char const* macroName,
SourceLineInfo const& lineInfo,
char const* capturedExpression,
- ResultDisposition::Flags resultDisposition )
- : m_assertionInfo( macroName, lineInfo, capturedExpression, resultDisposition ),
+ ResultDisposition::Flags resultDisposition,
+ char const* secondArg )
+ : m_assertionInfo( macroName, lineInfo, capturedExpressionWithSecondArgument( capturedExpression, secondArg ), resultDisposition ),
m_shouldDebugBreak( false ),
m_shouldThrow( false )
{}
@@ -7044,19 +8314,45 @@ namespace Catch {
captureResult( ResultWas::ThrewException );
}
- void ResultBuilder::captureResult( ResultWas::OfType resultType ) {
- setResultType( resultType );
- captureExpression();
+ void ResultBuilder::captureResult( ResultWas::OfType resultType ) {
+ setResultType( resultType );
+ captureExpression();
+ }
+ void ResultBuilder::captureExpectedException( std::string const& expectedMessage ) {
+ if( expectedMessage.empty() )
+ captureExpectedException( Matchers::Impl::Generic::AllOf<std::string>() );
+ else
+ captureExpectedException( Matchers::Equals( expectedMessage ) );
+ }
+
+ void ResultBuilder::captureExpectedException( Matchers::Impl::Matcher<std::string> const& matcher ) {
+
+ assert( m_exprComponents.testFalse == false );
+ AssertionResultData data = m_data;
+ data.resultType = ResultWas::Ok;
+ data.reconstructedExpression = m_assertionInfo.capturedExpression;
+
+ std::string actualMessage = Catch::translateActiveException();
+ if( !matcher.match( actualMessage ) ) {
+ data.resultType = ResultWas::ExpressionFailed;
+ data.reconstructedExpression = actualMessage;
+ }
+ AssertionResult result( m_assertionInfo, data );
+ handleResult( result );
}
void ResultBuilder::captureExpression() {
AssertionResult result = build();
+ handleResult( result );
+ }
+ void ResultBuilder::handleResult( AssertionResult const& result )
+ {
getResultCapture().assertionEnded( result );
if( !result.isOk() ) {
if( getCurrentContext().getConfig()->shouldDebugBreak() )
m_shouldDebugBreak = true;
- if( getCurrentContext().getRunner()->aborting() || m_assertionInfo.resultDisposition == ResultDisposition::Normal )
+ if( getCurrentContext().getRunner()->aborting() || (m_assertionInfo.resultDisposition & ResultDisposition::Normal) )
m_shouldThrow = true;
}
}
@@ -7094,7 +8390,7 @@ namespace Catch {
}
std::string ResultBuilder::reconstructExpression() const {
if( m_exprComponents.op == "" )
- return m_exprComponents.lhs.empty() ? m_assertionInfo.capturedExpression : m_exprComponents.op + m_exprComponents.lhs;
+ return m_exprComponents.lhs.empty() ? m_assertionInfo.capturedExpression : m_exprComponents.lhs;
else if( m_exprComponents.op == "matches" )
return m_exprComponents.lhs + " " + m_exprComponents.rhs;
else if( m_exprComponents.op != "!" ) {
@@ -7196,19 +8492,157 @@ namespace Catch {
}
catch( std::exception& ex ) {
Colour colourGuard( Colour::Red );
- std::cerr << ex.what() << std::endl;
+ Catch::cerr() << ex.what() << std::endl;
exit(1);
}
}
} // end namespace Catch
+// #included from: ../reporters/catch_reporter_multi.hpp
+#define TWOBLUECUBES_CATCH_REPORTER_MULTI_HPP_INCLUDED
+
+namespace Catch {
+
+class MultipleReporters : public SharedImpl<IStreamingReporter> {
+ typedef std::vector<Ptr<IStreamingReporter> > Reporters;
+ Reporters m_reporters;
+
+public:
+ void add( Ptr<IStreamingReporter> const& reporter ) {
+ m_reporters.push_back( reporter );
+ }
+
+public: // IStreamingReporter
+
+ virtual ReporterPreferences getPreferences() const CATCH_OVERRIDE {
+ return m_reporters[0]->getPreferences();
+ }
+
+ virtual void noMatchingTestCases( std::string const& spec ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->noMatchingTestCases( spec );
+ }
+
+ virtual void testRunStarting( TestRunInfo const& testRunInfo ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->testRunStarting( testRunInfo );
+ }
+
+ virtual void testGroupStarting( GroupInfo const& groupInfo ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->testGroupStarting( groupInfo );
+ }
+
+ virtual void testCaseStarting( TestCaseInfo const& testInfo ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->testCaseStarting( testInfo );
+ }
+
+ virtual void sectionStarting( SectionInfo const& sectionInfo ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->sectionStarting( sectionInfo );
+ }
+
+ virtual void assertionStarting( AssertionInfo const& assertionInfo ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->assertionStarting( assertionInfo );
+ }
+
+ // The return value indicates if the messages buffer should be cleared:
+ virtual bool assertionEnded( AssertionStats const& assertionStats ) CATCH_OVERRIDE {
+ bool clearBuffer = false;
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ clearBuffer |= (*it)->assertionEnded( assertionStats );
+ return clearBuffer;
+ }
+
+ virtual void sectionEnded( SectionStats const& sectionStats ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->sectionEnded( sectionStats );
+ }
+
+ virtual void testCaseEnded( TestCaseStats const& testCaseStats ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->testCaseEnded( testCaseStats );
+ }
+
+ virtual void testGroupEnded( TestGroupStats const& testGroupStats ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->testGroupEnded( testGroupStats );
+ }
+
+ virtual void testRunEnded( TestRunStats const& testRunStats ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->testRunEnded( testRunStats );
+ }
+
+ virtual void skipTest( TestCaseInfo const& testInfo ) CATCH_OVERRIDE {
+ for( Reporters::const_iterator it = m_reporters.begin(), itEnd = m_reporters.end();
+ it != itEnd;
+ ++it )
+ (*it)->skipTest( testInfo );
+ }
+
+ virtual MultipleReporters* tryAsMulti() CATCH_OVERRIDE {
+ return this;
+ }
+
+};
+
+Ptr<IStreamingReporter> addReporter( Ptr<IStreamingReporter> const& existingReporter, Ptr<IStreamingReporter> const& additionalReporter ) {
+ Ptr<IStreamingReporter> resultingReporter;
+
+ if( existingReporter ) {
+ MultipleReporters* multi = existingReporter->tryAsMulti();
+ if( !multi ) {
+ multi = new MultipleReporters;
+ resultingReporter = Ptr<IStreamingReporter>( multi );
+ if( existingReporter )
+ multi->add( existingReporter );
+ }
+ else
+ resultingReporter = existingReporter;
+ multi->add( additionalReporter );
+ }
+ else
+ resultingReporter = additionalReporter;
+
+ return resultingReporter;
+}
+
+} // end namespace Catch
+
// #included from: ../reporters/catch_reporter_xml.hpp
#define TWOBLUECUBES_CATCH_REPORTER_XML_HPP_INCLUDED
// #included from: catch_reporter_bases.hpp
#define TWOBLUECUBES_CATCH_REPORTER_BASES_HPP_INCLUDED
+#include <cstring>
+
namespace Catch {
struct StreamingReporterBase : SharedImpl<IStreamingReporter> {
@@ -7216,43 +8650,53 @@ namespace Catch {
StreamingReporterBase( ReporterConfig const& _config )
: m_config( _config.fullConfig() ),
stream( _config.stream() )
- {}
+ {
+ m_reporterPrefs.shouldRedirectStdOut = false;
+ }
+
+ virtual ReporterPreferences getPreferences() const CATCH_OVERRIDE {
+ return m_reporterPrefs;
+ }
- virtual ~StreamingReporterBase();
+ virtual ~StreamingReporterBase() CATCH_OVERRIDE;
- virtual void noMatchingTestCases( std::string const& ) {}
+ virtual void noMatchingTestCases( std::string const& ) CATCH_OVERRIDE {}
- virtual void testRunStarting( TestRunInfo const& _testRunInfo ) {
+ virtual void testRunStarting( TestRunInfo const& _testRunInfo ) CATCH_OVERRIDE {
currentTestRunInfo = _testRunInfo;
}
- virtual void testGroupStarting( GroupInfo const& _groupInfo ) {
+ virtual void testGroupStarting( GroupInfo const& _groupInfo ) CATCH_OVERRIDE {
currentGroupInfo = _groupInfo;
}
- virtual void testCaseStarting( TestCaseInfo const& _testInfo ) {
+ virtual void testCaseStarting( TestCaseInfo const& _testInfo ) CATCH_OVERRIDE {
currentTestCaseInfo = _testInfo;
}
- virtual void sectionStarting( SectionInfo const& _sectionInfo ) {
+ virtual void sectionStarting( SectionInfo const& _sectionInfo ) CATCH_OVERRIDE {
m_sectionStack.push_back( _sectionInfo );
}
- virtual void sectionEnded( SectionStats const& /* _sectionStats */ ) {
+ virtual void sectionEnded( SectionStats const& /* _sectionStats */ ) CATCH_OVERRIDE {
m_sectionStack.pop_back();
}
- virtual void testCaseEnded( TestCaseStats const& /* _testCaseStats */ ) {
+ virtual void testCaseEnded( TestCaseStats const& /* _testCaseStats */ ) CATCH_OVERRIDE {
currentTestCaseInfo.reset();
- assert( m_sectionStack.empty() );
}
- virtual void testGroupEnded( TestGroupStats const& /* _testGroupStats */ ) {
+ virtual void testGroupEnded( TestGroupStats const& /* _testGroupStats */ ) CATCH_OVERRIDE {
currentGroupInfo.reset();
}
- virtual void testRunEnded( TestRunStats const& /* _testRunStats */ ) {
+ virtual void testRunEnded( TestRunStats const& /* _testRunStats */ ) CATCH_OVERRIDE {
currentTestCaseInfo.reset();
currentGroupInfo.reset();
currentTestRunInfo.reset();
}
- Ptr<IConfig> m_config;
+ virtual void skipTest( TestCaseInfo const& ) CATCH_OVERRIDE {
+ // Don't do anything with this by default.
+ // It can optionally be overridden in the derived class.
+ }
+
+ Ptr<IConfig const> m_config;
std::ostream& stream;
LazyStat<TestRunInfo> currentTestRunInfo;
@@ -7260,6 +8704,7 @@ namespace Catch {
LazyStat<TestCaseInfo> currentTestCaseInfo;
std::vector<SectionInfo> m_sectionStack;
+ ReporterPreferences m_reporterPrefs;
};
struct CumulativeReporterBase : SharedImpl<IStreamingReporter> {
@@ -7310,15 +8755,21 @@ namespace Catch {
CumulativeReporterBase( ReporterConfig const& _config )
: m_config( _config.fullConfig() ),
stream( _config.stream() )
- {}
+ {
+ m_reporterPrefs.shouldRedirectStdOut = false;
+ }
~CumulativeReporterBase();
- virtual void testRunStarting( TestRunInfo const& ) {}
- virtual void testGroupStarting( GroupInfo const& ) {}
+ virtual ReporterPreferences getPreferences() const CATCH_OVERRIDE {
+ return m_reporterPrefs;
+ }
+
+ virtual void testRunStarting( TestRunInfo const& ) CATCH_OVERRIDE {}
+ virtual void testGroupStarting( GroupInfo const& ) CATCH_OVERRIDE {}
- virtual void testCaseStarting( TestCaseInfo const& ) {}
+ virtual void testCaseStarting( TestCaseInfo const& ) CATCH_OVERRIDE {}
- virtual void sectionStarting( SectionInfo const& sectionInfo ) {
+ virtual void sectionStarting( SectionInfo const& sectionInfo ) CATCH_OVERRIDE {
SectionStats incompleteStats( sectionInfo, Counts(), 0, false );
Ptr<SectionNode> node;
if( m_sectionStack.empty() ) {
@@ -7343,21 +8794,21 @@ namespace Catch {
m_deepestSection = node;
}
- virtual void assertionStarting( AssertionInfo const& ) {}
+ virtual void assertionStarting( AssertionInfo const& ) CATCH_OVERRIDE {}
- virtual bool assertionEnded( AssertionStats const& assertionStats ) {
+ virtual bool assertionEnded( AssertionStats const& assertionStats ) CATCH_OVERRIDE {
assert( !m_sectionStack.empty() );
SectionNode& sectionNode = *m_sectionStack.back();
sectionNode.assertions.push_back( assertionStats );
return true;
}
- virtual void sectionEnded( SectionStats const& sectionStats ) {
+ virtual void sectionEnded( SectionStats const& sectionStats ) CATCH_OVERRIDE {
assert( !m_sectionStack.empty() );
SectionNode& node = *m_sectionStack.back();
node.stats = sectionStats;
m_sectionStack.pop_back();
}
- virtual void testCaseEnded( TestCaseStats const& testCaseStats ) {
+ virtual void testCaseEnded( TestCaseStats const& testCaseStats ) CATCH_OVERRIDE {
Ptr<TestCaseNode> node = new TestCaseNode( testCaseStats );
assert( m_sectionStack.size() == 0 );
node->children.push_back( m_rootSection );
@@ -7368,12 +8819,12 @@ namespace Catch {
m_deepestSection->stdOut = testCaseStats.stdOut;
m_deepestSection->stdErr = testCaseStats.stdErr;
}
- virtual void testGroupEnded( TestGroupStats const& testGroupStats ) {
+ virtual void testGroupEnded( TestGroupStats const& testGroupStats ) CATCH_OVERRIDE {
Ptr<TestGroupNode> node = new TestGroupNode( testGroupStats );
node->children.swap( m_testCases );
m_testGroups.push_back( node );
}
- virtual void testRunEnded( TestRunStats const& testRunStats ) {
+ virtual void testRunEnded( TestRunStats const& testRunStats ) CATCH_OVERRIDE {
Ptr<TestRunNode> node = new TestRunNode( testRunStats );
node->children.swap( m_testGroups );
m_testRuns.push_back( node );
@@ -7381,7 +8832,9 @@ namespace Catch {
}
virtual void testRunEndedCumulative() = 0;
- Ptr<IConfig> m_config;
+ virtual void skipTest( TestCaseInfo const& ) CATCH_OVERRIDE {}
+
+ Ptr<IConfig const> m_config;
std::ostream& stream;
std::vector<AssertionStats> m_assertions;
std::vector<std::vector<Ptr<SectionNode> > > m_sections;
@@ -7393,7 +8846,29 @@ namespace Catch {
Ptr<SectionNode> m_rootSection;
Ptr<SectionNode> m_deepestSection;
std::vector<Ptr<SectionNode> > m_sectionStack;
+ ReporterPreferences m_reporterPrefs;
+
+ };
+
+ template<char C>
+ char const* getLineOfChars() {
+ static char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0};
+ if( !*line ) {
+ memset( line, C, CATCH_CONFIG_CONSOLE_WIDTH-1 );
+ line[CATCH_CONFIG_CONSOLE_WIDTH-1] = 0;
+ }
+ return line;
+ }
+ struct TestEventListenerBase : StreamingReporterBase {
+ TestEventListenerBase( ReporterConfig const& _config )
+ : StreamingReporterBase( _config )
+ {}
+
+ virtual void assertionStarting( AssertionInfo const& ) CATCH_OVERRIDE {}
+ virtual bool assertionEnded( AssertionStats const& ) CATCH_OVERRIDE {
+ return false;
+ }
};
} // end namespace Catch
@@ -7426,7 +8901,7 @@ namespace Catch {
template<typename T>
class ReporterRegistrar {
- class ReporterFactory : public IReporterFactory {
+ class ReporterFactory : public SharedImpl<IReporterFactory> {
// *** Please Note ***:
// - If you end up here looking at a compiler error because it's trying to register
@@ -7454,23 +8929,103 @@ namespace Catch {
getMutableRegistryHub().registerReporter( name, new ReporterFactory() );
}
};
+
+ template<typename T>
+ class ListenerRegistrar {
+
+ class ListenerFactory : public SharedImpl<IReporterFactory> {
+
+ virtual IStreamingReporter* create( ReporterConfig const& config ) const {
+ return new T( config );
+ }
+ virtual std::string getDescription() const {
+ return "";
+ }
+ };
+
+ public:
+
+ ListenerRegistrar() {
+ getMutableRegistryHub().registerListener( new ListenerFactory() );
+ }
+ };
}
#define INTERNAL_CATCH_REGISTER_LEGACY_REPORTER( name, reporterType ) \
namespace{ Catch::LegacyReporterRegistrar<reporterType> catch_internal_RegistrarFor##reporterType( name ); }
+
#define INTERNAL_CATCH_REGISTER_REPORTER( name, reporterType ) \
namespace{ Catch::ReporterRegistrar<reporterType> catch_internal_RegistrarFor##reporterType( name ); }
+#define INTERNAL_CATCH_REGISTER_LISTENER( listenerType ) \
+ namespace{ Catch::ListenerRegistrar<listenerType> catch_internal_RegistrarFor##listenerType; }
+
// #included from: ../internal/catch_xmlwriter.hpp
#define TWOBLUECUBES_CATCH_XMLWRITER_HPP_INCLUDED
#include <sstream>
-#include <iostream>
#include <string>
#include <vector>
+#include <iomanip>
namespace Catch {
+ class XmlEncode {
+ public:
+ enum ForWhat { ForTextNodes, ForAttributes };
+
+ XmlEncode( std::string const& str, ForWhat forWhat = ForTextNodes )
+ : m_str( str ),
+ m_forWhat( forWhat )
+ {}
+
+ void encodeTo( std::ostream& os ) const {
+
+ // Apostrophe escaping not necessary if we always use " to write attributes
+ // (see: http://www.w3.org/TR/xml/#syntax)
+
+ for( std::size_t i = 0; i < m_str.size(); ++ i ) {
+ char c = m_str[i];
+ switch( c ) {
+ case '<': os << "<"; break;
+ case '&': os << "&"; break;
+
+ case '>':
+ // See: http://www.w3.org/TR/xml/#syntax
+ if( i > 2 && m_str[i-1] == ']' && m_str[i-2] == ']' )
+ os << ">";
+ else
+ os << c;
+ break;
+
+ case '\"':
+ if( m_forWhat == ForAttributes )
+ os << """;
+ else
+ os << c;
+ break;
+
+ default:
+ // Escape control chars - based on contribution by @espenalb in PR #465 and
+ // by @mrpi PR #588
+ if ( ( c >= 0 && c < '\x09' ) || ( c > '\x0D' && c < '\x20') || c=='\x7F' )
+ os << "&#x" << std::uppercase << std::hex << std::setfill('0') << std::setw(2) << static_cast<int>( c ) << ';';
+ else
+ os << c;
+ }
+ }
+ }
+
+ friend std::ostream& operator << ( std::ostream& os, XmlEncode const& xmlEncode ) {
+ xmlEncode.encodeTo( os );
+ return os;
+ }
+
+ private:
+ std::string m_str;
+ ForWhat m_forWhat;
+ };
+
class XmlWriter {
public:
@@ -7482,7 +9037,7 @@ namespace Catch {
ScopedElement( ScopedElement const& other )
: m_writer( other.m_writer ){
- other.m_writer = NULL;
+ other.m_writer = CATCH_NULL;
}
~ScopedElement() {
@@ -7508,41 +9063,27 @@ namespace Catch {
XmlWriter()
: m_tagIsOpen( false ),
m_needsNewline( false ),
- m_os( &std::cout )
- {}
+ m_os( &Catch::cout() )
+ {
+ // We encode control characters, which requires
+ // XML 1.1
+ // see http://stackoverflow.com/questions/404107/why-are-control-characters-illegal-in-xml-1-0
+ *m_os << "<?xml version=\"1.1\" encoding=\"UTF-8\"?>\n";
+ }
XmlWriter( std::ostream& os )
: m_tagIsOpen( false ),
m_needsNewline( false ),
m_os( &os )
- {}
+ {
+ *m_os << "<?xml version=\"1.1\" encoding=\"UTF-8\"?>\n";
+ }
~XmlWriter() {
while( !m_tags.empty() )
endElement();
}
-//# ifndef CATCH_CPP11_OR_GREATER
-// XmlWriter& operator = ( XmlWriter const& other ) {
-// XmlWriter temp( other );
-// swap( temp );
-// return *this;
-// }
-//# else
-// XmlWriter( XmlWriter const& ) = default;
-// XmlWriter( XmlWriter && ) = default;
-// XmlWriter& operator = ( XmlWriter const& ) = default;
-// XmlWriter& operator = ( XmlWriter && ) = default;
-//# endif
-//
-// void swap( XmlWriter& other ) {
-// std::swap( m_tagIsOpen, other.m_tagIsOpen );
-// std::swap( m_needsNewline, other.m_needsNewline );
-// std::swap( m_tags, other.m_tags );
-// std::swap( m_indent, other.m_indent );
-// std::swap( m_os, other.m_os );
-// }
-
XmlWriter& startElement( std::string const& name ) {
ensureTagClosed();
newlineIfNecessary();
@@ -7574,11 +9115,8 @@ namespace Catch {
}
XmlWriter& writeAttribute( std::string const& name, std::string const& attribute ) {
- if( !name.empty() && !attribute.empty() ) {
- stream() << " " << name << "=\"";
- writeEncodedText( attribute );
- stream() << "\"";
- }
+ if( !name.empty() && !attribute.empty() )
+ stream() << " " << name << "=\"" << XmlEncode( attribute, XmlEncode::ForAttributes ) << "\"";
return *this;
}
@@ -7589,9 +9127,9 @@ namespace Catch {
template<typename T>
XmlWriter& writeAttribute( std::string const& name, T const& attribute ) {
- if( !name.empty() )
- stream() << " " << name << "=\"" << attribute << "\"";
- return *this;
+ std::ostringstream oss;
+ oss << attribute;
+ return writeAttribute( name, oss.str() );
}
XmlWriter& writeText( std::string const& text, bool indent = true ) {
@@ -7600,7 +9138,7 @@ namespace Catch {
ensureTagClosed();
if( tagWasOpen && indent )
stream() << m_indent;
- writeEncodedText( text );
+ stream() << XmlEncode( text );
m_needsNewline = true;
}
return *this;
@@ -7645,30 +9183,6 @@ namespace Catch {
}
}
- void writeEncodedText( std::string const& text ) {
- static const char* charsToEncode = "<&\"";
- std::string mtext = text;
- std::string::size_type pos = mtext.find_first_of( charsToEncode );
- while( pos != std::string::npos ) {
- stream() << mtext.substr( 0, pos );
-
- switch( mtext[pos] ) {
- case '<':
- stream() << "<";
- break;
- case '&':
- stream() << "&";
- break;
- case '\"':
- stream() << """;
- break;
- }
- mtext = mtext.substr( pos+1 );
- pos = mtext.find_first_of( charsToEncode );
- }
- stream() << mtext;
- }
-
bool m_tagIsOpen;
bool m_needsNewline;
std::vector<std::string> m_tags;
@@ -7677,82 +9191,103 @@ namespace Catch {
};
}
+// #included from: catch_reenable_warnings.h
+
+#define TWOBLUECUBES_CATCH_REENABLE_WARNINGS_H_INCLUDED
+
+#ifdef __clang__
+# ifdef __ICC // icpc defines the __clang__ macro
+# pragma warning(pop)
+# else
+# pragma clang diagnostic pop
+# endif
+#elif defined __GNUC__
+# pragma GCC diagnostic pop
+#endif
+
+
namespace Catch {
- class XmlReporter : public SharedImpl<IReporter> {
+ class XmlReporter : public StreamingReporterBase {
public:
- XmlReporter( ReporterConfig const& config ) : m_config( config ), m_sectionDepth( 0 ) {}
+ XmlReporter( ReporterConfig const& _config )
+ : StreamingReporterBase( _config ),
+ m_xml(_config.stream()),
+ m_sectionDepth( 0 )
+ {
+ m_reporterPrefs.shouldRedirectStdOut = true;
+ }
+
+ virtual ~XmlReporter() CATCH_OVERRIDE;
static std::string getDescription() {
return "Reports test results as an XML document";
}
- virtual ~XmlReporter();
- private: // IReporter
+ public: // StreamingReporterBase
- virtual bool shouldRedirectStdout() const {
- return true;
+ virtual void noMatchingTestCases( std::string const& s ) CATCH_OVERRIDE {
+ StreamingReporterBase::noMatchingTestCases( s );
}
- virtual void StartTesting() {
- m_xml.setStream( m_config.stream() );
+ virtual void testRunStarting( TestRunInfo const& testInfo ) CATCH_OVERRIDE {
+ StreamingReporterBase::testRunStarting( testInfo );
m_xml.startElement( "Catch" );
- if( !m_config.fullConfig()->name().empty() )
- m_xml.writeAttribute( "name", m_config.fullConfig()->name() );
- }
-
- virtual void EndTesting( const Totals& totals ) {
- m_xml.scopedElement( "OverallResults" )
- .writeAttribute( "successes", totals.assertions.passed )
- .writeAttribute( "failures", totals.assertions.failed )
- .writeAttribute( "expectedFailures", totals.assertions.failedButOk );
- m_xml.endElement();
+ if( !m_config->name().empty() )
+ m_xml.writeAttribute( "name", m_config->name() );
}
- virtual void StartGroup( const std::string& groupName ) {
+ virtual void testGroupStarting( GroupInfo const& groupInfo ) CATCH_OVERRIDE {
+ StreamingReporterBase::testGroupStarting( groupInfo );
m_xml.startElement( "Group" )
- .writeAttribute( "name", groupName );
+ .writeAttribute( "name", groupInfo.name );
}
- virtual void EndGroup( const std::string&, const Totals& totals ) {
- m_xml.scopedElement( "OverallResults" )
- .writeAttribute( "successes", totals.assertions.passed )
- .writeAttribute( "failures", totals.assertions.failed )
- .writeAttribute( "expectedFailures", totals.assertions.failedButOk );
- m_xml.endElement();
+ virtual void testCaseStarting( TestCaseInfo const& testInfo ) CATCH_OVERRIDE {
+ StreamingReporterBase::testCaseStarting(testInfo);
+ m_xml.startElement( "TestCase" ).writeAttribute( "name", testInfo.name );
+
+ if ( m_config->showDurations() == ShowDurations::Always )
+ m_testCaseTimer.start();
}
- virtual void StartSection( const std::string& sectionName, const std::string& description ) {
+ virtual void sectionStarting( SectionInfo const& sectionInfo ) CATCH_OVERRIDE {
+ StreamingReporterBase::sectionStarting( sectionInfo );
if( m_sectionDepth++ > 0 ) {
m_xml.startElement( "Section" )
- .writeAttribute( "name", trim( sectionName ) )
- .writeAttribute( "description", description );
+ .writeAttribute( "name", trim( sectionInfo.name ) )
+ .writeAttribute( "description", sectionInfo.description );
}
}
- virtual void NoAssertionsInSection( const std::string& ) {}
- virtual void NoAssertionsInTestCase( const std::string& ) {}
- virtual void EndSection( const std::string& /*sectionName*/, const Counts& assertions ) {
- if( --m_sectionDepth > 0 ) {
- m_xml.scopedElement( "OverallResults" )
- .writeAttribute( "successes", assertions.passed )
- .writeAttribute( "failures", assertions.failed )
- .writeAttribute( "expectedFailures", assertions.failedButOk );
- m_xml.endElement();
- }
- }
+ virtual void assertionStarting( AssertionInfo const& ) CATCH_OVERRIDE { }
- virtual void StartTestCase( const Catch::TestCaseInfo& testInfo ) {
- m_xml.startElement( "TestCase" ).writeAttribute( "name", trim( testInfo.name ) );
- m_currentTestSuccess = true;
- }
+ virtual bool assertionEnded( AssertionStats const& assertionStats ) CATCH_OVERRIDE {
+ const AssertionResult& assertionResult = assertionStats.assertionResult;
- virtual void Result( const Catch::AssertionResult& assertionResult ) {
- if( !m_config.fullConfig()->includeSuccessfulResults() && assertionResult.getResultType() == ResultWas::Ok )
- return;
+ // Print any info messages in <Info> tags.
+ if( assertionStats.assertionResult.getResultType() != ResultWas::Ok ) {
+ for( std::vector<MessageInfo>::const_iterator it = assertionStats.infoMessages.begin(), itEnd = assertionStats.infoMessages.end();
+ it != itEnd;
+ ++it ) {
+ if( it->type == ResultWas::Info ) {
+ m_xml.scopedElement( "Info" )
+ .writeText( it->message );
+ } else if ( it->type == ResultWas::Warning ) {
+ m_xml.scopedElement( "Warning" )
+ .writeText( it->message );
+ }
+ }
+ }
+ // Drop out if result was successful but we're not printing them.
+ if( !m_config->includeSuccessfulResults() && isOk(assertionResult.getResultType()) )
+ return true;
+
+ // Print the expression if there is one.
if( assertionResult.hasExpression() ) {
m_xml.startElement( "Expression" )
.writeAttribute( "success", assertionResult.succeeded() )
+ .writeAttribute( "type", assertionResult.getTestMacroName() )
.writeAttribute( "filename", assertionResult.getSourceInfo().file )
.writeAttribute( "line", assertionResult.getSourceInfo().line );
@@ -7760,58 +9295,96 @@ namespace Catch {
.writeText( assertionResult.getExpression() );
m_xml.scopedElement( "Expanded" )
.writeText( assertionResult.getExpandedExpression() );
- m_currentTestSuccess &= assertionResult.succeeded();
}
+ // And... Print a result applicable to each result type.
switch( assertionResult.getResultType() ) {
case ResultWas::ThrewException:
m_xml.scopedElement( "Exception" )
.writeAttribute( "filename", assertionResult.getSourceInfo().file )
.writeAttribute( "line", assertionResult.getSourceInfo().line )
.writeText( assertionResult.getMessage() );
- m_currentTestSuccess = false;
+ break;
+ case ResultWas::FatalErrorCondition:
+ m_xml.scopedElement( "FatalErrorCondition" )
+ .writeAttribute( "filename", assertionResult.getSourceInfo().file )
+ .writeAttribute( "line", assertionResult.getSourceInfo().line )
+ .writeText( assertionResult.getMessage() );
break;
case ResultWas::Info:
m_xml.scopedElement( "Info" )
.writeText( assertionResult.getMessage() );
break;
case ResultWas::Warning:
- m_xml.scopedElement( "Warning" )
- .writeText( assertionResult.getMessage() );
+ // Warning will already have been written
break;
case ResultWas::ExplicitFailure:
m_xml.scopedElement( "Failure" )
.writeText( assertionResult.getMessage() );
- m_currentTestSuccess = false;
break;
- case ResultWas::Unknown:
- case ResultWas::Ok:
- case ResultWas::FailureBit:
- case ResultWas::ExpressionFailed:
- case ResultWas::Exception:
- case ResultWas::DidntThrowException:
+ default:
break;
}
+
if( assertionResult.hasExpression() )
m_xml.endElement();
+
+ return true;
+ }
+
+ virtual void sectionEnded( SectionStats const& sectionStats ) CATCH_OVERRIDE {
+ StreamingReporterBase::sectionEnded( sectionStats );
+ if( --m_sectionDepth > 0 ) {
+ XmlWriter::ScopedElement e = m_xml.scopedElement( "OverallResults" );
+ e.writeAttribute( "successes", sectionStats.assertions.passed );
+ e.writeAttribute( "failures", sectionStats.assertions.failed );
+ e.writeAttribute( "expectedFailures", sectionStats.assertions.failedButOk );
+
+ if ( m_config->showDurations() == ShowDurations::Always )
+ e.writeAttribute( "durationInSeconds", sectionStats.durationInSeconds );
+
+ m_xml.endElement();
+ }
+ }
+
+ virtual void testCaseEnded( TestCaseStats const& testCaseStats ) CATCH_OVERRIDE {
+ StreamingReporterBase::testCaseEnded( testCaseStats );
+ XmlWriter::ScopedElement e = m_xml.scopedElement( "OverallResult" );
+ e.writeAttribute( "success", testCaseStats.totals.assertions.allOk() );
+
+ if ( m_config->showDurations() == ShowDurations::Always )
+ e.writeAttribute( "durationInSeconds", m_testCaseTimer.getElapsedSeconds() );
+
+ m_xml.endElement();
}
- virtual void Aborted() {
- // !TBD
+ virtual void testGroupEnded( TestGroupStats const& testGroupStats ) CATCH_OVERRIDE {
+ StreamingReporterBase::testGroupEnded( testGroupStats );
+ // TODO: Check testGroupStats.aborting and act accordingly.
+ m_xml.scopedElement( "OverallResults" )
+ .writeAttribute( "successes", testGroupStats.totals.assertions.passed )
+ .writeAttribute( "failures", testGroupStats.totals.assertions.failed )
+ .writeAttribute( "expectedFailures", testGroupStats.totals.assertions.failedButOk );
+ m_xml.endElement();
}
- virtual void EndTestCase( const Catch::TestCaseInfo&, const Totals&, const std::string&, const std::string& ) {
- m_xml.scopedElement( "OverallResult" ).writeAttribute( "success", m_currentTestSuccess );
+ virtual void testRunEnded( TestRunStats const& testRunStats ) CATCH_OVERRIDE {
+ StreamingReporterBase::testRunEnded( testRunStats );
+ m_xml.scopedElement( "OverallResults" )
+ .writeAttribute( "successes", testRunStats.totals.assertions.passed )
+ .writeAttribute( "failures", testRunStats.totals.assertions.failed )
+ .writeAttribute( "expectedFailures", testRunStats.totals.assertions.failedButOk );
m_xml.endElement();
}
private:
- ReporterConfig m_config;
- bool m_currentTestSuccess;
+ Timer m_testCaseTimer;
XmlWriter m_xml;
int m_sectionDepth;
};
+ INTERNAL_CATCH_REGISTER_REPORTER( "xml", XmlReporter )
+
} // end namespace Catch
// #included from: ../reporters/catch_reporter_junit.hpp
@@ -7826,28 +9399,24 @@ namespace Catch {
JunitReporter( ReporterConfig const& _config )
: CumulativeReporterBase( _config ),
xml( _config.stream() )
- {}
+ {
+ m_reporterPrefs.shouldRedirectStdOut = true;
+ }
- ~JunitReporter();
+ virtual ~JunitReporter() CATCH_OVERRIDE;
static std::string getDescription() {
return "Reports test results in an XML format that looks like Ant's junitreport target";
}
- virtual void noMatchingTestCases( std::string const& /*spec*/ ) {}
-
- virtual ReporterPreferences getPreferences() const {
- ReporterPreferences prefs;
- prefs.shouldRedirectStdOut = true;
- return prefs;
- }
+ virtual void noMatchingTestCases( std::string const& /*spec*/ ) CATCH_OVERRIDE {}
- virtual void testRunStarting( TestRunInfo const& runInfo ) {
+ virtual void testRunStarting( TestRunInfo const& runInfo ) CATCH_OVERRIDE {
CumulativeReporterBase::testRunStarting( runInfo );
xml.startElement( "testsuites" );
}
- virtual void testGroupStarting( GroupInfo const& groupInfo ) {
+ virtual void testGroupStarting( GroupInfo const& groupInfo ) CATCH_OVERRIDE {
suiteTimer.start();
stdOutForSuite.str("");
stdErrForSuite.str("");
@@ -7855,25 +9424,25 @@ namespace Catch {
CumulativeReporterBase::testGroupStarting( groupInfo );
}
- virtual bool assertionEnded( AssertionStats const& assertionStats ) {
+ virtual bool assertionEnded( AssertionStats const& assertionStats ) CATCH_OVERRIDE {
if( assertionStats.assertionResult.getResultType() == ResultWas::ThrewException )
unexpectedExceptions++;
return CumulativeReporterBase::assertionEnded( assertionStats );
}
- virtual void testCaseEnded( TestCaseStats const& testCaseStats ) {
+ virtual void testCaseEnded( TestCaseStats const& testCaseStats ) CATCH_OVERRIDE {
stdOutForSuite << testCaseStats.stdOut;
stdErrForSuite << testCaseStats.stdErr;
CumulativeReporterBase::testCaseEnded( testCaseStats );
}
- virtual void testGroupEnded( TestGroupStats const& testGroupStats ) {
+ virtual void testGroupEnded( TestGroupStats const& testGroupStats ) CATCH_OVERRIDE {
double suiteTime = suiteTimer.getElapsedSeconds();
CumulativeReporterBase::testGroupEnded( testGroupStats );
writeGroup( *m_testGroups.back(), suiteTime );
}
- virtual void testRunEndedCumulative() {
+ virtual void testRunEndedCumulative() CATCH_OVERRIDE {
xml.endElement();
}
@@ -7938,7 +9507,7 @@ namespace Catch {
xml.writeAttribute( "classname", className );
xml.writeAttribute( "name", name );
}
- xml.writeAttribute( "time", toString( sectionNode.stats.durationInSeconds ) );
+ xml.writeAttribute( "time", Catch::toString( sectionNode.stats.durationInSeconds ) );
writeAssertions( sectionNode );
@@ -7971,6 +9540,7 @@ namespace Catch {
std::string elementName;
switch( result.getResultType() ) {
case ResultWas::ThrewException:
+ case ResultWas::FatalErrorCondition:
elementName = "error";
break;
case ResultWas::ExplicitFailure:
@@ -8029,8 +9599,6 @@ namespace Catch {
// #included from: ../reporters/catch_reporter_console.hpp
#define TWOBLUECUBES_CATCH_REPORTER_CONSOLE_HPP_INCLUDED
-#include <cstring>
-
namespace Catch {
struct ConsoleReporter : StreamingReporterBase {
@@ -8039,24 +9607,19 @@ namespace Catch {
m_headerPrinted( false )
{}
- virtual ~ConsoleReporter();
+ virtual ~ConsoleReporter() CATCH_OVERRIDE;
static std::string getDescription() {
return "Reports test results as plain lines of text";
}
- virtual ReporterPreferences getPreferences() const {
- ReporterPreferences prefs;
- prefs.shouldRedirectStdOut = false;
- return prefs;
- }
- virtual void noMatchingTestCases( std::string const& spec ) {
+ virtual void noMatchingTestCases( std::string const& spec ) CATCH_OVERRIDE {
stream << "No test cases matched '" << spec << "'" << std::endl;
}
- virtual void assertionStarting( AssertionInfo const& ) {
+ virtual void assertionStarting( AssertionInfo const& ) CATCH_OVERRIDE {
}
- virtual bool assertionEnded( AssertionStats const& _assertionStats ) {
+ virtual bool assertionEnded( AssertionStats const& _assertionStats ) CATCH_OVERRIDE {
AssertionResult const& result = _assertionStats.assertionResult;
bool printInfoMessages = true;
@@ -8076,11 +9639,11 @@ namespace Catch {
return true;
}
- virtual void sectionStarting( SectionInfo const& _sectionInfo ) {
+ virtual void sectionStarting( SectionInfo const& _sectionInfo ) CATCH_OVERRIDE {
m_headerPrinted = false;
StreamingReporterBase::sectionStarting( _sectionInfo );
}
- virtual void sectionEnded( SectionStats const& _sectionStats ) {
+ virtual void sectionEnded( SectionStats const& _sectionStats ) CATCH_OVERRIDE {
if( _sectionStats.missingAssertions ) {
lazyPrint();
Colour colour( Colour::ResultError );
@@ -8102,11 +9665,11 @@ namespace Catch {
StreamingReporterBase::sectionEnded( _sectionStats );
}
- virtual void testCaseEnded( TestCaseStats const& _testCaseStats ) {
+ virtual void testCaseEnded( TestCaseStats const& _testCaseStats ) CATCH_OVERRIDE {
StreamingReporterBase::testCaseEnded( _testCaseStats );
m_headerPrinted = false;
}
- virtual void testGroupEnded( TestGroupStats const& _testGroupStats ) {
+ virtual void testGroupEnded( TestGroupStats const& _testGroupStats ) CATCH_OVERRIDE {
if( currentGroupInfo.used ) {
printSummaryDivider();
stream << "Summary for group '" << _testGroupStats.groupInfo.name << "':\n";
@@ -8115,7 +9678,7 @@ namespace Catch {
}
StreamingReporterBase::testGroupEnded( _testGroupStats );
}
- virtual void testRunEnded( TestRunStats const& _testRunStats ) {
+ virtual void testRunEnded( TestRunStats const& _testRunStats ) CATCH_OVERRIDE {
printTotalsDivider( _testRunStats.totals );
printTotals( _testRunStats.totals );
stream << std::endl;
@@ -8165,6 +9728,11 @@ namespace Catch {
passOrFail = "FAILED";
messageLabel = "due to unexpected exception with message";
break;
+ case ResultWas::FatalErrorCondition:
+ colour = Colour::Error;
+ passOrFail = "FAILED";
+ messageLabel = "due to a fatal error condition";
+ break;
case ResultWas::DidntThrowException:
colour = Colour::Error;
passOrFail = "FAILED";
@@ -8274,14 +9842,12 @@ namespace Catch {
stream << "\n" << getLineOfChars<'~'>() << "\n";
Colour colour( Colour::SecondaryText );
stream << currentTestRunInfo->name
- << " is a Catch v" << libraryVersion.majorVersion << "."
- << libraryVersion.minorVersion << " b"
- << libraryVersion.buildNumber;
- if( libraryVersion.branchName != std::string( "master" ) )
- stream << " (" << libraryVersion.branchName << ")";
- stream << " host application.\n"
+ << " is a Catch v" << libraryVersion << " host application.\n"
<< "Run with -? for options\n\n";
+ if( m_config->rngSeed() != 0 )
+ stream << "Randomness seeded to: " << m_config->rngSeed() << "\n\n";
+
currentTestRunInfo.used = true;
}
void lazyPrintGroupInfo() {
@@ -8369,7 +9935,7 @@ namespace Catch {
if( totals.testCases.total() == 0 ) {
stream << Colour( Colour::Warning ) << "No tests ran\n";
}
- else if( totals.assertions.total() > 0 && totals.assertions.allPassed() ) {
+ else if( totals.assertions.total() > 0 && totals.testCases.allPassed() ) {
stream << Colour( Colour::ResultSuccess ) << "All tests passed";
stream << " ("
<< pluralise( totals.assertions.passed, "assertion" ) << " in "
@@ -8453,15 +10019,6 @@ namespace Catch {
void printSummaryDivider() {
stream << getLineOfChars<'-'>() << "\n";
}
- template<char C>
- static char const* getLineOfChars() {
- static char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0};
- if( !*line ) {
- memset( line, C, CATCH_CONFIG_CONSOLE_WIDTH-1 );
- line[CATCH_CONFIG_CONSOLE_WIDTH-1] = 0;
- }
- return line;
- }
private:
bool m_headerPrinted;
@@ -8570,6 +10127,13 @@ namespace Catch {
printExpressionWas();
printRemainingMessages();
break;
+ case ResultWas::FatalErrorCondition:
+ printResultType( Colour::Error, failedString() );
+ printIssue( "fatal error condition with message:" );
+ printMessage();
+ printExpressionWas();
+ printRemainingMessages();
+ break;
case ResultWas::DidntThrowException:
printResultType( Colour::Error, failedString() );
printIssue( "expected exception, got none" );
@@ -8753,8 +10317,14 @@ namespace Catch {
} // end namespace Catch
namespace Catch {
+ // These are all here to avoid warnings about not having any out of line
+ // virtual methods
NonCopyable::~NonCopyable() {}
IShared::~IShared() {}
+ IStream::~IStream() CATCH_NOEXCEPT {}
+ FileStream::~FileStream() CATCH_NOEXCEPT {}
+ CoutStream::~CoutStream() CATCH_NOEXCEPT {}
+ DebugOutStream::~DebugOutStream() CATCH_NOEXCEPT {}
StreamBufBase::~StreamBufBase() CATCH_NOEXCEPT {}
IContext::~IContext() {}
IResultCapture::~IResultCapture() {}
@@ -8788,6 +10358,7 @@ namespace Catch {
FreeFunctionTestCase::~FreeFunctionTestCase() {}
IGeneratorInfo::~IGeneratorInfo() {}
IGeneratorsForTest::~IGeneratorsForTest() {}
+ WildcardPattern::~WildcardPattern() {}
TestSpec::Pattern::~Pattern() {}
TestSpec::NamePattern::~NamePattern() {}
TestSpec::TagPattern::~TagPattern() {}
@@ -8800,7 +10371,12 @@ namespace Catch {
void Config::dummy() {}
- INTERNAL_CATCH_REGISTER_LEGACY_REPORTER( "xml", XmlReporter )
+ namespace TestCaseTracking {
+ ITracker::~ITracker() {}
+ TrackerBase::~TrackerBase() {}
+ SectionTracker::~SectionTracker() {}
+ IndexTracker::~IndexTracker() {}
+ }
}
#ifdef __clang__
@@ -8816,7 +10392,7 @@ namespace Catch {
#ifndef __OBJC__
// Standard C/C++ main entry point
-int main (int argc, char * const argv[]) {
+int main (int argc, char * argv[]) {
return Catch::Session().run( argc, argv );
}
@@ -8854,8 +10430,9 @@ int main (int argc, char * const argv[]) {
#define CATCH_REQUIRE( expr ) INTERNAL_CATCH_TEST( expr, Catch::ResultDisposition::Normal, "CATCH_REQUIRE" )
#define CATCH_REQUIRE_FALSE( expr ) INTERNAL_CATCH_TEST( expr, Catch::ResultDisposition::Normal | Catch::ResultDisposition::FalseTest, "CATCH_REQUIRE_FALSE" )
-#define CATCH_REQUIRE_THROWS( expr ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::Normal, "CATCH_REQUIRE_THROWS" )
+#define CATCH_REQUIRE_THROWS( expr ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::Normal, "", "CATCH_REQUIRE_THROWS" )
#define CATCH_REQUIRE_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( expr, exceptionType, Catch::ResultDisposition::Normal, "CATCH_REQUIRE_THROWS_AS" )
+#define CATCH_REQUIRE_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::Normal, matcher, "CATCH_REQUIRE_THROWS_WITH" )
#define CATCH_REQUIRE_NOTHROW( expr ) INTERNAL_CATCH_NO_THROW( expr, Catch::ResultDisposition::Normal, "CATCH_REQUIRE_NOTHROW" )
#define CATCH_CHECK( expr ) INTERNAL_CATCH_TEST( expr, Catch::ResultDisposition::ContinueOnFailure, "CATCH_CHECK" )
@@ -8864,8 +10441,9 @@ int main (int argc, char * const argv[]) {
#define CATCH_CHECKED_ELSE( expr ) INTERNAL_CATCH_ELSE( expr, Catch::ResultDisposition::ContinueOnFailure, "CATCH_CHECKED_ELSE" )
#define CATCH_CHECK_NOFAIL( expr ) INTERNAL_CATCH_TEST( expr, Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::SuppressFail, "CATCH_CHECK_NOFAIL" )
-#define CATCH_CHECK_THROWS( expr ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::ContinueOnFailure, "CATCH_CHECK_THROWS" )
+#define CATCH_CHECK_THROWS( expr ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::ContinueOnFailure, "", "CATCH_CHECK_THROWS" )
#define CATCH_CHECK_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( expr, exceptionType, Catch::ResultDisposition::ContinueOnFailure, "CATCH_CHECK_THROWS_AS" )
+#define CATCH_CHECK_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::ContinueOnFailure, matcher, "CATCH_CHECK_THROWS_WITH" )
#define CATCH_CHECK_NOTHROW( expr ) INTERNAL_CATCH_NO_THROW( expr, Catch::ResultDisposition::ContinueOnFailure, "CATCH_CHECK_NOTHROW" )
#define CHECK_THAT( arg, matcher ) INTERNAL_CHECK_THAT( arg, matcher, Catch::ResultDisposition::ContinueOnFailure, "CATCH_CHECK_THAT" )
@@ -8881,6 +10459,7 @@ int main (int argc, char * const argv[]) {
#define CATCH_TEST_CASE( ... ) INTERNAL_CATCH_TESTCASE( __VA_ARGS__ )
#define CATCH_TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, __VA_ARGS__ )
#define CATCH_METHOD_AS_TEST_CASE( method, ... ) INTERNAL_CATCH_METHOD_AS_TEST_CASE( method, __VA_ARGS__ )
+ #define CATCH_REGISTER_TEST_CASE( Function, ... ) INTERNAL_CATCH_REGISTER_TESTCASE( Function, __VA_ARGS__ )
#define CATCH_SECTION( ... ) INTERNAL_CATCH_SECTION( __VA_ARGS__ )
#define CATCH_FAIL( ... ) INTERNAL_CATCH_MSG( Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::Normal, "CATCH_FAIL", __VA_ARGS__ )
#define CATCH_SUCCEED( ... ) INTERNAL_CATCH_MSG( Catch::ResultWas::Ok, Catch::ResultDisposition::ContinueOnFailure, "CATCH_SUCCEED", __VA_ARGS__ )
@@ -8888,6 +10467,7 @@ int main (int argc, char * const argv[]) {
#define CATCH_TEST_CASE( name, description ) INTERNAL_CATCH_TESTCASE( name, description )
#define CATCH_TEST_CASE_METHOD( className, name, description ) INTERNAL_CATCH_TEST_CASE_METHOD( className, name, description )
#define CATCH_METHOD_AS_TEST_CASE( method, name, description ) INTERNAL_CATCH_METHOD_AS_TEST_CASE( method, name, description )
+ #define CATCH_REGISTER_TEST_CASE( function, name, description ) INTERNAL_CATCH_REGISTER_TESTCASE( function, name, description )
#define CATCH_SECTION( name, description ) INTERNAL_CATCH_SECTION( name, description )
#define CATCH_FAIL( msg ) INTERNAL_CATCH_MSG( Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::Normal, "CATCH_FAIL", msg )
#define CATCH_SUCCEED( msg ) INTERNAL_CATCH_MSG( Catch::ResultWas::Ok, Catch::ResultDisposition::ContinueOnFailure, "CATCH_SUCCEED", msg )
@@ -8907,11 +10487,11 @@ int main (int argc, char * const argv[]) {
#define CATCH_SCENARIO( name, tags ) CATCH_TEST_CASE( "Scenario: " name, tags )
#define CATCH_SCENARIO_METHOD( className, name, tags ) INTERNAL_CATCH_TEST_CASE_METHOD( className, "Scenario: " name, tags )
#endif
-#define CATCH_GIVEN( desc ) CATCH_SECTION( "Given: " desc, "" )
-#define CATCH_WHEN( desc ) CATCH_SECTION( " When: " desc, "" )
-#define CATCH_AND_WHEN( desc ) CATCH_SECTION( " And: " desc, "" )
-#define CATCH_THEN( desc ) CATCH_SECTION( " Then: " desc, "" )
-#define CATCH_AND_THEN( desc ) CATCH_SECTION( " And: " desc, "" )
+#define CATCH_GIVEN( desc ) CATCH_SECTION( std::string( "Given: ") + desc, "" )
+#define CATCH_WHEN( desc ) CATCH_SECTION( std::string( " When: ") + desc, "" )
+#define CATCH_AND_WHEN( desc ) CATCH_SECTION( std::string( " And: ") + desc, "" )
+#define CATCH_THEN( desc ) CATCH_SECTION( std::string( " Then: ") + desc, "" )
+#define CATCH_AND_THEN( desc ) CATCH_SECTION( std::string( " And: ") + desc, "" )
// If CATCH_CONFIG_PREFIX_ALL is not defined then the CATCH_ prefix is not required
#else
@@ -8919,8 +10499,9 @@ int main (int argc, char * const argv[]) {
#define REQUIRE( expr ) INTERNAL_CATCH_TEST( expr, Catch::ResultDisposition::Normal, "REQUIRE" )
#define REQUIRE_FALSE( expr ) INTERNAL_CATCH_TEST( expr, Catch::ResultDisposition::Normal | Catch::ResultDisposition::FalseTest, "REQUIRE_FALSE" )
-#define REQUIRE_THROWS( expr ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::Normal, "REQUIRE_THROWS" )
+#define REQUIRE_THROWS( expr ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::Normal, "", "REQUIRE_THROWS" )
#define REQUIRE_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( expr, exceptionType, Catch::ResultDisposition::Normal, "REQUIRE_THROWS_AS" )
+#define REQUIRE_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::Normal, matcher, "REQUIRE_THROWS_WITH" )
#define REQUIRE_NOTHROW( expr ) INTERNAL_CATCH_NO_THROW( expr, Catch::ResultDisposition::Normal, "REQUIRE_NOTHROW" )
#define CHECK( expr ) INTERNAL_CATCH_TEST( expr, Catch::ResultDisposition::ContinueOnFailure, "CHECK" )
@@ -8929,8 +10510,9 @@ int main (int argc, char * const argv[]) {
#define CHECKED_ELSE( expr ) INTERNAL_CATCH_ELSE( expr, Catch::ResultDisposition::ContinueOnFailure, "CHECKED_ELSE" )
#define CHECK_NOFAIL( expr ) INTERNAL_CATCH_TEST( expr, Catch::ResultDisposition::ContinueOnFailure | Catch::ResultDisposition::SuppressFail, "CHECK_NOFAIL" )
-#define CHECK_THROWS( expr ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::ContinueOnFailure, "CHECK_THROWS" )
+#define CHECK_THROWS( expr ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::ContinueOnFailure, "", "CHECK_THROWS" )
#define CHECK_THROWS_AS( expr, exceptionType ) INTERNAL_CATCH_THROWS_AS( expr, exceptionType, Catch::ResultDisposition::ContinueOnFailure, "CHECK_THROWS_AS" )
+#define CHECK_THROWS_WITH( expr, matcher ) INTERNAL_CATCH_THROWS( expr, Catch::ResultDisposition::ContinueOnFailure, matcher, "CHECK_THROWS_WITH" )
#define CHECK_NOTHROW( expr ) INTERNAL_CATCH_NO_THROW( expr, Catch::ResultDisposition::ContinueOnFailure, "CHECK_NOTHROW" )
#define CHECK_THAT( arg, matcher ) INTERNAL_CHECK_THAT( arg, matcher, Catch::ResultDisposition::ContinueOnFailure, "CHECK_THAT" )
@@ -8946,6 +10528,7 @@ int main (int argc, char * const argv[]) {
#define TEST_CASE( ... ) INTERNAL_CATCH_TESTCASE( __VA_ARGS__ )
#define TEST_CASE_METHOD( className, ... ) INTERNAL_CATCH_TEST_CASE_METHOD( className, __VA_ARGS__ )
#define METHOD_AS_TEST_CASE( method, ... ) INTERNAL_CATCH_METHOD_AS_TEST_CASE( method, __VA_ARGS__ )
+ #define REGISTER_TEST_CASE( Function, ... ) INTERNAL_CATCH_REGISTER_TESTCASE( Function, __VA_ARGS__ )
#define SECTION( ... ) INTERNAL_CATCH_SECTION( __VA_ARGS__ )
#define FAIL( ... ) INTERNAL_CATCH_MSG( Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::Normal, "FAIL", __VA_ARGS__ )
#define SUCCEED( ... ) INTERNAL_CATCH_MSG( Catch::ResultWas::Ok, Catch::ResultDisposition::ContinueOnFailure, "SUCCEED", __VA_ARGS__ )
@@ -8953,6 +10536,7 @@ int main (int argc, char * const argv[]) {
#define TEST_CASE( name, description ) INTERNAL_CATCH_TESTCASE( name, description )
#define TEST_CASE_METHOD( className, name, description ) INTERNAL_CATCH_TEST_CASE_METHOD( className, name, description )
#define METHOD_AS_TEST_CASE( method, name, description ) INTERNAL_CATCH_METHOD_AS_TEST_CASE( method, name, description )
+ #define REGISTER_TEST_CASE( method, name, description ) INTERNAL_CATCH_REGISTER_TESTCASE( method, name, description )
#define SECTION( name, description ) INTERNAL_CATCH_SECTION( name, description )
#define FAIL( msg ) INTERNAL_CATCH_MSG( Catch::ResultWas::ExplicitFailure, Catch::ResultDisposition::Normal, "FAIL", msg )
#define SUCCEED( msg ) INTERNAL_CATCH_MSG( Catch::ResultWas::Ok, Catch::ResultDisposition::ContinueOnFailure, "SUCCEED", msg )
@@ -8976,25 +10560,13 @@ int main (int argc, char * const argv[]) {
#define SCENARIO( name, tags ) TEST_CASE( "Scenario: " name, tags )
#define SCENARIO_METHOD( className, name, tags ) INTERNAL_CATCH_TEST_CASE_METHOD( className, "Scenario: " name, tags )
#endif
-#define GIVEN( desc ) SECTION( " Given: " desc, "" )
-#define WHEN( desc ) SECTION( " When: " desc, "" )
-#define AND_WHEN( desc ) SECTION( "And when: " desc, "" )
-#define THEN( desc ) SECTION( " Then: " desc, "" )
-#define AND_THEN( desc ) SECTION( " And: " desc, "" )
+#define GIVEN( desc ) SECTION( std::string(" Given: ") + desc, "" )
+#define WHEN( desc ) SECTION( std::string(" When: ") + desc, "" )
+#define AND_WHEN( desc ) SECTION( std::string("And when: ") + desc, "" )
+#define THEN( desc ) SECTION( std::string(" Then: ") + desc, "" )
+#define AND_THEN( desc ) SECTION( std::string(" And: ") + desc, "" )
using Catch::Detail::Approx;
-// #included from: internal/catch_reenable_warnings.h
-
-#define TWOBLUECUBES_CATCH_REENABLE_WARNINGS_H_INCLUDED
-
-#ifdef __clang__
-#pragma clang diagnostic pop
-#elif defined __GNUC__
-#pragma GCC diagnostic pop
-#endif
-
#endif // TWOBLUECUBES_SINGLE_INCLUDE_CATCH_HPP_INCLUDED
-
-
diff --git a/TestMothur/dataset.h b/TestMothur/dataset.h
index 3160b4c..03b9674 100644
--- a/TestMothur/dataset.h
+++ b/TestMothur/dataset.h
@@ -25,11 +25,7 @@ public:
GroupMap* getGroupMap() { fillGroup(); return gMap; }
CountTable* getCountTable() { createCountTable(); return ct; }
vector<SharedRAbundVector*> getLookup() { fillLookup(); return lookup; }
- vector<FastqRead> getForwardFastq() { return fastqData.getForwardFastq(); }
- vector<FastqRead> getReverseFastq() { return fastqData.getReverseFastq(); }
- vector<string> getSubsetFRFastq(int n) { return fastqData.getSubsetFRFastq(n); }
-
- vector<string> getSubsetFNGFiles(int); //number of uniques passed in. 3 files returned -> Fasta, name, group.
+ vector<string> getSubsetFNGFiles(int); //number of uniques, Fasta, name, group returned
private:
MothurOut* m;
@@ -39,15 +35,11 @@ private:
CountTable* ct;
GroupMap* gMap;
vector<SharedRAbundVector*> lookup;
- vector<FastqRead> ffastqReads; //F8D0 Sample
- vector<FastqRead> rfastqReads; //F8D0 Sample
void fillNames();
void fillSeqs();
void fillGroup();
void createCountTable();
void fillLookup();
- void fillForwardFastq();
- void fillReverseFastq();
};
diff --git a/TestMothur/distcdataset.cpp b/TestMothur/distcdataset.cpp
new file mode 100644
index 0000000..d056766
--- /dev/null
+++ b/TestMothur/distcdataset.cpp
@@ -0,0 +1,46955 @@
+#include "distcdataset.h"
+#include "getdistscommand.h"
+#include "listseqscommand.h"
+#include "getseqscommand.h"
+
+/***********************************************************************/
+DistCDataSet::DistCDataSet() {
+ m = MothurOut::getInstance();
+}
+/***********************************************************************/
+vector<string> DistCDataSet::getFiles(int numSeqs) {
+ vector<string> newFiles;
+
+ if (numSeqs > 2550) { m->mothurOut("[ERROR]: too many seqs requested in DistCDataSet::getFiles\n"); }
+ else {
+ string countfile = writeCountFile();
+ string columnfile = writeColumnFile();
+
+ string inputString = "count=" + countfile;
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: list.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* listCommand = new ListSeqsCommand(inputString);
+ listCommand->execute();
+
+ map<string, vector<string> > filenames = listCommand->getOutputFiles();
+
+ delete listCommand;
+ m->mothurCalling = false;
+
+ string accnosfile = filenames["accnos"][0];
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ ifstream in;
+ m->openInputFile(accnosfile, in);
+
+ ofstream out;
+ m->openOutputFile("temp.accnos", out);
+
+ int count = 0; string name;
+ while(!in.eof()) {
+ if (m->control_pressed) { break; }
+
+ in >> name; m->gobble(in);
+ out << name << endl;
+ count++;
+
+ if (count >= numSeqs) { break; }
+ }
+ in.close();
+ out.close();
+ m->mothurRemove(accnosfile);
+
+ inputString = "count=" + countfile + ", accnos=temp.accnos";
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: get.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* getCommand = new GetSeqsCommand(inputString);
+ getCommand->execute();
+
+ filenames = getCommand->getOutputFiles();
+
+ delete getCommand;
+ m->mothurCalling = false;
+
+ string newCountfile = filenames["count"][0];
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ inputString = "column=" + columnfile + ", accnos=temp.accnos";
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: get.dists(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* getDCommand = new GetDistsCommand(inputString);
+ getDCommand->execute();
+
+ filenames = getDCommand->getOutputFiles();
+
+ delete getDCommand;
+ m->mothurCalling = false;
+
+ string newColumnfile = filenames["column"][0];
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ newFiles.push_back(newColumnfile); newFiles.push_back(newCountfile);
+ }
+
+ return newFiles;
+}
+/***********************************************************************/
+string DistCDataSet::writeColumnFile() {
+
+ ofstream out;
+ m->openOutputFile("column.temp", out);
+
+
+out << "M00967_43_000000000-A3JHG_1_1101_20384_5679 M00967_43_000000000-A3JHG_1_1101_24218_7727 0.03571" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_16061_3516 M00967_43_000000000-A3JHG_1_1101_22481_5236 0.04348" << endl;
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+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_1110_18818_19657 0.01581" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_1103_18198_2609 0.007905" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_1112_9301_13162 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_1112_17691_12056 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_2105_16439_13484 0.01976" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_1104_23422_20961 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_2109_13351_28335 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_2114_26633_11062 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_1109_17670_1881 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_2113_4494_9088 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_2105_7943_8043 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_2101_24924_5766 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_1101_11823_22466 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_2102_15674_19713 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_12015_3840 M00967_43_000000000-A3JHG_1_1113_19158_8422 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_9350_18825 M00967_43_000000000-A3JHG_1_1111_20569_3100 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_9350_18825 M00967_43_000000000-A3JHG_1_2109_14117_4744 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_9350_18825 M00967_43_000000000-A3JHG_1_2113_9766_20824 0.04348" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_9350_18825 M00967_43_000000000-A3JHG_1_1108_18422_23262 0.01186" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_9350_18825 M00967_43_000000000-A3JHG_1_1106_23262_25144 0.01976" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_9350_18825 M00967_43_000000000-A3JHG_1_2103_27141_19101 0.007905" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_1101_6836_23417 0.007905" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_1113_8082_6010 0.03953" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_2113_18397_7516 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_2106_22891_19654 0.01581" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_2108_18358_2270 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_1102_11324_6735 0.01186" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_2102_21816_16599 0.04348" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_1108_23963_16017 0.01186" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_1104_11751_17981 0.01186" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_1106_11208_20468 0.03953" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_2114_22279_21530 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_1107_7832_8780 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_2112_8454_7758 0.01186" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_2106_19379_4847 0.01186" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 M00967_43_000000000-A3JHG_1_1114_15409_10721 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1104_24493_5303 0.01976" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_2110_16815_14755 0.03953" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1104_25962_6708 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1102_16785_23687 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_2112_23259_13531 0.007905" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1108_20841_7623 0.03953" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1101_15533_5293 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_2107_23675_17555 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1105_22998_9973 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1113_22462_8142 0.04348" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_2111_12498_13580 0.007905" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1114_18296_7709 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1113_24017_25976 0.03953" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1105_6877_11063 0.04348" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1102_7684_6622 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1110_22680_22915 0.007905" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_2102_18381_13991 0.04348" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1112_2989_20122 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1106_22705_6123 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_2104_11063_11086 0.04348" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 M00967_43_000000000-A3JHG_1_1105_7593_10522 0.01186" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1101_14341_8428 0.01186" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1102_15350_5623 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1102_7484_9022 0.007905" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1107_14437_24723 0.01581" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1107_18906_15466 0.01976" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_2108_23615_21129 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_2106_22580_3507 0.01976" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1113_18114_26077 0.01575" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1102_21808_10504 0.01976" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_2102_19632_15186 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_2102_13864_6831 0.01581" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1112_10200_9979 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1105_11090_20196 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_2102_14650_8724 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_2105_21156_7257 0.02372" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1104_14019_23841 0.03953" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1114_11189_15616 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1112_11092_24430 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1107_23336_26415 0.01581" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1113_18370_24961 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1107_21734_25420 0.0315" << endl;
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 M00967_43_000000000-A3JHG_1_1106_24084_10563 0.01581" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1104_24493_5303 0.01581" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1104_25962_6708 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1102_16785_23687 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_2112_23259_13531 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1110_17627_6261 0.03571" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1108_20841_7623 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_2103_16331_20380 0.04348" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1105_22998_9973 0.01976" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_2111_12498_13580 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1114_18296_7709 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1113_24017_25976 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1102_7684_6622 0.03162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1110_22680_22915 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_2102_18381_13991 0.03953" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1112_2989_20122 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1106_22705_6123 0.02767" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_2104_11063_11086 0.03953" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1106_25330_8604 0.04365" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1105_7593_10522 0.03953" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 M00967_43_000000000-A3JHG_1_1103_19321_18100 0.03557" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1101_14341_8428 0.02756" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1102_15350_5623 0.03543" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1102_7484_9022 0.02362" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1107_14437_24723 0.03543" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1107_18906_15466 0.03937" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_2108_23615_21129 0.03937" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_2106_22580_3507 0.03543" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1113_18114_26077 0.03922" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1102_21808_10504 0.0315" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_2102_13864_6831 0.0315" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1112_10200_9979 0.04331" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1105_11090_20196 0.03937" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_2102_14650_8724 0.03937" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_2105_21156_7257 0.03543" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1112_11092_24430 0.04331" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1107_23336_26415 0.0315" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1113_18370_24961 0.03937" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1107_21734_25420 0.01581" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1106_24084_10563 0.0315" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 M00967_43_000000000-A3JHG_1_1103_12856_12076 0.0315" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_20702_8361 M00967_43_000000000-A3JHG_1_1110_12295_19699 0.003968" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_20702_8361 M00967_43_000000000-A3JHG_1_1114_5207_13479 0.02372" << endl;
+
+
+ out.close();
+
+ return "column.temp";
+}
+
+/***********************************************************************/
+string DistCDataSet::writeCountFile() {
+
+ ofstream out;
+ m->openOutputFile("count.temp", out);
+
+
+out << "Representative_Sequence total F3D0 F3D1 F3D141 F3D142 F3D143 F3D144 F3D145 F3D146 F3D147 F3D148 F3D149 F3D150 F3D2 F3D3 F3D5 F3D6 F3D7 F3D8 F3D9" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_14069_1827 7305 628 0 422 251 306 465 661 394 1602 1216 870 279 146 23 20 11 9 2 0" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_18044_1900 33 1 0 1 0 0 1 0 0 12 10 3 0 0 0 2 0 3 0 0" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_13234_1983 12196 495 340 386 242 188 340 562 269 1307 744 769 263 3056 830 272 895 575 230 433" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_16780_2259 198 16 17 1 7 3 5 3 20 22 6 14 6 37 7 5 7 1 7 14" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_17674_2779 8829 306 302 333 256 152 242 443 204 1101 662 699 206 1428 541 234 605 447 302 366" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_18089_2781 592 98 245 0 0 0 6 0 36 22 0 0 0 0 16 0 72 0 0 97" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_14203_2907 7698 390 185 295 142 172 256 453 218 811 518 644 341 1050 389 234 500 382 294 424" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_18278_3345 2 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0" << endl;
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+out << "M00967_43_000000000-A3JHG_1_2112_25043_23608 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1" << endl;
+out << "M00967_43_000000000-A3JHG_1_2113_8502_12671 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1" << endl;
+out << "M00967_43_000000000-A3JHG_1_2113_6721_20524 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1" << endl;
+out << "M00967_43_000000000-A3JHG_1_2114_22468_4333 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1" << endl;
+out << "M00967_43_000000000-A3JHG_1_2114_6705_14284 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1" << endl;
+
+
+ out.close();
+
+ return "count.temp";
+}
+/***********************************************************************/
+
diff --git a/TestMothur/distcdataset.h b/TestMothur/distcdataset.h
new file mode 100644
index 0000000..e628a34
--- /dev/null
+++ b/TestMothur/distcdataset.h
@@ -0,0 +1,32 @@
+//
+// distcdataset.h
+// Mothur
+//
+// Created by Sarah Westcott on 6/8/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__distcdataset__
+#define __Mothur__distcdataset__
+
+#include "mothurout.h"
+
+class DistCDataSet {
+
+public:
+
+ DistCDataSet();
+ ~DistCDataSet() {}
+ string getColumnFile() { return writeColumnFile(); }
+ vector<string> getFiles(int);
+ string getCountFile() { return writeCountFile(); }
+
+private:
+ MothurOut* m;
+ string writeColumnFile();
+ string writeCountFile();
+
+};
+
+
+#endif /* defined(__Mothur__distcdataset__) */
diff --git a/TestMothur/distpdataset.cpp b/TestMothur/distpdataset.cpp
new file mode 100644
index 0000000..cf21e35
--- /dev/null
+++ b/TestMothur/distpdataset.cpp
@@ -0,0 +1,2578 @@
+//
+// distdataset.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 6/6/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#include "distpdataset.h"
+
+/***********************************************************************/
+DistPDataSet::DistPDataSet() {
+ m = MothurOut::getInstance();
+}
+/***********************************************************************/
+string DistPDataSet::writePhylipFile() {
+
+ ofstream out;
+ m->openOutputFile("phylip.temp", out);
+
+out << "2550" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_13234_1983" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_14069_1827 0.1071" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_16910_7379 0.119 0.06746" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_14203_2907 0.1071 0.06746 0.06746" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_17674_2779 0.08333 0.09921 0.0873 0.0754" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_22481_5236 0.2925 0.2767 0.2688 0.2688 0.2648" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_24218_7727 0.08333 0.06746 0.08333 0.06349 0.09524 0.2846" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_9376_4054 0.2451 0.1937 0.2095 0.1779 0.2134 0.2569 0.2095" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_17656_27121 0.1937 0.2016 0.2016 0.1858 0.1818 0.253 0.2055 0.2253" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_20384_5679 0.0754 0.0754 0.09524 0.07143 0.09921 0.2885 0.03571 0.2134 0.1937" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_18415_21676 0.3043 0.2925 0.2767 0.2727 0.2727 0.1937 0.3004 0.2688 0.2174 0.2925" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_24025_14108 0.3043 0.3123 0.3004 0.3004 0.2925 0.1976 0.3162 0.2846 0.2372 0.3281 0.2016" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_25599_11475 0.2767 0.2372 0.2688 0.2411 0.2451 0.06324 0.2648 0.2292 0.2411 0.2727 0.1779 0.1976" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_21195_10623 0.2846 0.2609 0.2727 0.253 0.2609 0.04743 0.2767 0.2332 0.2372 0.2806 0.1581 0.1739 0.06324" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_11856_9674 0.3241 0.2767 0.2885 0.3083 0.3083 0.2451 0.2964 0.3123 0.2964 0.3083 0.2688 0.2213 0.2292 0.2451" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_20183_7496 0.2648 0.2648 0.2846 0.2609 0.2569 0.1739 0.2806 0.2411 0.253 0.2806 0.17 0.1897 0.1502 0.1423 0.2688" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_16061_3516 0.2885 0.2688 0.2767 0.2688 0.2727 0.04348 0.2806 0.249 0.253 0.2846 0.17 0.1976 0.04348 0.03953 0.2332 0.166" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_12395_11489 0.2846 0.249 0.2609 0.2451 0.2451 0.07115 0.2648 0.2174 0.2213 0.2767 0.1462 0.1542 0.06719 0.02767 0.2253 0.1383 0.05929" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_17084_15866 0.2885 0.2609 0.2806 0.2609 0.2688 0.04743 0.2806 0.2411 0.2451 0.2846 0.166 0.1897 0.04743 0.01581 0.2372 0.1462 0.02767 0.04348" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_28516_16324 0.1071 0.08333 0.0873 0.07143 0.09524 0.2846 0.07937 0.1897 0.2016 0.08333 0.2925 0.2925 0.2688 0.2688 0.2846 0.2806 0.2925 0.2609 0.2846" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_8084_12645 0.0754 0.08333 0.09127 0.04762 0.06746 0.2767 0.06349 0.2055 0.1937 0.07143 0.2964 0.3123 0.253 0.2688 0.3123 0.2569 0.2727 0.2569 0.2727 0.1032" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_18089_2781 0.2806 0.2372 0.2688 0.2332 0.253 0.1146 0.249 0.2213 0.2332 0.2569 0.1858 0.1897 0.083 0.08696 0.2609 0.17 0.1146 0.09486 0.1028 0.249 0.2451" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_21702_5444 0.3123 0.3202 0.2925 0.2925 0.2767 0.1937 0.3162 0.3004 0.2134 0.3123 0.1423 0.1225 0.1937 0.166 0.249 0.1976 0.1779 0.1502 0.1818 0.2925 0.3123 0.1897" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14077_24664 0.2925 0.2885 0.2964 0.2964 0.2964 0.1976 0.2846 0.2609 0.3083 0.2885 0.2451 0.2411 0.2095 0.1897 0.2024 0.2451 0.2016 0.1818 0.1976 0.2846 0.2964 0.1937 0.253" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_14168_10823 0.2964 0.249 0.249 0.2451 0.249 0.09881 0.2727 0.2095 0.249 0.2846 0.17 0.2134 0.1107 0.09486 0.2332 0.1423 0.09881 0.0751 0.1028 0.253 0.2648 0.1304 0.1976 0.1976" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_19252_7867 0.2835 0.248 0.2441 0.2441 0.248 0.1339 0.2638 0.2283 0.2402 0.2638 0.1693 0.2087 0.1457 0.1299 0.2598 0.1024 0.1339 0.122 0.1378 0.2717 0.2598 0.1654 0.2126 0.2126 0.09055" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_7265_9662 0.2648 0.2451 0.253 0.2451 0.2411 0.1542 0.2688 0.2292 0.2451 0.2609 0.1858 0.2095 0.1502 0.1502 0.249 0.1621 0.1462 0.1502 0.1502 0.2609 0.2569 0.1818 0.1897 0.2213 0.1383 0.1299" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_5370_21051 0.2846 0.2332 0.2688 0.2411 0.249 0.1304 0.2569 0.2411 0.2372 0.2688 0.1976 0.2055 0.1107 0.1265 0.249 0.166 0.1225 0.1067 0.1186 0.2609 0.249 0.1304 0.2016 0.2372 0.1265 0.1732 0.1858" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_14341_8428 0.3043 0.253 0.2727 0.2688 0.2767 0.1146 0.2688 0.2372 0.2451 0.2846 0.1897 0.1858 0.1067 0.1146 0.2451 0.1858 0.1107 0.1186 0.1146 0.2846 0.2806 0.09881 0.2016 0.2134 0.1225 0.1457 0.1502 0.1542" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_14198_21368 0.2846 0.2332 0.2648 0.2372 0.2569 0.1265 0.253 0.2174 0.249 0.2688 0.1858 0.1937 0.09486 0.1067 0.2332 0.1383 0.1107 0.08696 0.1067 0.2569 0.249 0.1067 0.1897 0.2134 0.09091 0.1378 0.1739 0.04743 0.1265" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_5883_17133 0.2964 0.2688 0.253 0.2569 0.253 0.05534 0.2806 0.2213 0.2332 0.2925 0.2095 0.1937 0.08696 0.083 0.2451 0.1858 0.083 0.07905 0.083 0.2609 0.2727 0.1186 0.1976 0.2016 0.1107 0.1496 0.1581 0.1304 0.1186 0.1344" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_7311_6821 0.2767 0.2332 0.2569 0.2411 0.2372 0.1186 0.249 0.2451 0.2292 0.2648 0.1542 0.1937 0.1028 0.1028 0.2213 0.1383 0.083 0.083 0.09091 0.2609 0.2411 0.1344 0.1818 0.2055 0.09091 0.1299 0.1581 0.0751 0.1304 0.0751 0.1304" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_13595_8524 0.2846 0.2411 0.2609 0.2411 0.249 0.07115 0.2609 0.2213 0.2372 0.2727 0.1739 0.1779 0.083 0.05138 0.2332 0.1344 0.07115 0.05534 0.06719 0.253 0.2569 0.083 0.1739 0.1858 0.09091 0.1339 0.1621 0.1146 0.09091 0.09486 0.083 0.083" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_15031_12738 0.2648 0.2213 0.249 0.2174 0.2332 0.1344 0.2372 0.1937 0.2253 0.249 0.1976 0.1897 0.1186 0.1067 0.253 0.1383 0.1265 0.08696 0.1225 0.2292 0.2292 0.1067 0.1818 0.2055 0.09881 0.1457 0.17 0.07115 0.1462 0.04743 0.1186 0.09881 0.09486" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_11381_14019 0.2767 0.2609 0.2727 0.2648 0.2609 0.1107 0.2569 0.2292 0.2253 0.2648 0.1739 0.1858 0.09091 0.09486 0.2451 0.1462 0.09881 0.07905 0.08696 0.2767 0.2688 0.1186 0.1779 0.2055 0.09881 0.1614 0.1581 0.1265 0.1265 0.1186 0.1107 0.1107 0.1107 0.1265" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_20653_21248 0.2688 0.2332 0.249 0.2372 0.2451 0.1542 0.253 0.2253 0.2411 0.253 0.1937 0.2055 0.1423 0.1502 0.2372 0.1621 0.1502 0.1462 0.1423 0.253 0.2451 0.1779 0.1976 0.2213 0.1502 0.1417 0.03162 0.1779 0.1542 0.166 0.1542 0.1542 0.1621 0.1621 0.1542" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_26181_9437 0.3123 0.336 0.3083 0.3043 0.2925 0.2174 0.3241 0.3004 0.2332 0.3202 0.1937 0.1225 0.1976 0.1897 0.2609 0.2174 0.1937 0.1739 0.2055 0.3083 0.3202 0.2055 0.0751 0.2569 0.2292 0.2323 0.2213 0.2213 0.2134 0.2095 0.2134 0.2095 0.1937 0.2055 0.2055 0.2134" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_6929_7655 0.1429 0.1151 0.1071 0.09524 0.1151 0.2648 0.1032 0.2253 0.2134 0.1151 0.2885 0.3083 0.2569 0.2648 0.2925 0.2727 0.2846 0.249 0.2727 0.09524 0.1071 0.249 0.3004 0.2925 0.2609 0.2717 0.249 0.2767 0.2727 0.2569 0.2727 0.249 0.249 0.249 0.2767 0.2292 0.3162" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_14218_8400 0.05556 0.0873 0.09524 0.07143 0.08333 0.2806 0.08333 0.2174 0.1858 0.06349 0.2806 0.3004 0.2727 0.2648 0.3162 0.253 0.2885 0.2688 0.2727 0.08333 0.08333 0.2648 0.3043 0.2885 0.2767 0.2638 0.249 0.2767 0.2846 0.2767 0.2727 0.2727 0.2609 0.2569 0.2727 0.249 0.3123 0.119" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_18922_4934 0.2806 0.2451 0.2846 0.253 0.2648 0.09881 0.2688 0.2372 0.2372 0.2727 0.1739 0.1937 0.06719 0.05929 0.2292 0.1423 0.06324 0.0751 0.05534 0.2688 0.2609 0.0751 0.1818 0.2095 0.1067 0.1535 0.1502 0.1186 0.09881 0.09881 0.1265 0.08696 0.06324 0.1107 0.1225 0.1383 0.2016 0.2688 0.2688" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_24493_5303 0.2767 0.2569 0.2767 0.2569 0.253 0.05138 0.2767 0.2411 0.2332 0.2806 0.1818 0.1976 0.04743 0.04743 0.2411 0.1621 0.04348 0.06324 0.03162 0.2806 0.2609 0.1107 0.1897 0.2134 0.1107 0.1417 0.1621 0.1067 0.1225 0.1028 0.08696 0.1028 0.09091 0.1265 0.1067 0.1502 0.2016 0.2727 0.2767 0.0751" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_28036_9037 0.3004 0.2727 0.2925 0.2727 0.2806 0.07115 0.2964 0.249 0.253 0.3004 0.1779 0.1976 0.05929 0.04348 0.249 0.17 0.03953 0.05534 0.03557 0.2964 0.2885 0.1186 0.1937 0.2253 0.09881 0.1535 0.1581 0.1225 0.1304 0.1107 0.1067 0.1107 0.09091 0.1344 0.09881 0.1542 0.2055 0.2885 0.2885 0.07115 0.04743" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_17656_7294 0.2648 0.2648 0.2846 0.2609 0.2569 0.1779 0.2648 0.2451 0.2253 0.2727 0.1818 0.1739 0.1462 0.1542 0.2688 0.06324 0.166 0.1383 0.1581 0.2806 0.249 0.1581 0.1937 0.2372 0.1581 0.1024 0.1976 0.1621 0.1818 0.1502 0.1739 0.1383 0.1383 0.1502 0.1344 0.1937 0.1937 0.2964 0.2609 0.1581 0.1621 0.1818" << endl;
+out << "M00967_43_000000000-A3JHG_1_1106_24475_12056 0.3071 0.2913 0.3031 0.2953 0.2913 0.185 0.3071 0.2441 0.2717 0.315 0.1654 0.2008 0.1693 0.1496 0.2835 0.1969 0.1772 0.1457 0.1654 0.3071 0.3071 0.1772 0.2165 0.2126 0.1969 0.1922 0.1693 0.2165 0.1929 0.1969 0.1969 0.1929 0.1732 0.2008 0.1811 0.1693 0.2165 0.2953 0.3031 0.1811 0.1732 0.1614 0.1929" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_17802_26911 0.2846 0.2609 0.2648 0.2688 0.2569 0.07905 0.2806 0.2411 0.2332 0.2925 0.1937 0.1858 0.0751 0.083 0.2253 0.166 0.0751 0.0751 0.0751 0.2767 0.2767 0.1107 0.1937 0.1818 0.08696 0.1142 0.1383 0.1462 0.09881 0.1265 0.07115 0.1146 0.07115 0.1383 0.1067 0.1344 0.2016 0.2688 0.2767 0.083 0.07905 0.09091 0.1423 0.1772" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_21761_13031 0.3162 0.2925 0.2727 0.2767 0.2925 0.2055 0.3004 0.2688 0.2569 0.3083 0.1739 0.2134 0.2213 0.1897 0.2292 0.1976 0.2055 0.1858 0.2055 0.2767 0.2925 0.2292 0.2213 0.2095 0.1937 0.1772 0.2213 0.2174 0.2372 0.1858 0.2174 0.1897 0.2016 0.2134 0.2332 0.2213 0.2411 0.2846 0.2964 0.2174 0.2055 0.2016 0.2095 0.2008 0.2134" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_10133_8460 0.2795 0.2441 0.2559 0.2441 0.2559 0.126 0.2559 0.2165 0.2559 0.2677 0.1693 0.2087 0.09843 0.09055 0.252 0.1378 0.09449 0.09449 0.09055 0.2559 0.2638 0.126 0.1929 0.1969 0.08268 0.1294 0.1457 0.122 0.122 0.07874 0.1339 0.09449 0.1102 0.1024 0.1024 0.1496 0.2165 0.2677 0.2638 0.09843 0.1142 0.09843 0.1614 0.1765 0.122 0.185" << endl;
+out << "M00967_43_000000000-A3JHG_1_1104_24665_17168 0.336 0.3004 0.2964 0.3004 0.3083 0.2727 0.3004 0.2925 0.2727 0.3123 0.2569 0.2292 0.2569 0.2569 0.2964 0.2727 0.2648 0.2411 0.2648 0.2885 0.3202 0.2134 0.2253 0.2806 0.2609 0.2874 0.253 0.2213 0.2332 0.2332 0.2688 0.2569 0.2411 0.2292 0.253 0.249 0.2213 0.2925 0.3162 0.2411 0.2648 0.2648 0.2609 0.2598 0.253 0.2411 0.2638" << endl;
+out << "M00967_43_000000000-A3JHG_1_1102_8473_5446 0.2767 0.2569 0.2648 0.2609 0.253 0.09881 0.2688 0.2213 0.2332 0.2767 0.1937 0.17 0.083 0.07905 0.2569 0.166 0.09486 0.07115 0.08696 0.2688 0.2688 0.08696 0.1858 0.2016 0.1265 0.1693 0.166 0.1383 0.1423 0.1344 0.0751 0.1383 0.07905 0.1067 0.083 0.1542 0.1976 0.2688 0.2688 0.09486 0.09486 0.1028 0.1502 0.1732 0.07115 0.2372 0.126 0.249" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_28553_10567 0.2756 0.2559 0.2795 0.248 0.252 0.1339 0.2677 0.252 0.2441 0.2717 0.2283 0.2244 0.122 0.126 0.2677 0.1654 0.126 0.1181 0.122 0.2756 0.2559 0.1339 0.2205 0.2559 0.1299 0.1725 0.185 0.09843 0.1614 0.1142 0.1299 0.126 0.1378 0.1142 0.126 0.185 0.2323 0.2913 0.2677 0.1102 0.09843 0.1142 0.1693 0.2275 0.1575 0.248 0.149 0.2402 0.1378" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_12259_21251 0.2806 0.2292 0.2569 0.2372 0.2451 0.1304 0.253 0.2213 0.2332 0.2648 0.1621 0.1937 0.1146 0.1107 0.2134 0.1344 0.09881 0.08696 0.1107 0.2569 0.2411 0.1383 0.1818 0.1858 0.06719 0.1181 0.1462 0.09091 0.1344 0.06324 0.1462 0.04743 0.09091 0.06719 0.1225 0.1462 0.2095 0.2569 0.2727 0.09486 0.1186 0.1225 0.1462 0.189 0.1186 0.1858 0.07874 0.249 0.1462 0.1299" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_11296_4480 0.249 0.2609 0.2609 0.2609 0.2688 0.1621 0.253 0.2767 0.2095 0.2688 0.1858 0.2134 0.1779 0.17 0.2885 0.1621 0.1818 0.1621 0.1739 0.2727 0.253 0.1779 0.2055 0.249 0.1739 0.1693 0.1502 0.1937 0.1779 0.166 0.1897 0.166 0.1739 0.1779 0.166 0.1542 0.2292 0.2372 0.2569 0.166 0.1858 0.1858 0.1739 0.185 0.1858 0.2055 0.1732 0.2806 0.2016 0.1969 0.17" << endl;
+out << "M00967_43_000000000-A3JHG_1_1101_8868_4602 0.1111 0.09921 0.1032 0.09127 0.1151 0.2648 0.09921 0.1897 0.1858 0.0873 0.2767 0.3004 0.2569 0.2648 0.2885 0.2609 0.2688 0.2609 0.2648 0.1032 0.1071 0.2648 0.3083 0.3004 0.2648 0.2559 0.2411 0.2609 0.2767 0.2609 0.253 0.2569 0.2569 0.2411 0.2727 0.2253 0.3083 0.119 0.0754 0.2569 0.2569 0.2767 0.2767 0.3031 0.2688 0.2885 0.2677 0.3004 0.2688 0.2638 0.2569 0.2609" << endl;
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+out << "M00967_43_000000000-A3JHG_1_1103_23279_25937 0.2885 0.2451 0.2727 0.249 0.253 0.1146 0.2688 0.2372 0.2332 0.2806 0.1976 0.1897 0.1028 0.1107 0.2648 0.1621 0.1067 0.09091 0.1028 0.2688 0.2609 0.1146 0.1858 0.2292 0.07905 0.1457 0.1739 0.0751 0.1265 0.05929 0.1304 0.07905 0.09881 0.0751 0.09881 0.166 0.2055 0.2648 0.2806 0.1028 0.1067 0.09881 0.1423 0.2126 0.1028 0.2332 0.1142 0.2411 0.1225 0.1142 0.083 0.17 0.2727 0.09881 0.1462 0.08696 0.07115 0.07115 0.1383 0.1581 0.2016 0.1423 [...]
+out << "M00967_43_000000000-A3JHG_1_1103_19321_18100 0.2648 0.2451 0.2648 0.2451 0.2411 0.07115 0.2648 0.2332 0.2134 0.2688 0.1897 0.2134 0.06719 0.06719 0.249 0.1779 0.06324 0.083 0.05138 0.2688 0.249 0.1304 0.2055 0.2213 0.1304 0.1575 0.1779 0.1186 0.1423 0.1225 0.1067 0.1146 0.1107 0.1383 0.1265 0.166 0.2174 0.2609 0.2648 0.09486 0.01976 0.06719 0.1779 0.189 0.09881 0.2174 0.1339 0.2767 0.1146 0.1181 0.1344 0.2016 0.2451 0.09091 0.1739 0.1265 0.09486 0.1265 0.1818 0.1818 0.2134 0.17 0 [...]
+out << "M00967_43_000000000-A3JHG_1_1103_12856_12076 0.3083 0.2569 0.2767 0.2727 0.2806 0.1186 0.2727 0.2451 0.249 0.2885 0.2016 0.1937 0.1146 0.1186 0.249 0.1937 0.1146 0.1225 0.1186 0.2885 0.2885 0.1107 0.2016 0.2174 0.1344 0.1535 0.1502 0.1581 0.01186 0.1304 0.1225 0.1344 0.09486 0.1462 0.1304 0.1542 0.2213 0.2767 0.2885 0.1107 0.1265 0.1344 0.1897 0.1929 0.1067 0.2451 0.1339 0.2332 0.1462 0.1654 0.1383 0.1858 0.2806 0.1107 0.1581 0.1067 0.1146 0.1344 0.1818 0.1581 0.2292 0.1818 0.134 [...]
+out << "M00967_43_000000000-A3JHG_1_1102_14586_9284 0.2767 0.253 0.2767 0.2609 0.249 0.06719 0.2727 0.2451 0.2372 0.2806 0.1897 0.2016 0.05534 0.06324 0.2372 0.17 0.05929 0.06719 0.04743 0.2767 0.2609 0.1186 0.1976 0.2174 0.1146 0.1535 0.17 0.1107 0.1186 0.1067 0.09091 0.1067 0.09486 0.1304 0.1107 0.1581 0.2095 0.2727 0.2767 0.08696 0.01581 0.06324 0.166 0.1772 0.083 0.2134 0.1181 0.2688 0.09881 0.1102 0.1225 0.1897 0.2569 0.0751 0.166 0.1146 0.07905 0.1186 0.17 0.17 0.2055 0.1542 0.0909 [...]
+out << "M00967_43_000000000-A3JHG_1_1102_11158_17229 0.3071 0.252 0.2677 0.2717 0.2756 0.1299 0.2717 0.2441 0.248 0.2874 0.2047 0.1929 0.126 0.1299 0.249 0.1969 0.126 0.1339 0.1299 0.2874 0.2874 0.122 0.2165 0.2292 0.1457 0.1647 0.1693 0.1693 0.02756 0.1417 0.1339 0.1457 0.09843 0.1614 0.1457 0.1732 0.2283 0.2717 0.2835 0.122 0.1378 0.1457 0.1929 0.2118 0.1181 0.2559 0.149 0.2402 0.1496 0.1765 0.1575 0.1969 0.2756 0.122 0.1693 0.126 0.126 0.1457 0.185 0.1693 0.2323 0.1929 0.1457 0.1693 0 [...]
+out << "M00967_43_000000000-A3JHG_1_1101_20702_8361 0.311 0.3189 0.3189 0.3228 0.2953 0.2323 0.3228 0.3228 0.311 0.3189 0.2402 0.2008 0.2126 0.2402 0.2806 0.2756 0.2205 0.2283 0.2323 0.3189 0.315 0.2441 0.2087 0.1976 0.2598 0.2706 0.2638 0.2362 0.2362 0.2362 0.2441 0.2323 0.2441 0.248 0.2283 0.2559 0.1929 0.3386 0.3228 0.2362 0.2244 0.2362 0.248 0.251 0.2283 0.2717 0.2431 0.2874 0.2362 0.2588 0.2362 0.2402 0.3307 0.2205 0.2598 0.2559 0.2165 0.2362 0.248 0.2402 0.2244 0.2323 0.2205 0.2559 [...]
+
+ out.close();
+
+ return "phylip.temp";
+}
+
+/***********************************************************************/
diff --git a/TestMothur/distpdataset.h b/TestMothur/distpdataset.h
new file mode 100644
index 0000000..a06cb75
--- /dev/null
+++ b/TestMothur/distpdataset.h
@@ -0,0 +1,30 @@
+//
+// distdataset.h
+// Mothur
+//
+// Created by Sarah Westcott on 6/6/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__distdataset__
+#define __Mothur__distdataset__
+
+#include "mothurout.h"
+
+class DistPDataSet {
+
+public:
+
+ DistPDataSet();
+ ~DistPDataSet() {}
+
+ string getPhylipFile() { return writePhylipFile(); }
+
+private:
+ MothurOut* m;
+ string writePhylipFile();
+
+};
+
+
+#endif /* defined(__Mothur__distdataset__) */
diff --git a/TestMothur/main.cpp b/TestMothur/main.cpp
index 1c86ead..c8acef9 100644
--- a/TestMothur/main.cpp
+++ b/TestMothur/main.cpp
@@ -15,11 +15,10 @@
To compile TestMothur you need to uncomment
- //CommandFactory* CommandFactory::_uniqueInstance; in commandfactory.cpp
+ CommandFactory* CommandFactory::_uniqueInstance; in commandfactory.cpp
- //MothurOut* MothurOut::_uniqueInstance; in mothurout.cpp
+ MothurOut* MothurOut::_uniqueInstance; in mothurout.cpp
- //ReferenceDB* ReferenceDB::myInstance; in referencedb.cpp
*/
//***********************************************************//
@@ -29,5 +28,3 @@ To compile TestMothur you need to uncomment
#define CATCH_CONFIG_MAIN // This tells Catch to provide a main() - only do this in one cpp file
#include "catch.hpp"
-
-
diff --git a/TestMothur/testclassifier/testphylotree.cpp b/TestMothur/testclassifier/testphylotree.cpp
new file mode 100644
index 0000000..f39c313
--- /dev/null
+++ b/TestMothur/testclassifier/testphylotree.cpp
@@ -0,0 +1,129 @@
+//
+// testphylotree.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 8/29/16.
+// Copyright © 2016 Schloss Lab. All rights reserved.
+//
+
+#include "catch.hpp"
+#include "testphylotree.hpp"
+
+/**************************************************************************************************/
+TestPhyloTree::TestPhyloTree() { //setup
+ m = MothurOut::getInstance();
+
+ string tax1WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
+ string tax2WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
+ string tax3WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
+ string tax4WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
+ string tax5WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
+
+ string tax1WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
+ string tax2WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
+ string tax3WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
+ string tax4WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
+ string tax5WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
+
+ phylo.addSeqToTree("seq1", tax1WithSpaces);
+ phylo.addSeqToTree("seq2", tax2WithSpaces);
+ phylo.addSeqToTree("seq3", tax3WithSpaces);
+ phylo.addSeqToTree("seq4", tax4WithSpaces);
+ phylo.addSeqToTree("seq5", tax5WithSpaces);
+ phylo.addSeqToTree("seq6", tax1WithOutSpaces);
+ phylo.addSeqToTree("seq7", tax2WithOutSpaces);
+ phylo.addSeqToTree("seq8", tax3WithOutSpaces);
+ phylo.addSeqToTree("seq9", tax4WithOutSpaces);
+ phylo.addSeqToTree("seq10", tax5WithOutSpaces);
+}
+/**************************************************************************************************/
+TestPhyloTree::~TestPhyloTree() {}
+/**************************************************************************************************/
+
+TEST_CASE("Testing PhyloTree Class") {
+ TestPhyloTree testPTree;
+
+ string tax1WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
+ string tax2WithSpaces = "Bacteria(100);Bacteroidetes 7(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
+ string tax3WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
+ string tax4WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
+ string tax5WithSpaces = "Bacteria(100);Firmicutes(100);Clostridia B(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
+
+ string tax1WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(100);Bacteroidales(100);S24-7(100);";
+ string tax2WithOutSpaces = "Bacteria(100);Bacteroidetes(100);Bacteroidia(98);Bacteroidales(98);Bacteroidaceae(98);Bacteroides(98);";
+ string tax3WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Blautia(92);";
+ string tax4WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Ruminococcaceae(100);Anaerotruncus(100);";
+ string tax5WithOutSpaces = "Bacteria(100);Firmicutes(100);Clostridia(100);Clostridiales(100);Lachnospiraceae(100);Incertae_Sedis(97);";
+
+ SECTION("Add Sequences to Tree") {
+ INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
+
+ CAPTURE(testPTree.addSeqToTree("seq1", tax1WithSpaces));
+ CHECK(testPTree.addSeqToTree("seq1", tax1WithSpaces) == 5);
+
+ CAPTURE(testPTree.addSeqToTree("seq2", tax2WithSpaces));
+ CHECK(testPTree.addSeqToTree("seq2", tax2WithSpaces) == 6);
+
+ CAPTURE(testPTree.addSeqToTree("seq3", tax3WithSpaces));
+ CHECK(testPTree.addSeqToTree("seq3", tax3WithSpaces) == 6);
+
+ CAPTURE(testPTree.addSeqToTree("seq4", tax4WithSpaces));
+ CHECK(testPTree.addSeqToTree("seq4", tax4WithSpaces) == 6);
+
+ CAPTURE(testPTree.addSeqToTree("seq5", tax5WithSpaces));
+ CHECK(testPTree.addSeqToTree("seq5", tax5WithSpaces) == 6);
+
+ CAPTURE(testPTree.addSeqToTree("seq6", tax1WithOutSpaces));
+ CHECK(testPTree.addSeqToTree("seq6", tax1WithOutSpaces) == 5);
+
+ CAPTURE(testPTree.addSeqToTree("seq7", tax2WithOutSpaces));
+ CHECK(testPTree.addSeqToTree("seq7", tax2WithOutSpaces) == 6);
+
+ CAPTURE(testPTree.addSeqToTree("seq8", tax3WithOutSpaces));
+ CHECK(testPTree.addSeqToTree("seq8", tax3WithOutSpaces) == 6);
+
+ CAPTURE(testPTree.addSeqToTree("seq9", tax4WithOutSpaces));
+ CHECK(testPTree.addSeqToTree("seq9", tax4WithOutSpaces) == 6);
+
+ CAPTURE(testPTree.addSeqToTree("seq10", tax5WithOutSpaces));
+ CHECK(testPTree.addSeqToTree("seq10", tax5WithOutSpaces) == 6);
+ }
+
+ SECTION("Get Seqs") {
+ INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
+
+ CAPTURE(testPTree.phylo.getSeqs("Bacteroidetes 7").size());
+ CHECK((testPTree.phylo.getSeqs("Bacteroidetes 7").size()) == 2);
+
+ vector<string> Bacteroidetes_7 = testPTree.phylo.getSeqs("Bacteroidetes 7");
+ CHECK(Bacteroidetes_7[0] == "seq1");
+ CHECK(Bacteroidetes_7[1] == "seq2");
+
+ CAPTURE(testPTree.phylo.getSeqs("Clostridia").size());
+ CHECK((testPTree.phylo.getSeqs("Clostridia").size()) == 3);
+
+ vector<string> Clostridia = testPTree.phylo.getSeqs("Clostridia");
+ CHECK(Clostridia[0] == "seq8");
+ CHECK(Clostridia[1] == "seq9");
+ CHECK(Clostridia[2] == "seq10");
+ }
+
+ SECTION("Get Genus Totals") {
+ INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
+
+ CAPTURE(testPTree.phylo.getGenusTotals().size());
+ CHECK(testPTree.phylo.getGenusTotals().size() == 10);
+ }
+
+ SECTION("Get Full Taxonomy") {
+ INFO("Using taxonomies with and without spaces") // Only appears on a FAIL
+
+ CAPTURE(testPTree.phylo.getFullTaxonomy("seq1"));
+ CHECK(testPTree.phylo.getFullTaxonomy("seq1") == "Bacteria;Bacteroidetes 7;Bacteroidia;Bacteroidales;S24-7;");
+
+ CAPTURE(testPTree.phylo.getFullTaxonomy("seq10"));
+ CHECK(testPTree.phylo.getFullTaxonomy("seq1") == "Bacteria;Firmicutes;Clostridia;Clostridiales;Lachnospiraceae;Incertae_Sedis;");
+ }
+
+}
+/**************************************************************************************************/
diff --git a/TestMothur/testclassifier/testphylotree.hpp b/TestMothur/testclassifier/testphylotree.hpp
new file mode 100644
index 0000000..bfac178
--- /dev/null
+++ b/TestMothur/testclassifier/testphylotree.hpp
@@ -0,0 +1,32 @@
+//
+// testphylotree.hpp
+// Mothur
+//
+// Created by Sarah Westcott on 8/29/16.
+// Copyright © 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef testphylotree_hpp
+#define testphylotree_hpp
+
+#include "phylotree.h"
+
+class TestPhyloTree : public PhyloTree {
+
+
+public:
+
+ TestPhyloTree();
+ ~TestPhyloTree();
+
+ MothurOut* m;
+
+ PhyloTree phylo;
+
+ //using PhyloTree::
+ //using PhyloTree::
+
+};
+
+
+#endif /* testphylotree_hpp */
diff --git a/TestMothur/testcontainers/testfastqread.cpp b/TestMothur/testcontainers/testfastqread.cpp
index 5184dd3..f48bf5e 100644
--- a/TestMothur/testcontainers/testfastqread.cpp
+++ b/TestMothur/testcontainers/testfastqread.cpp
@@ -13,7 +13,7 @@
/**************************************************************************************************/
TestFastqRead::TestFastqRead() { //setup
m = MothurOut::getInstance();
- TestDataSet data;
+ TestFastqDataSet data;
reads = data.getForwardFastq();
filenames = data.getSubsetFRFastq(100);
}
@@ -25,6 +25,7 @@ TestFastqRead::~TestFastqRead() {
/**************************************************************************************************/
TEST_CASE("Testing FastqRead Class") {
+ /*
TestFastqRead testFastq;
SECTION("Testing (Sequence, Quality) Constructor ") {
@@ -60,6 +61,6 @@ TEST_CASE("Testing FastqRead Class") {
CHECK(read.getScores()[0] == testFastq.reads[0].getScores()[0]);
}
-
+ */
}
/**************************************************************************************************/
diff --git a/TestMothur/testcontainers/testoptimatrix.cpp b/TestMothur/testcontainers/testoptimatrix.cpp
new file mode 100644
index 0000000..e3cbde6
--- /dev/null
+++ b/TestMothur/testcontainers/testoptimatrix.cpp
@@ -0,0 +1,101 @@
+//
+// testoptimatrix.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 6/6/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#include "catch.hpp"
+#include "testoptimatrix.h"
+#include "distancecommand.h"
+#include "dataset.h"
+
+/**************************************************************************************************/
+TestOptiMatrix::TestOptiMatrix() { //setup
+ m = MothurOut::getInstance();
+ TestDataSet data;
+ filenames = data.getSubsetFNGFiles(100); //Fasta, name, group returned
+
+ string inputString = "fasta=" + filenames[0];
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: dist.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* distCommand = new DistanceCommand(inputString);
+ distCommand->execute();
+
+ map<string, vector<string> > outputFilenames = distCommand->getOutputFiles();
+
+ delete distCommand;
+ m->mothurCalling = false;
+
+ columnFile = outputFilenames["column"][0];
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+
+ inputString = "fasta=" + filenames[0] + ", output=lt";
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: dist.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* dist2Command = new DistanceCommand(inputString);
+ dist2Command->execute();
+
+ outputFilenames = dist2Command->getOutputFiles();
+
+ delete dist2Command;
+ m->mothurCalling = false;
+
+ phylipFile = outputFilenames["phylip"][0];
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+}
+/**************************************************************************************************/
+TestOptiMatrix::~TestOptiMatrix() {
+ for (int i = 0; i < filenames.size(); i++) { m->mothurRemove(filenames[i]); } //teardown
+ m->mothurRemove(columnFile);
+ m->mothurRemove(phylipFile);
+}
+/**************************************************************************************************/
+TEST_CASE("Testing OptiMatrix Class") {
+ TestOptiMatrix testOMatrix;
+ OptiMatrix matrix(testOMatrix.columnFile, testOMatrix.filenames[1], "name", 0.03, false);
+ OptiMatrix pmatrix(testOMatrix.phylipFile, "", "", 0.03, false);
+
+ SECTION("Testing Column Read") {
+ INFO("Using First 100 sequences of final.fasta and final.names") // Only appears on a FAIL
+
+ CAPTURE(matrix.print(cout)); // Displays this variable on a FAIL
+
+ CHECK(matrix.print(cout) == 112); //numdists in matrix
+ }
+
+ SECTION("Testing Phylip Read") {
+ INFO("Using First 100 sequences of final.fasta and final.names") // Only appears on a FAIL
+
+ CAPTURE(pmatrix.print(cout)); // Displays this variable on a FAIL
+
+ CHECK(pmatrix.print(cout) == 112); //numdists in matrix
+ }
+
+ /* First few rows of matrix
+ 12 23 44
+ 10 23 32 36
+ 16 25 33 48
+ 38
+ 22 45 52
+ */
+
+ SECTION("Testing isClose") {
+ INFO("Sequences 0 and 1") // Only appears on a FAIL
+
+ CAPTURE(matrix.isClose(0, 12));
+ CHECK(matrix.isClose(0, 12) == true);
+ CAPTURE(matrix.isClose(0, 44));
+ CHECK(matrix.isClose(0, 44) == true);
+ CAPTURE(matrix.isClose(1, 23));
+ CHECK(matrix.isClose(1, 23) == true);
+ CAPTURE(matrix.isClose(1, 36));
+ CHECK(matrix.isClose(1, 36) == true);
+ }
+}
+/**************************************************************************************************/
diff --git a/TestMothur/testcontainers/testoptimatrix.h b/TestMothur/testcontainers/testoptimatrix.h
new file mode 100644
index 0000000..ba7b637
--- /dev/null
+++ b/TestMothur/testcontainers/testoptimatrix.h
@@ -0,0 +1,31 @@
+//
+// testoptimatrix.h
+// Mothur
+//
+// Created by Sarah Westcott on 6/6/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__testoptimatrix__
+#define __Mothur__testoptimatrix__
+
+#include "optimatrix.h"
+
+class TestOptiMatrix : public OptiMatrix {
+
+public:
+
+ TestOptiMatrix();
+ ~TestOptiMatrix();
+
+ using OptiMatrix::getCloseSeqs;
+ using OptiMatrix::findDistFormat;
+ using OptiMatrix::readPhylip;
+ using OptiMatrix::readColumn;
+
+ string columnFile, phylipFile;
+ vector<string> filenames;
+
+};
+
+#endif /* defined(__Mothur__testoptimatrix__) */
diff --git a/TestMothur/testopticluster.cpp b/TestMothur/testopticluster.cpp
new file mode 100644
index 0000000..46bd941
--- /dev/null
+++ b/TestMothur/testopticluster.cpp
@@ -0,0 +1,132 @@
+//
+// testopticluster.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 6/15/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#include "testopticluster.h"
+#include "catch.hpp"
+#include "optimatrix.h"
+#include "distancecommand.h"
+#include "dataset.h"
+
+/**************************************************************************************************/
+TestOptiCluster::TestOptiCluster() { //setup
+ m = MothurOut::getInstance();
+ TestDataSet data;
+ filenames = data.getSubsetFNGFiles(100); //Fasta, name, group returned
+
+ string inputString = "fasta=" + filenames[0];
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: dist.seqs(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* distCommand = new DistanceCommand(inputString);
+ distCommand->execute();
+
+ map<string, vector<string> > outputFilenames = distCommand->getOutputFiles();
+
+ delete distCommand;
+ m->mothurCalling = false;
+
+ columnFile = outputFilenames["column"][0];
+}
+/**************************************************************************************************/
+TestOptiCluster::~TestOptiCluster() {
+ for (int i = 0; i < filenames.size(); i++) { m->mothurRemove(filenames[i]); } //teardown
+ m->mothurRemove(columnFile);
+}
+/**************************************************************************************************/
+TEST_CASE("Testing OptiCluster Class") {
+ TestOptiCluster testOcluster;
+ OptiMatrix matrix(testOcluster.columnFile, testOcluster.filenames[1], "name", "column", 0.03, false);
+ testOcluster.setVariables(&matrix, "mcc");
+
+ SECTION("Testing Initialize") {
+ INFO("Using First 100 sequences of final.fasta and final.names") // Only appears on a FAIL
+
+ double initialMetricValue;
+
+ CAPTURE(testOcluster.initialize(initialMetricValue, true, "singleton")); //
+
+ CHECK(testOcluster.initialize(initialMetricValue, true, "singleton") == 0); //metric value
+ }
+
+ SECTION("Testing calcMCC") {
+ INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+
+ long long tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+
+ CAPTURE(testOcluster.calcMCC(tp,tn,fp,fn)); // Displays this variable on a FAIL
+
+ CHECK((int)(testOcluster.calcMCC(tp,tn,fp,fn)*10000) == 9694); //metric value
+ }
+
+ SECTION("Testing calcSens") {
+ INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+
+ long long tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+
+ CAPTURE(testOcluster.calcSens(tp,tn,fp,fn)); // Displays this variable on a FAIL
+
+ CHECK((int)(testOcluster.calcSens(tp,tn,fp,fn)*10000) == 9615); //metric value
+ }
+
+ SECTION("Testing calcSpec") {
+ INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+
+ long long tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+
+ CAPTURE(testOcluster.calcSpec(tp,tn,fp,fn)); // Displays this variable on a FAIL
+
+ CHECK((int)(testOcluster.calcSpec(tp,tn,fp,fn)*10000) == 9990); //metric value
+ }
+
+ SECTION("Testing calcTPTN") {
+ INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+
+ long long tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+
+ CAPTURE(testOcluster.calcTPTN(tp,tn,fp,fn)); // Displays this variable on a FAIL
+
+ CHECK((int)(testOcluster.calcTPTN(tp,tn,fp,fn)*10000) == 9861); //metric value
+ }
+
+ SECTION("Testing calcFPFN") {
+ INFO("Using tp=5000, tn=10000, fp=10, fn=200") // Only appears on a FAIL
+
+ double tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+
+ CAPTURE(testOcluster.calcFPFN(tp,tn,fp,fn)); // Displays this variable on a FAIL
+
+ CHECK((int)(testOcluster.calcFPFN(tp,tn,fp,fn)*10000) == 9861); //metric value
+ }
+
+ SECTION("Testing moveAdjustTFValues") {
+ INFO("Using tp=5000, tn=10000, fp=10, fn=200 and mcc") // Only appears on a FAIL
+
+ long long tp,tn,fp,fn; tp=5000; tn=10000; fp=10; fn=200;
+ double initialMetricValue;
+ testOcluster.initialize(initialMetricValue, false, "singleton"); //no randomization
+
+ CAPTURE(testOcluster.moveAdjustTFValues(0, 10, 1, tp,tn,fp,fn)); // Displays this variable on a FAIL
+
+ CHECK((int)(testOcluster.moveAdjustTFValues(0, 10, 1, tp,tn,fp,fn)*10000) == 9700); //metric value
+ }
+
+ SECTION("Testing update") {
+ INFO("Using mcc") // Only appears on a FAIL
+
+ double initialMetricValue;
+ testOcluster.initialize(initialMetricValue, false, "singleton"); //no randomization
+ testOcluster.update(initialMetricValue);
+
+ CAPTURE(initialMetricValue); // Displays this variable on a FAIL
+
+ CHECK((int)(initialMetricValue*10000) == 7853); //metric value
+ }
+
+}
+/**************************************************************************************************/
diff --git a/TestMothur/testopticluster.h b/TestMothur/testopticluster.h
new file mode 100644
index 0000000..021b9f9
--- /dev/null
+++ b/TestMothur/testopticluster.h
@@ -0,0 +1,35 @@
+//
+// testopticluster.h
+// Mothur
+//
+// Created by Sarah Westcott on 6/15/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__testopticluster__
+#define __Mothur__testopticluster__
+
+#include "opticluster.h"
+
+class TestOptiCluster : public OptiCluster {
+
+public:
+
+ TestOptiCluster();
+ ~TestOptiCluster();
+
+ MothurOut* m;
+ string columnFile, phylipFile;
+ vector<string> filenames;
+
+ using OptiCluster::calcMCC;
+ using OptiCluster::calcSens;
+ using OptiCluster::calcSpec;
+ using OptiCluster::calcTPTN;
+ using OptiCluster::calcFPFN;
+ using OptiCluster::moveAdjustTFValues;
+ using OptiCluster::setVariables;
+
+};
+
+#endif /* defined(__Mothur__testopticluster__) */
diff --git a/TestMothur/testtrimoligos.hpp b/TestMothur/testtrimoligos.hpp
index e150c3d..91ef92a 100644
--- a/TestMothur/testtrimoligos.hpp
+++ b/TestMothur/testtrimoligos.hpp
@@ -29,8 +29,8 @@ public:
map<int, oligosPair> pairedPrimers;
map<int, oligosPair> pairedBarcodes;
- using TrimOligos::compareDNASeq(string, string);
- using TrimOligos::countDiffs(string, string);
+ //using TrimOligos::compareDNASeq(string, string);
+ //using TrimOligos::countDiffs(string, string);
};
diff --git a/TestMothur/testvsearchfileparser.cpp b/TestMothur/testvsearchfileparser.cpp
index dd5dbd9..84af895 100644
--- a/TestMothur/testvsearchfileparser.cpp
+++ b/TestMothur/testvsearchfileparser.cpp
@@ -101,13 +101,13 @@ TEST_CASE("Testing VsearchParser Class") {
ifstream in2;
testVParser.m->openInputFile("temp.list", in2);
- ListVector list(in2);
+ ListVector list2(in2);
in2.close();
testVParser.m->mothurRemove("temp.list"); testVParser.m->mothurRemove("temp.rabund"); testVParser.m->mothurRemove("temp.sabund");
//for each bin
- for (int i = 0; i < list.getNumBins(); i++) {
- string binnames = list.get(i);
+ for (int i = 0; i < list2.getNumBins(); i++) {
+ string binnames = list2.get(i);
CAPTURE(binnames);
diff --git a/TestMothur/testvsearchfileparser.h b/TestMothur/testvsearchfileparser.h
index 46103cf..3d93aea 100644
--- a/TestMothur/testvsearchfileparser.h
+++ b/TestMothur/testvsearchfileparser.h
@@ -22,7 +22,6 @@ public:
~TestVsearchFileParser();
MothurOut* m;
- TestDataSet data;
vector<string> filenames;
CountTable* ct;
diff --git a/makefile-internal b/makefile-internal
index f7bf6f8..e319fae 100644
--- a/makefile-internal
+++ b/makefile-internal
@@ -1,12 +1,14 @@
64BIT_VERSION ?= yes
USEREADLINE ?= yes
USEBOOST ?= yes
-RELEASE_DATE = "\"7/20/2016\""
-VERSION = "\"1.38.0\""
+RELEASE_DATE = "\"1/23/2017\""
+VERSION = "\"1.39.0\""
# Optimize to level 3:
CXXFLAGS += -O3
+#CPP_11
+ CXXFLAGS += -std=c++11
ifeq ($(strip $(64BIT_VERSION)),yes)
#if you are a mac user use the following line
diff --git a/source/calculators/filters.h b/source/calculators/filters.h
index b00cb35..32df327 100644
--- a/source/calculators/filters.h
+++ b/source/calculators/filters.h
@@ -62,6 +62,18 @@ public:
}
}
+
+ void doVerticalAllBases() {
+
+ for(int i=0;i<alignmentLength;i++){
+ if(gap[i] == numSeqs) { filter[i] = '0'; }
+ else if(a[i] == numSeqs) { filter[i] = '0'; }
+ else if(t[i] == numSeqs) { filter[i] = '0'; }
+ else if(c[i] == numSeqs) { filter[i] = '0'; }
+ else if(g[i] == numSeqs) { filter[i] = '0'; }
+ }
+
+ }
void doTrump(Sequence seq) {
diff --git a/source/chimera/chimeracheckrdp.cpp b/source/chimera/chimeracheckrdp.cpp
index 9e91a96..72b4a79 100644
--- a/source/chimera/chimeracheckrdp.cpp
+++ b/source/chimera/chimeracheckrdp.cpp
@@ -20,7 +20,7 @@ ChimeraCheckRDP::ChimeraCheckRDP(string filename, string temp, string n, bool s,
kmerSize = k;
outputDir = o;
- templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0, rand());
+ templateDB = new AlignmentDB(templateFileName, "kmer", kmerSize, 0.0,0.0,0.0,0.0, rand(), true);
m->mothurOutEndLine();
kmer = new Kmer(kmerSize);
diff --git a/source/classifier/classify.cpp b/source/classifier/classify.cpp
index 3bec5d1..53c1756 100644
--- a/source/classifier/classify.cpp
+++ b/source/classifier/classify.cpp
@@ -101,7 +101,6 @@ void Classify::generateDatabaseAndNames(string tfile, string tempFile, string me
m->mothurOut("DONE."); m->mothurOutEndLine();
m->mothurOut("It took " + toString(time(NULL) - start) + " seconds generate search database. "); m->mothurOutEndLine();
-
readTaxonomy(taxFile);
//sanity check
diff --git a/source/classifier/phylosummary.cpp b/source/classifier/phylosummary.cpp
index 3d12efc..0be3cb7 100644
--- a/source/classifier/phylosummary.cpp
+++ b/source/classifier/phylosummary.cpp
@@ -177,6 +177,8 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
while (seqTaxonomy != "") {
+ level++;
+
if (m->control_pressed) { return 0; }
//somehow the parent is getting one too many accnos
@@ -287,15 +289,10 @@ int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
break;
}
}
-
- level++;
-
- if (level > maxLevel) { maxLevel = level; }
-
- if ((seqTaxonomy == "") && (level < maxLevel)) { //if you think you are done and you are not.
- for (int k = level; k < maxLevel; k++) { seqTaxonomy += "unclassified;"; }
- }
- }
+ }
+
+ if (level > maxLevel) { maxLevel = level; }
+
return 0;
}
catch(exception& e) {
@@ -321,6 +318,8 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, map<string, bool> containsGro
while (seqTaxonomy != "") {
+ level++;
+
if (m->control_pressed) { return 0; }
//somehow the parent is getting one too many accnos
@@ -346,7 +345,7 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, map<string, bool> containsGro
int index = tree.size() - 1;
tree[index].parent = currentNode;
- tree[index].level = (level+1);
+ tree[index].level = level;
tree[index].total = 1;
tree[currentNode].children[taxon] = index;
@@ -363,15 +362,10 @@ int PhyloSummary::addSeqToTree(string seqTaxonomy, map<string, bool> containsGro
break;
}
}
-
- level++;
-
- if (level > maxLevel) { maxLevel = level; }
-
- if ((seqTaxonomy == "") && (level < maxLevel)) { //if you think you are done and you are not.
- for (int k = level; k < maxLevel; k++) { seqTaxonomy += "unclassified;"; }
- }
}
+
+ if (level > maxLevel) { maxLevel = level; }
+
return 0;
}
catch(exception& e) {
@@ -755,13 +749,15 @@ void PhyloSummary::readTreeStruct(ifstream& in){
//read the tree file
for (int i = 0; i < tree.size(); i++) {
- in >> tree[i].level >> tree[i].name >> num; //num contains the number of children tree[i] has
-
+ in >> tree[i].level >> num; m->gobble(in); //num contains the number of children tree[i] has
+ tree[i].name = m->getline(in); m->gobble(in);
+
//set children
string childName;
int childIndex;
for (int j = 0; j < num; j++) {
- in >> childName >> childIndex;
+ in >> childIndex; m->gobble(in);
+ childName = m->getline(in); m->gobble(in);
tree[i].children[childName] = childIndex;
}
diff --git a/source/classifier/phylotree.cpp b/source/classifier/phylotree.cpp
index 1985725..d738cb3 100644
--- a/source/classifier/phylotree.cpp
+++ b/source/classifier/phylotree.cpp
@@ -46,7 +46,8 @@ PhyloTree::PhyloTree(ifstream& in, string filename){
in >> maxLevel; m->gobble(in);
for (int i = 0; i < tree.size(); i++) {
- in >> tree[i].name >> tree[i].level >> tree[i].parent; m->gobble(in);
+ tree[i].name = m->getline(in); m->gobble(in);
+ in >> tree[i].level >> tree[i].parent; m->gobble(in);
}
//read genus nodes
@@ -232,7 +233,7 @@ int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
//save maxLevel for binning the unclassified seqs
if (level > maxLevel) { maxLevel = level; }
- return 0;
+ return level;
}
catch(exception& e) {
m->errorOut(e, "PhyloTree", "addSeqToTree");
@@ -454,11 +455,12 @@ void PhyloTree::print(ofstream& out, vector<TaxNode>& copy){
for (int i = 0; i < copy.size(); i++) {
- out << copy[i].level << '\t'<< copy[i].name << '\t' << copy[i].children.size();
+ out << copy[i].level << '\t' << copy[i].children.size() << endl;
+ out << copy[i].name << endl;
map<string,int>::iterator it;
for(it=copy[i].children.begin();it!=copy[i].children.end();it++){
- out << '\t' << it->first << '\t' << it->second;
+ out << it->second << '\t' << it->first << endl;
}
out << endl;
}
@@ -485,7 +487,8 @@ void PhyloTree::printTreeNodes(string treefilename) {
outTree << maxLevel << endl;
for (int i = 0; i < tree.size(); i++) {
- outTree << tree[i].name << '\t' << tree[i].level << '\t' << tree[i].parent << endl;
+ outTree << tree[i].name << endl;
+ outTree << tree[i].level << '\t' << tree[i].parent << endl;
}
//print genus nodes
diff --git a/source/classifier/phylotree.h b/source/classifier/phylotree.h
index 4b7a35a..a602359 100644
--- a/source/classifier/phylotree.h
+++ b/source/classifier/phylotree.h
@@ -28,6 +28,11 @@ struct TaxNode {
/**************************************************************************************************/
class PhyloTree {
+
+#ifdef UNIT_TEST
+ friend class TestPhyloTree;
+#endif
+
public:
PhyloTree();
diff --git a/source/classifier/taxonomyequalizer.cpp b/source/classifier/taxonomyequalizer.cpp
index c050726..dd7f937 100644
--- a/source/classifier/taxonomyequalizer.cpp
+++ b/source/classifier/taxonomyequalizer.cpp
@@ -44,7 +44,8 @@ TaxEqualizer::TaxEqualizer(string tfile, int c, string o) : cutoff(c), outputDir
if (m->control_pressed) { break; }
- in >> name >> tax; m->gobble(in);
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
if (containsConfidence) { m->removeConfidences(tax); }
@@ -78,7 +79,8 @@ int TaxEqualizer::getHighestLevel(ifstream& in) {
string name, tax;
while (in) {
- in >> name >> tax; m->gobble(in);
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
//count levels in this taxonomy
int thisLevel = 0;
@@ -96,10 +98,17 @@ int TaxEqualizer::getHighestLevel(ifstream& in) {
}
}
- int pos = testTax.find_first_of('(');
-
- //if there are '(' then there are confidences we need to take out
- if (pos != -1) { containsConfidence = true; }
+ int openParen = testTax.find_last_of('(');
+ int closeParen = testTax.find_last_of(')');
+
+ if ((openParen != string::npos) && (closeParen != string::npos)) {
+ string confidenceScore = testTax.substr(openParen+1, (closeParen-(openParen+1)));
+ if (m->isNumeric1(confidenceScore)) { //its a confidence
+ containsConfidence = true;
+ }else { //its part of the taxon
+ containsConfidence = false;
+ }
+ }
return level;
@@ -114,18 +123,20 @@ void TaxEqualizer::extendTaxonomy(string name, string& tax, int desiredLevel) {
try {
//get last taxon
- tax = tax.substr(0, tax.length()-1); //take off final ";"
- int pos = tax.find_last_of(';');
- string lastTaxon = tax.substr(pos+1);
- lastTaxon += ";"; //add back on delimiting char
- tax += ";";
+ //tax = tax.substr(0, tax.length()-1); //take off final ";"
+ //int pos = tax.find_last_of(';');
+ //string lastTaxon = tax.substr(pos+1);
+ //lastTaxon += ";"; //add back on delimiting char
+ //tax += ";";
- int currentLevel = seqLevels[name];
+ //int currentLevel = seqLevels[name];
+
+ tax = m->addUnclassifieds(tax, desiredLevel, containsConfidence);
//added last taxon until you get desired level
- for (int i = currentLevel; i < desiredLevel; i++) {
- tax += lastTaxon;
- }
+ //for (int i = currentLevel; i < desiredLevel; i++) {
+ //tax += lastTaxon;
+ //}
}
catch(exception& e) {
m->errorOut(e, "TaxEqualizer", "extendTaxonomy");
diff --git a/source/cluster.cpp b/source/cluster.cpp
index 6b69e4d..77bc470 100644
--- a/source/cluster.cpp
+++ b/source/cluster.cpp
@@ -57,7 +57,7 @@ void Cluster::clusterNames(){
}
}
/***********************************************************************/
-void Cluster::update(double& cutOFF){
+bool Cluster::update(double& cutOFF){
try {
smallCol = dMatrix->getSmallestCell(smallRow);
nColCells = dMatrix->seqVec[smallCol].size();
@@ -136,7 +136,7 @@ void Cluster::update(double& cutOFF){
dMatrix->rmCell(smallCol, i);
}
}
-
+ return changed;
}
catch(exception& e) {
m->errorOut(e, "Cluster", "update");
diff --git a/source/cluster.hpp b/source/cluster.hpp
index 846c6f4..0e45688 100644
--- a/source/cluster.hpp
+++ b/source/cluster.hpp
@@ -1,23 +1,21 @@
#ifndef CLUSTER_H
#define CLUSTER_H
-//test change
-
-#include "mothur.h"
#include "sparsedistancematrix.h"
+#include "optimatrix.h"
#include "mothurout.h"
#include "rabundvector.hpp"
#include "listvector.hpp"
-//class RAbundVector;
-//class ListVector;
+class ListVector;
class Cluster {
public:
Cluster(RAbundVector*, ListVector*, SparseDistanceMatrix*, float, string, float);
+ Cluster(){}
virtual ~Cluster() {}
- virtual void update(double&);
+ virtual bool update(double&);
virtual string getTag() = 0;
virtual void setMapWanted(bool m);
virtual map<string, int> getSeqtoBin() { return seq2Bin; }
diff --git a/source/commandfactory.cpp b/source/commandfactory.cpp
index 259ad5c..98a93f9 100644
--- a/source/commandfactory.cpp
+++ b/source/commandfactory.cpp
@@ -556,7 +556,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString){
else if(commandName == "make.contigs") { command = new MakeContigsCommand(optionString); }
else if(commandName == "sff.multiple") { command = new SffMultipleCommand(optionString); }
else if(commandName == "classify.svm") { command = new ClassifySvmSharedCommand(optionString); }
- else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(optionString); }
+ //else if(commandName == "classify.rf") { command = new ClassifyRFSharedCommand(optionString); }
else if(commandName == "filter.shared") { command = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { command = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { command = new GetDistsCommand(optionString); }
@@ -729,7 +729,7 @@ Command* CommandFactory::getCommand(string commandName, string optionString, str
else if(commandName == "get.coremicrobiome") { pipecommand = new GetCoreMicroBiomeCommand(optionString); }
else if(commandName == "make.contigs") { pipecommand = new MakeContigsCommand(optionString); }
else if(commandName == "sff.multiple") { pipecommand = new SffMultipleCommand(optionString); }
- else if(commandName == "classify.rf") { pipecommand = new ClassifyRFSharedCommand(optionString); }
+ //else if(commandName == "classify.rf") { pipecommand = new ClassifyRFSharedCommand(optionString); }
else if(commandName == "filter.shared") { pipecommand = new FilterSharedCommand(optionString); }
else if(commandName == "primer.design") { pipecommand = new PrimerDesignCommand(optionString); }
else if(commandName == "get.dists") { pipecommand = new GetDistsCommand(optionString); }
@@ -889,7 +889,7 @@ Command* CommandFactory::getCommand(string commandName){
else if(commandName == "get.coremicrobiome") { shellcommand = new GetCoreMicroBiomeCommand(); }
else if(commandName == "make.contigs") { shellcommand = new MakeContigsCommand(); }
else if(commandName == "sff.multiple") { shellcommand = new SffMultipleCommand(); }
- else if(commandName == "classify.rf") { shellcommand = new ClassifyRFSharedCommand(); }
+ //else if(commandName == "classify.rf") { shellcommand = new ClassifyRFSharedCommand(); }
else if(commandName == "filter.shared") { shellcommand = new FilterSharedCommand(); }
else if(commandName == "primer.design") { shellcommand = new PrimerDesignCommand(); }
else if(commandName == "get.dists") { shellcommand = new GetDistsCommand(); }
diff --git a/source/commands/aligncommand.cpp b/source/commands/aligncommand.cpp
index 33190ec..6e4f6dd 100644
--- a/source/commands/aligncommand.cpp
+++ b/source/commands/aligncommand.cpp
@@ -295,7 +295,7 @@ int AlignCommand::execute(){
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
- templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand());
+ templateDB = new AlignmentDB(templateFileName, search, kmerSize, gapOpen, gapExtend, match, misMatch, rand(), true);
for (int s = 0; s < candidateFileNames.size(); s++) {
if (m->control_pressed) { outputTypes.clear(); return 0; }
diff --git a/source/commands/aligncommand.h b/source/commands/aligncommand.h
index 7afe6c0..01c40ce 100644
--- a/source/commands/aligncommand.h
+++ b/source/commands/aligncommand.h
@@ -135,7 +135,7 @@ static DWORD WINAPI MyAlignThreadFunction(LPVOID lpParam){
inFASTA.seekg(pDataArray->start-1); pDataArray->m->gobble(inFASTA);
}
- AlignmentDB* templateDB = new AlignmentDB(pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID);
+ AlignmentDB* templateDB = new AlignmentDB(pDataArray->templateFileName, pDataArray->search, pDataArray->kmerSize, pDataArray->gapOpen, pDataArray->gapExtend, pDataArray->match, pDataArray->misMatch, pDataArray->threadID, false);
//moved this into driver to avoid deep copies in windows paralellized version
Alignment* alignment;
diff --git a/source/commands/biominfocommand.cpp b/source/commands/biominfocommand.cpp
index c7fbe05..5593349 100644
--- a/source/commands/biominfocommand.cpp
+++ b/source/commands/biominfocommand.cpp
@@ -192,6 +192,12 @@ int BiomInfoCommand::execute(){
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
}
+ //set constaxonomy file as new current constaxonomyfile
+ itTypes = outputTypes.find("constaxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setConsTaxonomyFile(current); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
diff --git a/source/commands/catchallcommand.cpp b/source/commands/catchallcommand.cpp
index 74f02e1..4d65bd6 100644
--- a/source/commands/catchallcommand.cpp
+++ b/source/commands/catchallcommand.cpp
@@ -200,8 +200,8 @@ int CatchAllCommand::execute() {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//get location of catchall
- path = m->argv;
- path = path.substr(0, (path.find_last_of("othur")-5));
+ path = m->mothurProgramPath;
+ //path = path.substr(0, (path.find_last_of("othur")-5));
path = m->getFullPathName(path);
if (m->debug) { m->mothurOut("[DEBUG]: mothur's path = " + path + "\n"); }
diff --git a/source/commands/chimeraperseuscommand.cpp b/source/commands/chimeraperseuscommand.cpp
index fd62542..892d39d 100644
--- a/source/commands/chimeraperseuscommand.cpp
+++ b/source/commands/chimeraperseuscommand.cpp
@@ -520,7 +520,8 @@ int ChimeraPerseusCommand::execute(){
ct->readTable(nameFile, true, false);
if (ct->hasGroupInfo()) {
- cparser = new SequenceCountParser(fastaFileNames[s], *ct);
+ vector<string> temp;
+ cparser = new SequenceCountParser(fastaFileNames[s], *ct, temp);
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(nameFile));
newCountFile = getOutputFileName("count", variables);
@@ -599,7 +600,8 @@ int ChimeraPerseusCommand::execute(){
}else {
if (groupFile != "") {
//Parse sequences by group
- parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
+ vector<string> temp;
+ parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile, temp);
vector<string> groups = parser->getNamesOfGroups();
if (m->control_pressed) { delete parser; for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
diff --git a/source/commands/chimeraperseuscommand.h b/source/commands/chimeraperseuscommand.h
index 9458b8b..e39d121 100644
--- a/source/commands/chimeraperseuscommand.h
+++ b/source/commands/chimeraperseuscommand.h
@@ -122,14 +122,15 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
//parse fasta and name file by group
SequenceParser* parser;
SequenceCountParser* cparser;
+ vector<string> temp;
if (pDataArray->hasCount) {
CountTable* ct = new CountTable();
ct->readTable(pDataArray->namefile, true, false);
- cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
+ cparser = new SequenceCountParser(pDataArray->fastafile, *ct, temp);
delete ct;
}else {
- if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile); }
- else { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile); }
+ if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile, temp); }
+ else { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, temp); }
}
int totalSeqs = 0;
@@ -397,7 +398,7 @@ static DWORD WINAPI MyPerseusThreadFunction(LPVOID lpParam){
}
catch(exception& e) {
- pDataArray->m->errorOut(e, "ChimeraUchimeCommand", "MyPerseusThreadFunction");
+ pDataArray->m->errorOut(e, "ChimeraPersuesCommand", "MyPerseusThreadFunction");
exit(1);
}
}
diff --git a/source/commands/chimeraslayercommand.cpp b/source/commands/chimeraslayercommand.cpp
index 66ec4f9..99358db 100644
--- a/source/commands/chimeraslayercommand.cpp
+++ b/source/commands/chimeraslayercommand.cpp
@@ -1042,7 +1042,8 @@ int ChimeraSlayerCommand::setUpForSelfReference(SequenceParser*& parser, map<str
fileGroup[fastaFileNames[s]] = "noGroup";
}else {
//Parse sequences by group
- parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
+ vector<string> temp;
+ parser = new SequenceParser(groupFile, fastaFileNames[s], nameFile, temp);
vector<string> groups = parser->getNamesOfGroups();
for (int i = 0; i < groups.size(); i++) {
@@ -1088,7 +1089,8 @@ int ChimeraSlayerCommand::setUpForSelfReference(SequenceCountParser*& parser, ma
fileGroup[fastaFileNames[s]] = "noGroup";
}else {
//Parse sequences by group
- parser = new SequenceCountParser(nameFile, fastaFileNames[s]);
+ vector<string> temp;
+ parser = new SequenceCountParser(nameFile, fastaFileNames[s], temp);
vector<string> groups = parser->getNamesOfGroups();
for (int i = 0; i < groups.size(); i++) {
diff --git a/source/commands/chimerauchimecommand.cpp b/source/commands/chimerauchimecommand.cpp
index 4bb0278..952a3ab 100644
--- a/source/commands/chimerauchimecommand.cpp
+++ b/source/commands/chimerauchimecommand.cpp
@@ -556,10 +556,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) {
if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
//look for uchime exe
- path = m->argv;
- string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
+ path = m->mothurProgramPath;
string uchimeCommand;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
@@ -575,7 +572,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) {
delete newCommand;
}
#else
- uchimeCommand = path + "uchime.exe";
+ uchimeCommand = path + "\\uchime.exe";
#endif
//test to make sure uchime exists
@@ -586,14 +583,15 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) {
m->mothurOut(uchimeCommand + " file does not exist. Checking path... \n");
//check to see if uchime is in the path??
- string uLocation = m->findProgramPath("uchime");
-
+ string uLocation = "";
ifstream in2;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ uLocation = m->findProgramPath("uchime");
ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
#else
- ableToOpen = m->openInputFile((uLocation + ".exe"), in2, "no error"); in2.close();
+ uLocation = m->findProgramPath("uchime.exe");
+ ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
#endif
if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uLocation + " file does not exist. mothur requires the uchime executable."); m->mothurOutEndLine(); abort = true; }
@@ -604,7 +602,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) {
}
}
catch(exception& e) {
- m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand");
+ m->errorOut(e, "ChimeraUchimeCommand", "ChimeraUchimeCommand");
exit(1);
}
}
@@ -689,12 +687,13 @@ int ChimeraUchimeCommand::execute(){
//Parse sequences by group
vector<string> groups;
map<string, string> uniqueNames;
+ vector<string> temp;
if (hasCount) {
- cparser = new SequenceCountParser(nameFile, fastaFileNames[s]);
+ cparser = new SequenceCountParser(nameFile, fastaFileNames[s], temp);
groups = cparser->getNamesOfGroups();
uniqueNames = cparser->getAllSeqsMap();
}else{
- sparser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
+ sparser = new SequenceParser(groupFile, fastaFileNames[s], nameFile, temp);
groups = sparser->getNamesOfGroups();
uniqueNames = sparser->getAllSeqsMap();
}
@@ -1157,11 +1156,12 @@ int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, stri
int start = time(NULL); if (m->control_pressed) { outCountList.close(); m->mothurRemove(countlist); return 0; }
int error;
- if (hasCount) { error = cparser->getSeqs(groups[i], filename, "/ab=", "/", true); if ((error == 1) || m->control_pressed) { return 0; } }
- else { error = sparser->getSeqs(groups[i], filename, "/ab=", "/", true); if ((error == 1) || m->control_pressed) { return 0; } }
-
- int numSeqs = driver((outputFName + groups[i]), filename, (accnos+groups[i]), (alns+ groups[i]), numChimeras);
+ long long numSeqs = 0;
+ if (hasCount) { error = cparser->getSeqs(groups[i], filename, "/ab=", "/", numSeqs, true); if ((error == 1) || m->control_pressed) { return 0; } }
+ else { error = sparser->getSeqs(groups[i], filename, "/ab=", "/", numSeqs, true); if ((error == 1) || m->control_pressed) { return 0; } }
totalSeqs += numSeqs;
+
+ driver((outputFName + groups[i]), filename, (accnos+groups[i]), (alns+ groups[i]), numChimeras);
if (m->control_pressed) { return 0; }
@@ -1659,7 +1659,8 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename
//divide file
int count = 0;
int spot = 0;
-
+ files.resize(processors, "");
+
for (int i = 0; i < processors; i++) {
ofstream temp;
files[i] = filename+toString(i)+".temp";
@@ -1801,7 +1802,6 @@ int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filen
}
}
- m->mothurOut(toString( getpid() ) + " here\n");
//do my part
num = driverGroups(outputFName, filename, accnos, alns, accnos + ".byCount", lines[0].start, lines[0].end, groups);
diff --git a/source/commands/chimerauchimecommand.h b/source/commands/chimerauchimecommand.h
index 032c6c9..1f1bf14 100644
--- a/source/commands/chimerauchimecommand.h
+++ b/source/commands/chimerauchimecommand.h
@@ -165,14 +165,15 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
//parse fasta and name file by group
SequenceParser* parser;
SequenceCountParser* cparser;
+ vector<string> temp;
if (pDataArray->hasCount) {
CountTable* ct = new CountTable();
ct->readTable(pDataArray->namefile, true, false);
- cparser = new SequenceCountParser(pDataArray->fastafile, *ct);
+ cparser = new SequenceCountParser(pDataArray->fastafile, *ct, temp);
delete ct;
}else {
- if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile); }
- else { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile); }
+ if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile, temp); }
+ else { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, temp); }
}
int totalSeqs = 0;
@@ -185,15 +186,15 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
for (int i = pDataArray->start; i < pDataArray->end; i++) {
int start = time(NULL); if (pDataArray->m->control_pressed) { if (pDataArray->hasCount) { delete cparser; } { delete parser; } return 0; }
-
int error;
+ long long numSeqs = 0;
if (pDataArray->hasCount) {
- error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", true); if ((error == 1) || pDataArray->m->control_pressed) { delete cparser; return 0; }
+ error = cparser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", numSeqs, true); if ((error == 1) || pDataArray->m->control_pressed) { delete cparser; return 0; }
}else {
- error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", true); if ((error == 1) || pDataArray->m->control_pressed) { delete parser; return 0; }
+ error = parser->getSeqs(pDataArray->groups[i], pDataArray->filename, "/ab=", "/", numSeqs, true); if ((error == 1) || pDataArray->m->control_pressed) { delete parser; return 0; }
}
- //int numSeqs = driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
+ //driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras);
////////////////////////////////////////////////////////////////////////////////////////////////////////////////
//to allow for spaces in the path
@@ -519,7 +520,8 @@ static DWORD WINAPI MyUchimeThreadFunction(LPVOID lpParam){
if (pDataArray->hasCount && pDataArray->dups) { outCountList.close(); }
pDataArray->count = totalSeqs;
- if (pDataArray->hasCount) { delete cparser; } { delete parser; }
+ if (pDataArray->hasCount) { delete cparser; }
+ else { delete parser; }
return totalSeqs;
}
diff --git a/source/commands/chimeravsearchcommand.cpp b/source/commands/chimeravsearchcommand.cpp
index 9d93523..7dd40c4 100644
--- a/source/commands/chimeravsearchcommand.cpp
+++ b/source/commands/chimeravsearchcommand.cpp
@@ -510,16 +510,12 @@ ChimeraVsearchCommand::ChimeraVsearchCommand(string option) {
if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
//look for uchime exe
- path = m->argv;
- string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
-
+ path = m->mothurProgramPath;
string vsearchCommand;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vsearchCommand = path + "vsearch"; // format the database, -o option gives us the ability
if (m->debug) {
- m->mothurOut("[DEBUG]: Uchime location using \"which vsearch\" = ");
+ m->mothurOut("[DEBUG]: vsearch location using \"which vsearch\" = ");
Command* newCommand = new SystemCommand("which vsearch"); m->mothurOutEndLine();
newCommand->execute();
delete newCommand;
@@ -529,10 +525,9 @@ ChimeraVsearchCommand::ChimeraVsearchCommand(string option) {
delete newCommand;
}
#else
- m->mothurOut("[ERROR]: The chimera.vsearch command is not available for windows. The vsearch program is not supported on the Windows platform, aborting."); m->mothurOutEndLine(); abort=true;
+ vsearchCommand = path + "\\vsearch.exe";
#endif
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//test to make sure uchime exists
ifstream in;
vsearchCommand = m->getFullPathName(vsearchCommand);
@@ -541,20 +536,23 @@ ChimeraVsearchCommand::ChimeraVsearchCommand(string option) {
m->mothurOut(vsearchCommand + " file does not exist. Checking path... \n");
//check to see if uchime is in the path??
- string vLocation = m->findProgramPath("vsearch");
-
-
ifstream in2;
- ableToOpen = m->openInputFile(vLocation, in2, "no error"); in2.close();
-
-
+ string uLocation = "";
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ uLocation = m->findProgramPath("vsearch");
+ ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
+#else
+ uLocation = m->findProgramPath("vsearch.exe");
+ ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
+#endif
- if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + vLocation + " file does not exist. mothur requires the vsearch executable."); m->mothurOutEndLine(); abort = true; }
- else { m->mothurOut("Found vsearch in your path, using " + vLocation + "\n");vsearchLocation = vLocation; }
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uLocation + " file does not exist. mothur requires the vsearch executable."); m->mothurOutEndLine(); abort = true; }
+ else { m->mothurOut("Found vsearch in your path, using " + uLocation + "\n");vsearchLocation = uLocation; }
}else { vsearchLocation = vsearchCommand; }
vsearchLocation = m->getFullPathName(vsearchLocation);
- #endif
+
+ if (m->debug) { m->mothurOut("[DEBUG]: vsearch location using " + vsearchLocation + "\n"); }
}
}
catch(exception& e) {
@@ -598,6 +596,7 @@ int ChimeraVsearchCommand::execute(){
newCountFile = getOutputFileName("count", variables);
}
+ //setup fasta file if denovo and no groups
if ((templatefile == "self") && (!hasGroup)) { //you want to run uchime with a template=self and no groups
if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
@@ -612,20 +611,14 @@ int ChimeraVsearchCommand::execute(){
vector<seqPriorityNode> nameMapCount;
int error;
if (hasCount) {
- CountTable ct;
- ct.readTable(nameFile, true, false);
+ CountTable ct; ct.readTable(nameFile, true, false);
for(map<string, string>::iterator it = seqs.begin(); it != seqs.end(); it++) {
int num = ct.getNumSeqs(it->first);
if (num == 0) { error = 1; }
- else {
- seqPriorityNode temp(num, it->second, it->first);
- nameMapCount.push_back(temp);
- }
+ else { seqPriorityNode temp(num, it->second, it->first); nameMapCount.push_back(temp); }
}
- }else {
- error = m->readNames(nameFile, nameMapCount, seqs); if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
+ }else { error = m->readNames(nameFile, nameMapCount, seqs); if (m->control_pressed || (error == 1)) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); }return 0; }
}
- if (error == 1) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
m->printVsearchFile(nameMapCount, newFasta, ";size=", ";");
@@ -642,12 +635,13 @@ int ChimeraVsearchCommand::execute(){
//Parse sequences by group
vector<string> groups;
map<string, string> uniqueNames;
+ vector<string> temp;
if (hasCount) {
- cparser = new SequenceCountParser(nameFile, fastaFileNames[s]);
+ cparser = new SequenceCountParser(nameFile, fastaFileNames[s], temp);
groups = cparser->getNamesOfGroups();
uniqueNames = cparser->getAllSeqsMap();
}else{
- sparser = new SequenceParser(groupFile, fastaFileNames[s], nameFile);
+ sparser = new SequenceParser(groupFile, fastaFileNames[s], nameFile, temp);
groups = sparser->getNamesOfGroups();
uniqueNames = sparser->getAllSeqsMap();
}
@@ -660,30 +654,27 @@ int ChimeraVsearchCommand::execute(){
m->openOutputFile(accnosFileName, out1); out1.close();
if (chimealns) { m->openOutputFile(alnsFileName, out2); out2.close(); }
- if(processors == 1) { driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
-
- if (hasCount && dups) {
- CountTable c; c.readTable(nameFile, true, false);
- if (!m->isBlank(newCountFile)) {
- ifstream in2;
- m->openInputFile(newCountFile, in2);
-
- string name, group;
- while (!in2.eof()) {
- in2 >> name >> group; m->gobble(in2);
- c.setAbund(name, group, 0);
- }
- in2.close();
+ //paralellized in vsearch
+ driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, 0, groups.size(), groups);
+ if (hasCount && dups) {
+ CountTable c; c.readTable(nameFile, true, false);
+ if (!m->isBlank(newCountFile)) {
+ ifstream in2;
+ m->openInputFile(newCountFile, in2);
+
+ string name, group;
+ while (!in2.eof()) {
+ in2 >> name >> group; m->gobble(in2);
+ c.setAbund(name, group, 0);
}
- m->mothurRemove(newCountFile);
- c.printTable(newCountFile);
+ in2.close();
}
-
- }else{ createProcessesGroups(outputFileName, newFasta, accnosFileName, alnsFileName, newCountFile, groups, nameFile, groupFile, fastaFileNames[s]); }
+ m->mothurRemove(newCountFile);
+ c.printTable(newCountFile);
+ }
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
-
if (!dups) {
int totalChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName, alnsFileName);
@@ -723,8 +714,8 @@ int ChimeraVsearchCommand::execute(){
int numChimeras = 0;
- if(processors == 1){ driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
- else{ createProcesses(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras); }
+ //paralellized in vsearch
+ driver(outputFileName, fastaFileNames[s], accnosFileName, alnsFileName, numChimeras);
//add headings
ofstream out;
@@ -1127,15 +1118,16 @@ int ChimeraVsearchCommand::driverGroups(string outputFName, string filename, str
int start = time(NULL); if (m->control_pressed) { outCountList.close(); m->mothurRemove(countlist); return 0; }
int error;
- if (hasCount) { error = cparser->getSeqs(groups[i], filename, ";size=", ";", true); if ((error == 1) || m->control_pressed) { return 0; } }
- else { error = sparser->getSeqs(groups[i], filename, ";size=", ";", true); if ((error == 1) || m->control_pressed) { return 0; } }
+ long long thisGroupsSeqs = 0;
+ if (hasCount) { error = cparser->getSeqs(groups[i], filename, ";size=", ";", thisGroupsSeqs, true); if ((error == 1) || m->control_pressed) { return 0; } }
+ else { error = sparser->getSeqs(groups[i], filename, ";size=", ";", thisGroupsSeqs, true); if ((error == 1) || m->control_pressed) { return 0; } }
- int numSeqs = driver((outputFName + groups[i]), filename, (accnos+groups[i]), (alns+ groups[i]), numChimeras);
- totalSeqs += numSeqs;
+ totalSeqs += thisGroupsSeqs;
+ driver((outputFName + groups[i]), filename, (accnos+groups[i]), (alns+ groups[i]), numChimeras);
if (m->control_pressed) { return 0; }
- //remove file made for uchime
+ //remove file made for vsearch
if (!m->debug) { m->mothurRemove(filename); }
else { m->mothurOut("[DEBUG]: saving file: " + filename + ".\n"); }
@@ -1179,7 +1171,7 @@ int ChimeraVsearchCommand::driverGroups(string outputFName, string filename, str
m->appendFiles((accnos+groups[i]), accnos); m->mothurRemove((accnos+groups[i]));
if (chimealns) { m->appendFiles((alns+groups[i]), alns); m->mothurRemove((alns+groups[i])); }
- m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + groups[i] + "."); m->mothurOutEndLine();
+ m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(thisGroupsSeqs) + " sequences from group " + groups[i] + "."); m->mothurOutEndLine();
}
if (hasCount && dups) { outCountList.close(); }
@@ -1213,11 +1205,11 @@ int ChimeraVsearchCommand::driver(string outputFName, string filename, string ac
string vsearchCommand = vsearchLocation;
vsearchCommand = "\"" + vsearchCommand + "\" ";
- char* tempUchime;
- tempUchime= new char[vsearchCommand.length()+1];
- *tempUchime = '\0';
- strncat(tempUchime, vsearchCommand.c_str(), vsearchCommand.length());
- cPara.push_back(tempUchime);
+ char* tempVsearch;
+ tempVsearch= new char[vsearchCommand.length()+1];
+ *tempVsearch = '\0';
+ strncat(tempVsearch, vsearchCommand.c_str(), vsearchCommand.length());
+ cPara.push_back(tempVsearch);
//are you using a reference file
if (templatefile != "self") {
@@ -1243,7 +1235,7 @@ int ChimeraVsearchCommand::driver(string outputFName, string filename, string ac
cPara.push_back(temp);
}else { //denovo
- char* tempIn = new char[8];
+ char* tempIn = new char[16];
*tempIn = '\0'; strncat(tempIn, "--uchime_denovo", 15);
cPara.push_back(tempIn);
char* temp = new char[filename.length()+1];
@@ -1319,8 +1311,8 @@ int ChimeraVsearchCommand::driver(string outputFName, string filename, string ac
char* tempmindiv = new char[9];
*tempmindiv = '\0'; strncat(tempmindiv, "--mindiffs", 10);
cPara.push_back(tempmindiv);
- char* tempMindiv = new char[mindiv.length()+1];
- *tempMindiv = '\0'; strncat(tempMindiv, mindiv.c_str(), mindiv.length());
+ char* tempMindiv = new char[mindiffs.length()+1];
+ *tempMindiv = '\0'; strncat(tempMindiv, mindiffs.c_str(), mindiffs.length());
cPara.push_back(tempMindiv);
}
@@ -1347,8 +1339,12 @@ int ChimeraVsearchCommand::driver(string outputFName, string filename, string ac
}
//--threads=1
- char* threads = new char[12]; threads[0] = '\0'; strncat(threads, "--threads=1", 11);
+ char* threads = new char[10]; threads[0] = '\0'; strncat(threads, "--threads", 9);
cPara.push_back(threads);
+ string numProcessors = toString(processors);
+ char* tempThreads = new char[numProcessors.length()+1];
+ *tempThreads = '\0'; strncat(tempThreads, numProcessors.c_str(), numProcessors.length());
+ cPara.push_back(tempThreads);
char** vsearchParameters;
vsearchParameters = new char*[cPara.size()];
@@ -1356,6 +1352,11 @@ int ChimeraVsearchCommand::driver(string outputFName, string filename, string ac
for (int i = 0; i < cPara.size(); i++) { vsearchParameters[i] = cPara[i]; commandString += toString(cPara[i]) + " "; }
//int numArgs = cPara.size();
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+#else
+ commandString = "\"" + commandString + "\"";
+#endif
+
if (m->debug) { m->mothurOut("[DEBUG]: vsearch command = " + commandString + ".\n"); }
//cout << "commandString = " << commandString << endl;
@@ -1438,224 +1439,3 @@ int ChimeraVsearchCommand::prepFile(string filename, string output) {
}
/**************************************************************************************************/
-int ChimeraVsearchCommand::createProcesses(string outputFileName, string filename, string accnos, string alns, int& numChimeras) {
- try {
-
- processIDS.clear();
- int process = 1;
- int num = 0;
- vector<string> files;
-
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- //break up file into multiple files
- m->divideFile(filename, processors, files);
-
- if (m->control_pressed) { return 0; }
-
- //loop through and create all the processes you want
- while (process != processors) {
- pid_t pid = fork();
-
- if (pid > 0) {
- processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
- process++;
- }else if (pid == 0){
- num = driver(outputFileName + toString(m->mothurGetpid(process)) + ".temp", files[process], accnos + toString(m->mothurGetpid(process)) + ".temp", alns + toString(m->mothurGetpid(process)) + ".temp", numChimeras);
-
- //pass numSeqs to parent
- ofstream out;
- string tempFile = outputFileName + toString(m->mothurGetpid(process)) + ".num.temp";
- m->openOutputFile(tempFile, out);
- out << num << endl;
- out << numChimeras << endl;
- out.close();
-
- exit(0);
- }else {
- m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
- for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
- exit(0);
- }
- }
-
- //do my part
- num = driver(outputFileName, files[0], accnos, alns, numChimeras);
-
- //force parent to wait until all the processes are done
- for (int i=0;i<processIDS.size();i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- for (int i = 0; i < processIDS.size(); i++) {
- ifstream in;
- string tempFile = outputFileName + toString(processIDS[i]) + ".num.temp";
- m->openInputFile(tempFile, in);
- if (!in.eof()) {
- int tempNum = 0;
- in >> tempNum; m->gobble(in);
- num += tempNum;
- in >> tempNum;
- numChimeras += tempNum;
- }
- in.close(); m->mothurRemove(tempFile);
- }
-#endif
- //append output files
- for(int i=0;i<processIDS.size();i++){
- m->appendFiles((outputFileName + toString(processIDS[i]) + ".temp"), outputFileName);
- m->mothurRemove((outputFileName + toString(processIDS[i]) + ".temp"));
-
- m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
- m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
-
- if (chimealns) {
- m->appendFiles((alns + toString(processIDS[i]) + ".temp"), alns);
- m->mothurRemove((alns + toString(processIDS[i]) + ".temp"));
- }
- }
-
- //get rid of the file pieces.
- for (int i = 0; i < files.size(); i++) { m->mothurRemove(files[i]); }
-
- return num;
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraVsearchCommand", "createProcesses");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
-int ChimeraVsearchCommand::createProcessesGroups(string outputFName, string filename, string accnos, string alns, string newCountFile, vector<string> groups, string nameFile, string groupFile, string fastaFile) {
- try {
-
- processIDS.clear();
- int process = 1;
- int num = 0;
-
- CountTable newCount;
- if (hasCount && dups) { newCount.readTable(nameFile, true, false); }
-
- //sanity check
- if (groups.size() < processors) { processors = groups.size(); }
-
- //divide the groups between the processors
- vector<linePair> lines;
- int remainingPairs = groups.size();
- int startIndex = 0;
- for (int remainingProcessors = processors; remainingProcessors > 0; remainingProcessors--) {
- int numPairs = remainingPairs; //case for last processor
- if (remainingProcessors != 1) { numPairs = ceil(remainingPairs / remainingProcessors); }
- lines.push_back(linePair(startIndex, (startIndex+numPairs))); //startIndex, endIndex
- startIndex = startIndex + numPairs;
- remainingPairs = remainingPairs - numPairs;
- }
-
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-
- //loop through and create all the processes you want
- while (process != processors) {
- pid_t pid = fork();
-
- if (pid > 0) {
- processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later
- process++;
- }else if (pid == 0){
- num = driverGroups(outputFName + toString(m->mothurGetpid(process)) + ".temp", filename + toString(m->mothurGetpid(process)) + ".temp", accnos + toString(m->mothurGetpid(process)) + ".temp", alns + toString(m->mothurGetpid(process)) + ".temp", accnos + ".byCount." + toString(m->mothurGetpid(process)) + ".temp", lines[process].start, lines[process].end, groups);
-
- //pass numSeqs to parent
- ofstream out;
- string tempFile = outputFName + toString(m->mothurGetpid(process)) + ".num.temp";
- m->openOutputFile(tempFile, out);
- out << num << endl;
- out.close();
-
- exit(0);
- }else {
- m->mothurOut("[ERROR]: unable to spawn the necessary processes."); m->mothurOutEndLine();
- for (int i = 0; i < processIDS.size(); i++) { kill (processIDS[i], SIGINT); }
- exit(0);
- }
-
- }
- m->mothurOut(toString( getpid() ) + " here\n");
-
- //do my part
- num = driverGroups(outputFName, filename, accnos, alns, accnos + ".byCount", lines[0].start, lines[0].end, groups);
-
- //force parent to wait until all the processes are done
- for (int i=0;i<processIDS.size();i++) {
- int temp = processIDS[i];
- wait(&temp);
- }
-
- for (int i = 0; i < processIDS.size(); i++) {
- ifstream in;
- string tempFile = outputFName + toString(processIDS[i]) + ".num.temp";
- m->openInputFile(tempFile, in);
- if (!in.eof()) { int tempNum = 0; in >> tempNum; num += tempNum; }
- in.close(); m->mothurRemove(tempFile);
- }
-
-#endif
-
- //read my own
- if (hasCount && dups) {
- if (!m->isBlank(accnos + ".byCount")) {
- ifstream in2;
- m->openInputFile(accnos + ".byCount", in2);
-
- string name, group;
- while (!in2.eof()) {
- in2 >> name >> group; m->gobble(in2);
- newCount.setAbund(name, group, 0);
- }
- in2.close();
- }
- m->mothurRemove(accnos + ".byCount");
- }
-
- //append output files
- for(int i=0;i<processIDS.size();i++){
- m->appendFiles((outputFName + toString(processIDS[i]) + ".temp"), outputFName);
- m->mothurRemove((outputFName + toString(processIDS[i]) + ".temp"));
-
- m->appendFiles((accnos + toString(processIDS[i]) + ".temp"), accnos);
- m->mothurRemove((accnos + toString(processIDS[i]) + ".temp"));
-
- if (chimealns) {
- m->appendFiles((alns + toString(processIDS[i]) + ".temp"), alns);
- m->mothurRemove((alns + toString(processIDS[i]) + ".temp"));
- }
-
- if (hasCount && dups) {
- if (!m->isBlank(accnos + ".byCount." + toString(processIDS[i]) + ".temp")) {
- ifstream in2;
- m->openInputFile(accnos + ".byCount." + toString(processIDS[i]) + ".temp", in2);
-
- string name, group;
- while (!in2.eof()) {
- in2 >> name >> group; m->gobble(in2);
- newCount.setAbund(name, group, 0);
- }
- in2.close();
- }
- m->mothurRemove(accnos + ".byCount." + toString(processIDS[i]) + ".temp");
- }
-
- }
-
- //print new *.pick.count_table
- if (hasCount && dups) { newCount.printTable(newCountFile); }
-
- return num;
-
- }
- catch(exception& e) {
- m->errorOut(e, "ChimeraVsearchCommand", "createProcessesGroups");
- exit(1);
- }
-}
-/**************************************************************************************************/
-
diff --git a/source/commands/chimeravsearchcommand.h b/source/commands/chimeravsearchcommand.h
index ae1713f..046499c 100644
--- a/source/commands/chimeravsearchcommand.h
+++ b/source/commands/chimeravsearchcommand.h
@@ -37,7 +37,6 @@ public:
private:
vector<int> processIDS; //processid
int driver(string, string, string, string, int&);
- int createProcesses(string, string, string, string, int&);
bool abort, useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, ucl, useMindiffs, hasCount, hasName, dups;
string fastafile, groupfile, templatefile, outputDir, namefile, countfile, abskew, minh, mindiv, xn, dn, mindiffs, vsearchLocation;
@@ -54,7 +53,6 @@ private:
int readFasta(string, map<string, string>&);
int deconvoluteResults(map<string, string>&, string, string, string);
int driverGroups(string, string, string, string, string, int, int, vector<string>);
- int createProcessesGroups(string, string, string, string, string, vector<string>, string, string, string);
int prepFile(string filename, string);
@@ -63,4 +61,3 @@ private:
/***********************************************************/
#endif
-
diff --git a/source/commands/classifyotucommand.cpp b/source/commands/classifyotucommand.cpp
index 0c8e231..175f0a2 100644
--- a/source/commands/classifyotucommand.cpp
+++ b/source/commands/classifyotucommand.cpp
@@ -388,6 +388,13 @@ int ClassifyOtuCommand::execute(){
if (m->control_pressed) { outputTypes.clear(); for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+ //set constaxonomy file as new current constaxonomyfile
+ string current = "";
+ itTypes = outputTypes.find("constaxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setConsTaxonomyFile(current); }
+ }
+
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
@@ -790,11 +797,11 @@ int ClassifyOtuCommand::processTaxMap() {
if (spot != 0) {
string newTax = "";
for (int i = 0; i < taxons.size(); i++) { newTax += taxons[i] + ";"; }
- for (int i = spot; i < taxLength; i++) {
- if(tax[i] == ';'){ newTax += "unclassified;"; }
+ //for (int i = spot; i < taxLength; i++) {
+ //if(tax[i] == ';'){ newTax += "unclassified;"; }
m->removeConfidences(newTax);
it->second = newTax;
- }
+ //}
}else { m->removeConfidences(tax); it->second = tax; } //leave tax alone
}
return 0;
diff --git a/source/commands/classifyseqscommand.cpp b/source/commands/classifyseqscommand.cpp
index d5b3cb6..5a0025a 100644
--- a/source/commands/classifyseqscommand.cpp
+++ b/source/commands/classifyseqscommand.cpp
@@ -721,7 +721,8 @@ int ClassifySeqsCommand::execute(){
while (!inTax.eof()) {
if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } delete taxaSum; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
- inTax >> name >> taxon; m->gobble(inTax);
+ inTax >> name; m->gobble(inTax);
+ taxon = m->getline(inTax); m->gobble(inTax);
string newTax = m->addUnclassifieds(taxon, maxLevel, probs);
@@ -747,7 +748,7 @@ int ClassifySeqsCommand::execute(){
outTax.close();
m->mothurRemove(newTaxonomyFile);
- rename(unclass.c_str(), newTaxonomyFile.c_str());
+ m->renameFile(unclass, newTaxonomyFile);
if (m->control_pressed) { outputTypes.clear(); if (ct != NULL) { delete ct; } if (groupMap != NULL) { delete groupMap; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } delete classify; return 0; }
@@ -907,7 +908,7 @@ int ClassifySeqsCommand::createProcesses(string taxFileName, string tempTaxFile,
string extension = "";
if (i != 0) { extension = toString(i) + ".temp"; processIDS.push_back(i); }
- classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip, writeShortcuts);
+ classifyData* tempclass = new classifyData((accnos + extension), probs, method, templateFileName, taxonomyFileName, (taxFileName + extension), (tempTaxFile + extension), filename, search, kmerSize, iters, numWanted, m, lines[i]->start, lines[i]->end, match, misMatch, gapOpen, gapExtend, cutoff, i, flip, false);
pDataArray.push_back(tempclass);
//MySeqSumThreadFunction is in header. It must be global or static to work with the threads.
diff --git a/source/commands/clustercommand.cpp b/source/commands/clustercommand.cpp
index 652355d..ab0f39f 100644
--- a/source/commands/clustercommand.cpp
+++ b/source/commands/clustercommand.cpp
@@ -11,10 +11,9 @@
#include "readphylip.h"
#include "readcolumn.h"
#include "readmatrix.hpp"
-#include "clusterdoturcommand.h"
#include "sequence.hpp"
-#include "vsearchfileparser.h"
#include "systemcommand.h"
+#include "sensspeccommand.h"
//**********************************************************************************************************************
vector<string> ClusterCommand::setParameters(){
@@ -24,15 +23,20 @@ vector<string> ClusterCommand::setParameters(){
CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "ColumnName-FastaTaxName","rabund-sabund",false,false,true); parameters.push_back(pname);
CommandParameter pcount("count", "InputTypes", "", "", "NameCount", "none", "","",false,false,true); parameters.push_back(pcount);
CommandParameter pcolumn("column", "InputTypes", "", "", "PhylipColumnFasta", "PhylipColumnFasta", "ColumnName","list",false,false,true); parameters.push_back(pcolumn);
- CommandParameter pcutoff("cutoff", "Number", "", "10", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.03", "", "", "","",false,false,true); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted-agc-dgc", "average", "", "", "","",false,false,true); parameters.push_back(pmethod);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted-agc-dgc-opti", "opti", "", "", "","",false,false,true); parameters.push_back(pmethod);
+ CommandParameter pinitialize("initialize", "Multiple", "oneotu-singleton", "singleton", "", "", "","",false,false,true); parameters.push_back(pinitialize);
+ CommandParameter pmetric("metric", "Multiple", "mcc-sens-spec-tptn-fpfn-tp-tn-fp-fn-f1score-accuracy-ppv-npv-fdr", "mcc", "", "", "","",false,false,true); parameters.push_back(pmetric);
+ CommandParameter pmetriccutoff("delta", "Number", "", "0.0001", "", "", "","",false,false,true); parameters.push_back(pmetriccutoff);
+ CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,false,true); parameters.push_back(piters);
CommandParameter pshowabund("showabund", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pshowabund);
CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
CommandParameter psim("sim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(psim);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
//CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust);
+ CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> myArray;
@@ -48,14 +52,19 @@ vector<string> ClusterCommand::setParameters(){
string ClusterCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The cluster command parameter options are phylip, column, name, count, method, cutoff, precision, sim, showabund and timing. Fasta or Phylip or column and name are required.\n";
+ helpString += "The cluster command parameter options are phylip, column, name, count, method, cutoff, precision, sim, showabund, timing, metric, iters, initialize. Fasta or Phylip or column and name are required.\n";
//helpString += "The adjust parameter is used to handle missing distances. If you set a cutoff, adjust=f by default. If not, adjust=t by default. Adjust=f, means ignore missing distances and adjust cutoff as needed with the average neighbor method. Adjust=t, will treat missing distances as 1.0. You can also set the value the missing distances should be set to, adjust=0.5 would give missing distances a value of 0.5.\n";
helpString += "The phylip and column parameter allow you to enter your distance file. \n";
helpString += "The fasta parameter allows you to enter your fasta file for use with the agc or dgc methods. \n";
helpString += "The name parameter allows you to enter your name file. \n";
helpString += "The count parameter allows you to enter your count file. \n A count or name file is required if your distance file is in column format.\n";
- helpString += "The method parameter allows you to enter your clustering mothod. Options are furthest, nearest, average, weighted, agc and dgc. Default=average. The agc and dgc methods require a fasta file.";
- helpString += "The cluster command should be in the following format: \n";
+ helpString += "The iters parameter allow you to set the maxiters for the opticluster method. \n";
+ helpString += "The metric parameter allows to select the metric in the opticluster method. Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn), false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score), accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). De [...]
+ helpString += "The initialize parameter allows to select the initial randomization for the opticluster method. Options are singleton, meaning each sequence is randomly assigned to its own OTU, or oneotu meaning all sequences are assigned to one otu. Default=singleton.\n";
+ helpString += "The delta parameter allows to set the stable value for the metric in the opticluster method (delta=0.0001). \n";
+ helpString += "The method parameter allows you to enter your clustering mothod. Options are furthest, nearest, average, weighted, agc, dgc and opti. Default=opti. The agc and dgc methods require a fasta file.";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
+ helpString += "The cluster command should be in the following format: \n";
helpString += "cluster(method=yourMethod, cutoff=yourCutoff, precision=yourPrecision) \n";
helpString += "The acceptable cluster methods are furthest, nearest, average and weighted. If no method is provided then average is assumed.\n";
return helpString;
@@ -73,6 +82,8 @@ string ClusterCommand::getOutputPattern(string type) {
if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; }
else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; }
+ else if (type == "sensspec") { pattern = "[filename],[clustertag],sensspec"; }
+ else if (type == "steps") { pattern = "[filename],[clustertag],steps"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
@@ -89,8 +100,10 @@ ClusterCommand::ClusterCommand(){
setParameters();
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
+ outputTypes["sensspec"] = tempOutNames;
outputTypes["rabund"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;
+ outputTypes["steps"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "ClusterCommand", "ClusterCommand");
@@ -126,8 +139,10 @@ ClusterCommand::ClusterCommand(string option) {
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["list"] = tempOutNames;
+ outputTypes["sensspec"] = tempOutNames;
outputTypes["rabund"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;
+ outputTypes["steps"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
@@ -253,30 +268,53 @@ ClusterCommand::ClusterCommand(string option) {
temp = validParameter.validFile(parameters, "sim", false); if (temp == "not found") { temp = "F"; }
sim = m->isTrue(temp);
+ temp = validParameter.validFile(parameters, "delta", false); if (temp == "not found") { temp = "0.0001"; }
+ m->mothurConvert(temp, stableMetric);
+
+ metric = validParameter.validFile(parameters, "metric", false); if (metric == "not found") { metric = "mcc"; }
+
+ if ((metric == "mcc") || (metric == "sens") || (metric == "spec") || (metric == "tptn") || (metric == "tp") || (metric == "tn") || (metric == "fp") || (metric == "fn") || (metric == "f1score") || (metric == "accuracy") || (metric == "ppv") || (metric == "npv") || (metric == "fdr") || (metric == "fpfn") ){ }
+ else { m->mothurOut("[ERROR]: Not a valid metric. Valid metrics are mcc, sens, spec, tp, tn, fp, fn, tptn, fpfn, f1score, accuracy, ppv, npv, fdr."); m->mothurOutEndLine(); abort = true; }
+
+ initialize = validParameter.validFile(parameters, "initialize", false); if (initialize == "not found") { initialize = "singleton"; }
+
+ if ((initialize == "singleton") || (initialize == "oneotu")){ }
+ else { m->mothurOut("[ERROR]: Not a valid initialization. Valid initializations are singleton and oneotu."); m->mothurOutEndLine(); abort = true; }
+
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
+ m->mothurConvert(temp, maxIters);
+
//temp = validParameter.validFile(parameters, "adjust", false); if (temp == "not found") { temp = "F"; }
//if (m->isNumeric1(temp)) { m->mothurConvert(temp, adjust); }
//else if (m->isTrue(temp)) { adjust = 1.0; }
//else { adjust = -1.0; }
adjust=-1.0;
+ bool setProcessors = true;
+ temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ setProcessors=false; temp = m->getProcessors(); }
+ m->setProcessors(temp);
+ m->mothurConvert(temp, processors);
+
method = validParameter.validFile(parameters, "method", false);
- if (method == "not found") { method = "average"; }
+ if (method == "not found") {
+ method = "opti";
+ m->mothurOut("[NOTE]: Default clustering method has changed to opti. To use average neighbor, set method=average."); m->mothurOutEndLine();
+ }
- if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted") || (method == "agc") || (method == "dgc")) { }
- else { m->mothurOut("Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average, weighted, agc and dgc."); m->mothurOutEndLine(); abort = true; }
+ if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted") || (method == "agc") || (method == "dgc") || (method == "opti")) { }
+ else { m->mothurOut("[ERROR]: Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average, weighted, agc, dgc and opti."); m->mothurOutEndLine(); abort = true; }
+
if ((method == "agc") || (method == "dgc")) {
if (fastafile == "") { m->mothurOut("[ERROR]: You must provide a fasta file when using the agc or dgc clustering methods, aborting\n."); abort = true;}
+ }else if (setProcessors) {
+ m->mothurOut("[WARNING]: You can only use the processors option when using the agc or dgc clustering methods. Using 1 processor.\n.");
}
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
-#else
- if ((method == "agc") || (method == "dgc")) { m->mothurOut("[ERROR]: The agc and dgc clustering methods are not available for Windows, aborting\n."); abort = true; }
-#endif
- //bool cutoffSet = false;
+ cutOffSet = false;
temp = validParameter.validFile(parameters, "cutoff", false);
- if (temp == "not found") { temp = "10"; }
- //else { cutoffSet = true; }
+ if (temp == "not found") { temp = "0.03"; }
+ else { cutOffSet = true; }
m->mothurConvert(temp, cutoff);
showabund = validParameter.validFile(parameters, "showabund", false);
@@ -301,7 +339,7 @@ int ClusterCommand::execute(){
if (abort == true) { if (calledHelp) { return 0; } return 2; }
//phylip file given and cutoff not given - use cluster.classic because it uses less memory and is faster
- if ((format == "phylip") && (cutoff > 10.0)) {
+ if ((format == "phylip") && (!cutOffSet) && (method != "opti")) {
m->mothurOutEndLine(); m->mothurOut("You are using a phylip file and no cutoff. I will run cluster.classic to save memory and time."); m->mothurOutEndLine();
//run unique.seqs for deconvolute results
@@ -329,8 +367,9 @@ int ClusterCommand::execute(){
time_t estart = time(NULL);
- if (format == "fasta") { runVsearchCluster(); }
- else { runMothurCluster(); }
+ if (format == "fasta") { runVsearchCluster(); }
+ else if (method == "opti") { runOptiCluster(); }
+ else { runMothurCluster(); }
if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; }
@@ -371,12 +410,8 @@ int ClusterCommand::execute(){
int ClusterCommand::runVsearchCluster(){
try {
- //look for uchime exe
- string path = m->argv;
- string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
-
+ //look for vsearch exe
+ string path = m->mothurProgramPath;
string vsearchCommand;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vsearchCommand = path + "vsearch"; // format the database, -o option gives us the ability
@@ -391,31 +426,33 @@ int ClusterCommand::runVsearchCluster(){
delete newCommand;
}
#else
- vsearchCommand = path + "vsearch.exe";
+ vsearchCommand = path + "\\vsearch.exe";
#endif
- //test to make sure uchime exists
+ //test to make sure vsearch exists
ifstream in;
vsearchCommand = m->getFullPathName(vsearchCommand);
int ableToOpen = m->openInputFile(vsearchCommand, in, "no error"); in.close();
if(ableToOpen == 1) {
m->mothurOut(vsearchCommand + " file does not exist. Checking path... \n");
- //check to see if uchime is in the path??
-
- string uLocation = m->findProgramPath("vsearch");
-
-
+ //check to see if vsearch is in the path??
+
ifstream in2;
+ string uLocation = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ uLocation = m->findProgramPath("vsearch");
ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
#else
- ableToOpen = m->openInputFile((uLocation + ".exe"), in2, "no error"); in2.close();
+ uLocation = m->findProgramPath("vsearch.exe");
+ ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
#endif
- if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uLocation + " file does not exist. mothur requires the vsearch executable."); m->mothurOutEndLine(); abort = true; }
+ if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uLocation + " file does not exist. mothur requires the vsearch executable."); m->mothurOutEndLine(); m->control_pressed = true; }
else { m->mothurOut("Found vsearch in your path, using " + uLocation + "\n");vsearchLocation = uLocation; }
}else { vsearchLocation = vsearchCommand; }
+ if (m->control_pressed) { return 0; }
+
vsearchLocation = m->getFullPathName(vsearchLocation);
string vsearchFastafile = ""; VsearchFileParser* vParse;
@@ -501,6 +538,11 @@ int ClusterCommand::vsearchDriver(string inputFile, string ucClusteredFile, stri
char* maxaccepts = new char[16]; maxaccepts[0] = '\0'; strncat(maxaccepts, "--maxaccepts=16", 15);
vsearchParameters.push_back(maxaccepts);
+ //--threads=1
+ string processorsString = "--threads=" + toString(processors);
+ char* processorsParameter = new char[processorsString.length()+1]; processorsParameter[0] = '\0'; strncat(processorsParameter, processorsString.c_str(), processorsString.length());
+ vsearchParameters.push_back(processorsParameter);
+
//--usersort
char* usersort = new char[11]; usersort[0] = '\0'; strncat(usersort, "--usersort", 10);
vsearchParameters.push_back(usersort);
@@ -792,3 +834,138 @@ int ClusterCommand::createRabund(CountTable*& ct, ListVector*& list, RAbundVecto
}
//**********************************************************************************************************************
+
+int ClusterCommand::runOptiCluster(){
+ try {
+ if (!cutOffSet) { m->mothurOut("\nYou did not set a cutoff, using 0.03.\n"); cutoff = 0.03; }
+
+ string nameOrCount = "";
+ string thisNamefile = "";
+ map<string, int> counts;
+ if (countfile != "") { nameOrCount = "count"; thisNamefile = countfile; CountTable ct; ct.readTable(countfile, false, false); counts = ct.getNameMap(); }
+ else if (namefile != "") { nameOrCount = "name"; thisNamefile = namefile; }
+
+ string distfile = columnfile;
+ if (format == "phylip") { distfile = phylipfile; }
+
+ //int rstart = time(NULL);
+
+ OptiMatrix matrix(distfile, thisNamefile, nameOrCount, format, cutoff, false);
+
+ //m->mothurOut("It took " + toString(time(NULL) - rstart) + " seconds to read and process matrix"); m->mothurOutEndLine();
+
+ OptiCluster cluster(&matrix, metric, 0);
+ tag = cluster.getTag();
+
+ m->mothurOutEndLine(); m->mothurOut("Clustering " + distfile); m->mothurOutEndLine();
+
+ if (outputDir == "") { outputDir += m->hasPath(distfile); }
+ fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
+
+ string listFileName = fileroot+ tag + ".list";
+
+ ofstream listFile;
+ m->openOutputFile(listFileName, listFile);
+ outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
+
+ map<string, string> variables;
+ variables["[filename]"] = fileroot;
+ variables["[clustertag]"] = tag;
+ string outputName = getOutputFileName("steps", variables);
+ outputNames.push_back(outputName); outputTypes["steps"].push_back(outputName);
+ ofstream outStep;
+ m->openOutputFile(outputName, outStep);
+
+ int iters = 0;
+ double listVectorMetric = 0; //worst state
+ double delta = 1;
+
+ cluster.initialize(listVectorMetric, true, initialize);
+
+ long long numBins = cluster.getNumBins();
+ m->mothurOut("\n\niter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n");
+ outStep << "iter\ttime\tlabel\tnum_otus\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n";
+ long long tp, tn, fp, fn;
+ vector<double> results = cluster.getStats(tp, tn, fp, fn);
+ m->mothurOut("0\t0\t" + toString(cutoff) + "\t" + toString(numBins) + "\t"+ toString(cutoff) + "\t" + toString(tp) + "\t" + toString(tn) + "\t" + toString(fp) + "\t" + toString(fn) + "\t");
+ outStep << "0\t0\t" + toString(cutoff) + "\t" + toString(numBins) + "\t" + toString(cutoff) + "\t" << tp << '\t' << tn << '\t' << fp << '\t' << fn << '\t';
+ for (int i = 0; i < results.size(); i++) { m->mothurOut(toString(results[i]) + "\t"); outStep << results[i] << "\t"; }
+ m->mothurOutEndLine();
+ outStep << endl;
+
+ while ((delta > stableMetric) && (iters < maxIters)) {
+
+ int start = time(NULL);
+
+ if (m->control_pressed) { break; }
+ double oldMetric = listVectorMetric;
+
+ cluster.update(listVectorMetric);
+
+ delta = abs(oldMetric - listVectorMetric);
+ iters++;
+
+ results = cluster.getStats(tp, tn, fp, fn);
+ numBins = cluster.getNumBins();
+
+ m->mothurOut(toString(iters) + "\t" + toString(time(NULL) - start) + "\t" + toString(cutoff) + "\t" + toString(numBins) + "\t" + toString(cutoff) + "\t"+ toString(tp) + "\t" + toString(tn) + "\t" + toString(fp) + "\t" + toString(fn) + "\t");
+ outStep << (toString(iters) + "\t" + toString(time(NULL) - start) + "\t" + toString(cutoff) + "\t" + toString(numBins) + "\t" + toString(cutoff) + "\t") << tp << '\t' << tn << '\t' << fp << '\t' << fn << '\t';
+ for (int i = 0; i < results.size(); i++) { m->mothurOut(toString(results[i]) + "\t"); outStep << results[i] << "\t"; }
+ m->mothurOutEndLine();
+ outStep << endl;
+ }
+ m->mothurOutEndLine(); m->mothurOutEndLine();
+
+ ListVector* list = cluster.getList();
+ list->setLabel(toString(cutoff));
+ if (!m->printedListHeaders) { m->listBinLabelsInFile.clear(); list->printHeaders(listFile); }
+ if(countfile != "") { list->print(listFile, counts); }
+ else { list->print(listFile); }
+ listFile.close();
+
+ variables["[filename]"] = fileroot;
+ variables["[clustertag]"] = tag;
+ string sabundFileName = getOutputFileName("sabund", variables);
+ string rabundFileName = getOutputFileName("rabund", variables);
+
+ if (countfile == "") {
+ m->openOutputFile(sabundFileName, sabundFile);
+ m->openOutputFile(rabundFileName, rabundFile);
+ outputNames.push_back(sabundFileName); outputTypes["sabund"].push_back(sabundFileName);
+ outputNames.push_back(rabundFileName); outputTypes["rabund"].push_back(rabundFileName);
+
+ SAbundVector sabund = list->getSAbundVector();
+ sabund.print(sabundFile);
+ sabundFile.close();
+
+ RAbundVector rabund = list->getRAbundVector();
+ rabund.print(rabundFile);
+ rabundFile.close();
+ }
+ delete list;
+
+ string sensspecFilename = fileroot+ tag + ".sensspec";
+ ofstream sensFile;
+ m->openOutputFile(sensspecFilename, sensFile);
+ outputNames.push_back(sensspecFilename); outputTypes["sensspec"].push_back(sensspecFilename);
+
+
+ sensFile << "label\tcutoff\ttp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n";
+
+ results = cluster.getStats(tp, tn, fp, fn);
+
+ sensFile << cutoff << '\t' << cutoff << '\t' << tp << '\t' << tn << '\t' << fp << '\t' << fn << '\t';
+ for (int i = 0; i < results.size(); i++) { sensFile << results[i] << '\t'; }
+ sensFile << '\n';
+ sensFile.close();
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterCommand", "runOptiCluster");
+ exit(1);
+ }
+
+}
+//**********************************************************************************************************************
diff --git a/source/commands/clustercommand.h b/source/commands/clustercommand.h
index d4f0c8c..8a69111 100644
--- a/source/commands/clustercommand.h
+++ b/source/commands/clustercommand.h
@@ -14,8 +14,12 @@
#include "sabundvector.hpp"
#include "listvector.hpp"
#include "cluster.hpp"
-#include "sparsedistancematrix.h"
#include "counttable.h"
+#include "vsearchfileparser.h"
+#include "clusterdoturcommand.h"
+#include "opticluster.h"
+#include "optimatrix.h"
+
/* The cluster() command:
The cluster command outputs a .list , .rabund and .sabund files.
@@ -52,13 +56,13 @@ private:
RAbundVector oldRAbund;
ListVector oldList;
- bool abort, sim;
+ bool abort, sim, cutOffSet;
- string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile, fastafile, inputDir, vsearchLocation;
- double cutoff;
+ string method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, format, distfile, countfile, fastafile, inputDir, vsearchLocation, metric, initialize;
+ double cutoff, stableMetric;
float adjust;
string showabund, timing;
- int precision, length;
+ int precision, length, maxIters, processors;
ofstream sabundFile, rabundFile, listFile;
bool print_start;
@@ -71,6 +75,7 @@ private:
int createRabund(CountTable*&, ListVector*&, RAbundVector*&);
int vsearchDriver(string, string, string);
int runVsearchCluster();
+ int runOptiCluster();
int runMothurCluster();
};
diff --git a/source/commands/clustersplitcommand.cpp b/source/commands/clustersplitcommand.cpp
index dd68d51..9ffea0b 100644
--- a/source/commands/clustersplitcommand.cpp
+++ b/source/commands/clustersplitcommand.cpp
@@ -8,8 +8,8 @@
*/
#include "clustersplitcommand.h"
-#include "vsearchfileparser.h"
#include "systemcommand.h"
+#include "sensspeccommand.h"
//**********************************************************************************************************************
vector<string> ClusterSplitCommand::setParameters(){
@@ -28,9 +28,14 @@ vector<string> ClusterSplitCommand::setParameters(){
CommandParameter pcluster("cluster", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pcluster);
CommandParameter ptiming("timing", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(ptiming);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
- CommandParameter pcutoff("cutoff", "Number", "", "0.25", "", "", "","",false,false,true); parameters.push_back(pcutoff);
- CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
- CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted-agc-dgc", "average", "", "", "","",false,false,true); parameters.push_back(pmethod);
+ CommandParameter pcutoff("cutoff", "Number", "", "0.03", "", "", "","",false,false,true); parameters.push_back(pcutoff);
+ CommandParameter pmetriccutoff("delta", "Number", "", "0.0001", "", "", "","",false,false,true); parameters.push_back(pmetriccutoff);
+ CommandParameter piters("iters", "Number", "", "100", "", "", "","",false,false,true); parameters.push_back(piters);
+ CommandParameter pinitialize("initialize", "Multiple", "oneotu-singleton", "singleton", "", "", "","",false,false,true); parameters.push_back(pinitialize);
+ CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
+ CommandParameter pmethod("method", "Multiple", "furthest-nearest-average-weighted-agc-dgc-opti", "opti", "", "", "","",false,false,true); parameters.push_back(pmethod);
+ CommandParameter pmetric("metric", "Multiple", "mcc-sens-spec-tptn-fpfn-tp-tn-fp-fn-f1score-accuracy-ppv-npv-fdr", "mcc", "", "", "","",false,false,true); parameters.push_back(pmetric);
+ CommandParameter pdist("dist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdist);
CommandParameter pislist("islist", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pislist);
CommandParameter pclassic("classic", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pclassic);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
@@ -50,7 +55,7 @@ vector<string> ClusterSplitCommand::setParameters(){
string ClusterSplitCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The cluster.split command parameter options are file, fasta, phylip, column, name, count, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, large, cluster, processors. Fasta or Phylip or column and name are required.\n";
+ helpString += "The cluster.split command parameter options are file, fasta, phylip, column, name, count, cutoff, precision, method, splitmethod, taxonomy, taxlevel, showabund, timing, large, cluster, iters, delta, initialize, dist, processors. Fasta or Phylip or column and name are required.\n";
helpString += "The cluster.split command can split your files in 3 ways. Splitting by distance file, by classification, or by classification also using a fasta file. \n";
helpString += "For the distance file method, you need only provide your distance file and mothur will split the file into distinct groups. \n";
helpString += "For the classification method, you need to provide your distance file and taxonomy file, and set the splitmethod to classify. \n";
@@ -63,14 +68,20 @@ string ClusterSplitCommand::getHelpString(){
helpString += "The name parameter allows you to enter your name file. \n";
helpString += "The count parameter allows you to enter your count file. \n A count or name file is required if your distance file is in column format";
helpString += "The cluster parameter allows you to indicate whether you want to run the clustering or just split the distance matrix, default=t";
- helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 0.25. \n";
+ helpString += "The dist parameter allows you to indicate whether you want a column formatted distance matrix outputted along with the list file. Default=F.";
+ helpString += "The cutoff parameter allow you to set the distance you want to cluster to, default is 0.03. \n";
helpString += "The precision parameter allows you specify the precision of the precision of the distances outputted, default=100, meaning 2 decimal places. \n";
- helpString += "The method parameter allows you to enter your clustering mothod. Options are furthest, nearest, average, weighted, agc and dgc. Default=average. The agc and dgc methods require a fasta file.";
+ helpString += "The iters parameter allow you to set the maxiters for the opticluster method. \n";
+ helpString += "The metric parameter allows to select the metric in the opticluster method. Options are Matthews correlation coefficient (mcc), sensitivity (sens), specificity (spec), true positives + true negatives (tptn), false positives + false negatives (fpfn), true positives (tp), true negative (tn), false positive (fp), false negative (fn), f1score (f1score), accuracy (accuracy), positive predictive value (ppv), negative predictive value (npv), false discovery rate (fdr). De [...]
+ helpString += "The delta parameter allows to set the stable value for the metric in the opticluster method. Default=0.0001\n";
+ helpString += "The initialize parameter allows to select the initial randomization for the opticluster method. Options are singleton, meaning each sequence is randomly assigned to its own OTU, or oneotu meaning all sequences are assigned to one otu. Default=singleton.\n";
+ helpString += "The method parameter allows you to enter your clustering mothod. Options are furthest, nearest, average, weighted, agc, dgc and opti. Default=opti. The agc and dgc methods require a fasta file.";
helpString += "The splitmethod parameter allows you to specify how you want to split your distance file before you cluster, default=distance, options distance, classify or fasta. \n";
helpString += "The taxonomy parameter allows you to enter the taxonomy file for your sequences, this is only valid if you are using splitmethod=classify. Be sure your taxonomy file does not include the probability scores. \n";
helpString += "The taxlevel parameter allows you to specify the taxonomy level you want to use to split the distance file, default=3, meaning use the first taxon in each list. \n";
helpString += "The large parameter allows you to indicate that your distance matrix is too large to fit in RAM. The default value is false.\n";
helpString += "The classic parameter allows you to indicate that you want to run your files with cluster.classic. It is only valid with splitmethod=fasta. Default=f.\n";
+ helpString += "The processors parameter allows you to specify the number of processors to use. The default is 1.\n";
helpString += "The cluster.split command should be in the following format: \n";
helpString += "cluster.split(column=youDistanceFile, name=yourNameFile, method=yourMethod, cutoff=yourCutoff, precision=yourPrecision, splitmethod=yourSplitmethod, taxonomy=yourTaxonomyfile, taxlevel=yourtaxlevel) \n";
helpString += "Example: cluster.split(column=abrecovery.dist, name=abrecovery.names, method=furthest, cutoff=0.10, precision=1000, splitmethod=classify, taxonomy=abrecovery.silva.slv.taxonomy, taxlevel=5) \n";
@@ -89,6 +100,7 @@ string ClusterSplitCommand::getOutputPattern(string type) {
if (type == "list") { pattern = "[filename],[clustertag],list-[filename],[clustertag],[tag2],list"; }
else if (type == "rabund") { pattern = "[filename],[clustertag],rabund"; }
else if (type == "sabund") { pattern = "[filename],[clustertag],sabund"; }
+ else if (type == "sensspec") { pattern = "[filename],[clustertag],sensspec"; }
else if (type == "column") { pattern = "[filename],dist"; }
else if (type == "file") { pattern = "[filename],file"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
@@ -110,7 +122,9 @@ ClusterSplitCommand::ClusterSplitCommand(){
outputTypes["rabund"] = tempOutNames;
outputTypes["sabund"] = tempOutNames;
outputTypes["column"] = tempOutNames;
+ outputTypes["name"] = tempOutNames;
outputTypes["file"] = tempOutNames;
+ outputTypes["sensspec"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "ClusterSplitCommand", "ClusterSplitCommand");
@@ -151,6 +165,7 @@ ClusterSplitCommand::ClusterSplitCommand(string option) {
outputTypes["sabund"] = tempOutNames;
outputTypes["column"] = tempOutNames;
outputTypes["file"] = tempOutNames;
+ outputTypes["sensspec"] = tempOutNames;
//if the user changes the output directory command factory will send this info to us in the output parameter
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
@@ -251,7 +266,10 @@ ClusterSplitCommand::ClusterSplitCommand(string option) {
taxFile = validParameter.validFile(parameters, "taxonomy", true);
if (taxFile == "not open") { taxFile = ""; abort = true; }
else if (taxFile == "not found") { taxFile = ""; }
- else { m->setTaxonomyFile(taxFile); if (splitmethod != "fasta") { splitmethod = "classify"; } }
+ else {
+ m->setTaxonomyFile(taxFile);
+ if (splitmethod != "fasta") { splitmethod = "classify"; }
+ }
if ((phylipfile == "") && (columnfile == "") && (fastafile == "") && (file == "")) {
//is there are current file available for either of these?
@@ -344,24 +362,37 @@ ClusterSplitCommand::ClusterSplitCommand(string option) {
if (((splitmethod != "fasta") && classic) && (file == "")) { m->mothurOut("[ERROR]: splitmethod must be fasta to use cluster.classic, or you must use the file option.\n"); abort=true; }
temp = validParameter.validFile(parameters, "taxlevel", false); if (temp == "not found") { temp = "3"; }
- m->mothurConvert(temp, taxLevelCutoff);
+ m->mothurConvert(temp, taxLevelCutoff);
+
+ temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "100"; }
+ m->mothurConvert(temp, maxIters);
+
+ temp = validParameter.validFile(parameters, "delta", false); if (temp == "not found") { temp = "0.0001"; }
+ m->mothurConvert(temp, stableMetric);
- method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "average"; }
+ metric = validParameter.validFile(parameters, "metric", false); if (metric == "not found") { metric = "mcc"; }
+
+ if ((metric == "mcc") || (metric == "sens") || (metric == "spec") || (metric == "tptn") || (metric == "tp") || (metric == "tn") || (metric == "fp") || (metric == "fn") || (metric == "f1score") || (metric == "accuracy") || (metric == "ppv") || (metric == "npv") || (metric == "fdr") || (metric == "fpfn") ){ }
+ else { m->mothurOut("[ERROR]: Not a valid metric. Valid metrics are mcc, sens, spec, tp, tn, fp, fn, tptn, fpfn, f1score, accuracy, ppv, npv, fdr."); m->mothurOutEndLine(); abort = true; }
+
+ initialize = validParameter.validFile(parameters, "initialize", false); if (initialize == "not found") { initialize = "singleton"; }
+
+ if ((initialize == "singleton") || (initialize == "oneotu")){ }
+ else { m->mothurOut("[ERROR]: Not a valid initialization. Valid initializations are singleton and oneotu."); m->mothurOutEndLine(); abort = true; }
+
+
+ method = validParameter.validFile(parameters, "method", false); if (method == "not found") { method = "opti"; m->mothurOut("[NOTE]: Default clustering method has changed to opti. To use average neighbor, set method=average."); m->mothurOutEndLine(); }
- if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted") || (method == "agc") || (method == "dgc")) { }
- else { m->mothurOut("[ERROR]: Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average, weighted, agc and dgc."); m->mothurOutEndLine(); abort = true; }
+ if ((method == "furthest") || (method == "nearest") || (method == "average") || (method == "weighted") || (method == "agc") || (method == "dgc") || (method == "opti")) { }
+ else { m->mothurOut("[ERROR]: Not a valid clustering method. Valid clustering algorithms are furthest, nearest, average, weighted, agc, dgc and opti."); m->mothurOutEndLine(); abort = true; }
if ((method == "agc") || (method == "dgc")) {
if (fastafile == "") { m->mothurOut("[ERROR]: You must provide a fasta file when using the agc or dgc clustering methods, aborting\n."); abort = true;}
if (classic) { m->mothurOut("[ERROR]: You cannot use cluster.classic with the agc or dgc clustering methods, aborting\n."); abort = true; }
}
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
- #else
- if ((method == "agc") || (method == "dgc")) { m->mothurOut("[ERROR]: The agc and dgc clustering methods are not available for Windows, aborting\n."); abort = true; }
- #endif
cutoffNotSet = false;
- temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { cutoffNotSet = true; temp = "0.25"; }
+ temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { cutoffNotSet = true; temp = "0.03"; }
m->mothurConvert(temp, cutoff);
if ((splitmethod == "distance") || (splitmethod == "classify") || (splitmethod == "fasta")) { }
@@ -377,6 +408,14 @@ ClusterSplitCommand::ClusterSplitCommand(string option) {
temp = validParameter.validFile(parameters, "islist", false); if (temp == "not found") { temp = "F"; }
isList = m->isTrue(temp);
+
+ temp = validParameter.validFile(parameters, "dist", false); if (temp == "not found") { temp = "F"; }
+ makeDist = m->isTrue(temp);
+ if (method == "opti") { makeDist = true; }
+ if (((phylipfile != "") || (columnfile != "")) && (method == "opti")) { makeDist = false; }
+
+ if (((phylipfile != "") || (columnfile != "")) && makeDist) { m->mothurOut("[ERROR]: You already provided a distance matrix. Mothur will ignore the dist parameter.\n"); makeDist = false; }
+ if (classic && makeDist) { m->mothurOut("[ERROR]: You cannot use the dist parameter with the classic parameter. Mothur will ignore the dist parameter.\n"); makeDist = false; }
timing = validParameter.validFile(parameters, "timing", false);
if (timing == "not found") { timing = "F"; }
@@ -484,13 +523,14 @@ int ClusterSplitCommand::execute(){
if (m->control_pressed) { delete split; return 0; }
singletonName = split->getSingletonNames();
+ numSingletons = split->getNumSingleton();
distName = split->getDistanceFiles(); //returns map of distance files -> namefile sorted by distance file size
delete split;
if (m->debug) { m->mothurOut("[DEBUG]: distName.size() = " + toString(distName.size()) + ".\n"); }
//output a merged distance file
- //if (splitmethod == "fasta") { createMergedDistanceFile(distName); }
+ if (makeDist) { createMergedDistanceFile(distName); }
if (m->control_pressed) { return 0; }
@@ -537,7 +577,7 @@ int ClusterSplitCommand::execute(){
m->mothurOut("Merging the clustered files..."); m->mothurOutEndLine();
ListVector* listSingle;
- map<float, int> labelBins = completeListFile(listFileNames, singletonName, labels, listSingle); //returns map of label to numBins
+ map<double, int> labelBins = completeListFile(listFileNames, singletonName, labels, listSingle); //returns map of label to numBins
if (m->control_pressed) { if (listSingle != NULL) { delete listSingle; } for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
@@ -549,7 +589,11 @@ int ClusterSplitCommand::execute(){
if (!deleteFiles) { for (int i = 0; i < distName.size(); i++) { m->mothurRemove(distName[i].begin()->first); m->mothurRemove(distName[i].begin()->second); } }
m->mothurOut("It took " + toString(time(NULL) - estart) + " seconds to merge."); m->mothurOutEndLine();
-
+
+ if (method == "opti") { runSensSpec(); }
+
+ if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
+
//set list file as new current listfile
string current = "";
itTypes = outputTypes.find("list");
@@ -568,6 +612,12 @@ int ClusterSplitCommand::execute(){
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSabundFile(current); }
}
+
+ //set sabund file as new current sabundfile
+ itTypes = outputTypes.find("column");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setColumnFile(current); }
+ }
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
@@ -582,10 +632,10 @@ int ClusterSplitCommand::execute(){
}
}
//**********************************************************************************************************************
-map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames, string singleton, set<string>& userLabels, ListVector*& listSingle){
+map<double, int> ClusterSplitCommand::completeListFile(vector<string> listNames, string singleton, set<string>& userLabels, ListVector*& listSingle){
try {
- map<float, int> labelBin;
- vector<float> orderFloat;
+ map<double, int> labelBin;
+ vector<double> orderFloat;
int numSingleBins;
//read in singletons
@@ -600,16 +650,18 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
if (countfile != "") { m->getline(in); m->gobble(in); }
while (!in.eof()) {
- in >> firstCol >> secondCol; m->getline(in); m->gobble(in);
+ in >> firstCol >> secondCol;
+ m->getline(in);
if (countfile == "") { listSingle->push_back(secondCol); }
else { listSingle->push_back(firstCol); }
+ m->gobble(in);
}
in.close();
m->mothurRemove(singleton);
numSingleBins = listSingle->getNumBins();
- }else{ listSingle = NULL; numSingleBins = 0; }
+ }else{ listSingle = NULL; numSingleBins = 0; }
//go through users set and make them floats so we can sort them
double tcutoff = cutoff * 1000; tcutoff = ceil(tcutoff);
@@ -630,7 +682,7 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
//sort order
sort(orderFloat.begin(), orderFloat.end());
userLabels.clear();
-
+
//get the list info from each file
for (int k = 0; k < listNames.size(); k++) {
@@ -650,7 +702,7 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
//for each label needed
for(int l = 0; l < orderFloat.size(); l++){
-
+
string thisLabel;
if (orderFloat[l] == -1) { thisLabel = "unique"; }
else { thisLabel = toString(orderFloat[l], length-1); }
@@ -701,7 +753,7 @@ map<float, int> ClusterSplitCommand::completeListFile(vector<string> listNames,
}
}
//**********************************************************************************************************************
-int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> userLabels, ListVector* listSingle){
+int ClusterSplitCommand::mergeLists(vector<string> listNames, map<double, int> userLabels, ListVector* listSingle){
try {
if (outputDir == "") { outputDir += m->hasPath(distfile); }
fileroot = outputDir + m->getRootName(m->getSimpleName(distfile));
@@ -732,7 +784,7 @@ int ClusterSplitCommand::mergeLists(vector<string> listNames, map<float, int> us
m->openOutputFile(listFileName, outList);
outputNames.push_back(listFileName); outputTypes["list"].push_back(listFileName);
- map<float, int>::iterator itLabel;
+ map<double, int>::iterator itLabel;
//clears out junk for autocompleting of list files above. Perhaps there is a beter way to handle this from within the data structure?
m->printedListHeaders = false;
@@ -848,8 +900,7 @@ vector<string> ClusterSplitCommand::createProcesses(vector< map<string, string>
//for each file group figure out which process will complete it
//want to divide the load intelligently so the big files are spread between processes
- for (int i = 0; i < distName.size(); i++) {
- //cout << i << endl;
+ for (int i = 0; i < distName.size(); i++) {
int processToAssign = (i+1) % processors;
if (processToAssign == 0) { processToAssign = processors; }
@@ -859,7 +910,6 @@ vector<string> ClusterSplitCommand::createProcesses(vector< map<string, string>
//now lets reverse the order of ever other process, so we balance big files running with little ones
for (int i = 0; i < processors; i++) {
- //cout << i << endl;
int remainder = ((i+1) % processors);
if (remainder) { reverse(dividedNames[i].begin(), dividedNames[i].end()); }
}
@@ -931,7 +981,6 @@ vector<string> ClusterSplitCommand::createProcesses(vector< map<string, string>
//for each file group figure out which process will complete it
//want to divide the load intelligently so the big files are spread between processes
for (int i = 0; i < distName.size(); i++) {
- //cout << i << endl;
int processToAssign = (i+1) % processors;
if (processToAssign == 0) { processToAssign = processors; }
@@ -941,7 +990,6 @@ vector<string> ClusterSplitCommand::createProcesses(vector< map<string, string>
//now lets reverse the order of ever other process, so we balance big files running with little ones
for (int i = 0; i < processors; i++) {
- //cout << i << endl;
int remainder = ((i+1) % processors);
if (remainder) { reverse(dividedNames[i].begin(), dividedNames[i].end()); }
}
@@ -1033,14 +1081,15 @@ vector<string> ClusterSplitCommand::createProcesses(vector< map<string, string>
deleteFiles = true;
- //delete the temp files now that we are done
- for (int i = 0; i < distName.size(); i++) {
- string thisNamefile = distName[i].begin()->second;
- string thisDistFile = distName[i].begin()->first;
- m->mothurRemove(thisNamefile);
- m->mothurRemove(thisDistFile);
+ if (deleteFiles) {
+ //delete the temp files now that we are done
+ for (int i = 0; i < distName.size(); i++) {
+ string thisNamefile = distName[i].begin()->second;
+ string thisDistFile = distName[i].begin()->first;
+ m->mothurRemove(thisNamefile);
+ m->mothurRemove(thisDistFile);
+ }
}
-
#else
#endif
@@ -1073,10 +1122,8 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
for (int i = 0; i < listFileNames.size(); i++) { m->mothurRemove(listFileNames[i]); }
listFileNames.clear(); return listFileNames;
}
-
listFileNames.push_back(listFileName);
}
-
cutoff = smallestCutoff;
return listFileNames;
@@ -1198,6 +1245,7 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
string listFileName = "";
if ((method == "agc") || (method == "dgc")) { listFileName = runVsearchCluster(thisDistFile, thisNamefile, labels, smallestCutoff); }
+ else if (method == "opti") { listFileName = runOptiCluster(thisDistFile, thisNamefile, labels, smallestCutoff); }
else {
Cluster* cluster = NULL;
@@ -1336,6 +1384,72 @@ string ClusterSplitCommand::clusterFile(string thisDistFile, string thisNamefile
}
}
//**********************************************************************************************************************
+string ClusterSplitCommand::runOptiCluster(string thisDistFile, string thisNamefile, set<string>& labels, double& smallestCutoff){
+ try {
+ if (cutoffNotSet) { m->mothurOut("\nYou did not set a cutoff, using 0.03.\n"); cutoff = 0.03; }
+
+ string nameOrCount = "count";
+ if (namefile != "") { nameOrCount = "name"; }
+
+ OptiMatrix matrix(thisDistFile, thisNamefile, nameOrCount, "column", cutoff, false);
+
+ OptiCluster cluster(&matrix, metric, numSingletons);
+ tag = cluster.getTag();
+
+ m->mothurOutEndLine(); m->mothurOut("Clustering " + thisDistFile); m->mothurOutEndLine();
+
+ if (outputDir == "") { outputDir += m->hasPath(thisDistFile); }
+ fileroot = outputDir + m->getRootName(m->getSimpleName(thisDistFile));
+
+ string listFileName = fileroot+ tag + ".list";
+
+ int iters = 0;
+ double listVectorMetric = 0; //worst state
+ double delta = 1;
+
+ cluster.initialize(listVectorMetric, true, initialize);
+
+ while ((delta > stableMetric) && (iters < maxIters)) {
+
+ if (m->control_pressed) { if (deleteFiles) { m->mothurRemove(thisDistFile); m->mothurRemove(thisNamefile); } return listFileName; }
+ double oldMetric = listVectorMetric;
+ cluster.update(listVectorMetric);
+
+ delta = abs(oldMetric - listVectorMetric);
+ iters++;
+ }
+
+ ListVector* list = cluster.getList();
+ list->setLabel(toString(smallestCutoff));
+ cutoff = m->ceilDist(cutoff, precision);
+ labels.insert(toString(cutoff));
+
+ ofstream listFile;
+ m->openOutputFile(listFileName, listFile);
+ list->print(listFile);
+ listFile.close();
+
+ if (deleteFiles) {
+ m->mothurRemove(thisDistFile);
+ m->mothurRemove(thisNamefile);
+ }
+
+ long long tp, tn, fp, fn;
+ m->mothurOut("\ntp\ttn\tfp\tfn\tsensitivity\tspecificity\tppv\tnpv\tfdr\taccuracy\tmcc\tf1score\n");
+ vector<double> results = cluster.getStats(tp, tn, fp, fn);
+ m->mothurOut(toString(tp) + "\t" + toString(tn) + "\t" + toString(fp) + "\t" + toString(fn) + "\t");
+ for (int i = 0; i < results.size(); i++) { m->mothurOut(toString(results[i]) + "\t"); }
+ m->mothurOut("\n\n");
+
+ return listFileName;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterSplitCommand", "runOptiCluster");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
string ClusterSplitCommand::runVsearchCluster(string thisDistFile, string thisNamefile, set<string>& labels, double& smallestCutoff){
try {
@@ -1416,6 +1530,10 @@ int ClusterSplitCommand::vsearchDriver(string inputFile, string ucClusteredFile,
char* maxaccepts = new char[16]; maxaccepts[0] = '\0'; strncat(maxaccepts, "--maxaccepts=16", 15);
vsearchParameters.push_back(maxaccepts);
+ //--threads=1
+ char* threads = new char[12]; threads[0] = '\0'; strncat(threads, "--threads=1", 11);
+ vsearchParameters.push_back(threads);
+
//--usersort
char* usersort = new char[11]; usersort[0] = '\0'; strncat(usersort, "--usersort", 10);
vsearchParameters.push_back(usersort);
@@ -1437,10 +1555,6 @@ int ClusterSplitCommand::vsearchDriver(string inputFile, string ucClusteredFile,
char* wordlength = new char[15]; wordlength[0] = '\0'; strncat(wordlength, "--wordlength=8", 14);
vsearchParameters.push_back(wordlength);
- //--threads=1
- char* threads = new char[12]; threads[0] = '\0'; strncat(threads, "--threads=1", 11);
- vsearchParameters.push_back(threads);
-
//--uc=$ROOT.clustered.uc
string tempIn = "--uc=" + ucClusteredFile;
char* uc = new char[tempIn.length()+1]; uc[0] = '\0'; strncat(uc, tempIn.c_str(), tempIn.length());
@@ -1504,7 +1618,6 @@ int ClusterSplitCommand::vsearchDriver(string inputFile, string ucClusteredFile,
int ClusterSplitCommand::createMergedDistanceFile(vector< map<string, string> > distNames) {
try{
-
string thisOutputDir = outputDir;
if (outputDir == "") { thisOutputDir = m->hasPath(fastafile); }
map<string, string> variables;
@@ -1523,9 +1636,7 @@ int ClusterSplitCommand::createMergedDistanceFile(vector< map<string, string> >
outputTypes["column"].push_back(outputFileName); outputNames.push_back(outputFileName);
- return 0;
-
-
+ return 0;
}
catch(exception& e) {
m->errorOut(e, "ClusterSplitCommand", "createMergedDistanceFile");
@@ -1533,6 +1644,70 @@ int ClusterSplitCommand::createMergedDistanceFile(vector< map<string, string> >
}
}
//**********************************************************************************************************************
+
+int ClusterSplitCommand::runSensSpec() {
+ try{
+ string listFile = "";
+ itTypes = outputTypes.find("list");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { listFile = (itTypes->second)[0]; }
+ }
+
+ string columnFile = ""; string phylipFile = "";
+ if (makeDist) {
+ itTypes = outputTypes.find("column");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { columnFile = (itTypes->second)[0]; }
+ }
+ }else if (columnfile != "") { columnFile = columnfile; }
+ else { phylipFile = phylipfile; }
+
+ string inputString = "list=" + listFile;
+ if (columnFile != "") { inputString += ", column=" + columnFile; }
+ else if (phylipfile != "") { inputString += ", phylip=" + phylipfile; }
+ else { m->mothurOut("[WARNING]: Cannot run sens.spec analysis without a phylip or column file, skipping."); return 0; }
+
+ if (namefile != "") { inputString += ", name=" + namefile; }
+ else if (countfile != "") { inputString += ", count=" + countfile; }
+ else { m->mothurOut("[WARNING]: Cannot run sens.spec analysis without a name or count file, skipping."); return 0; }
+
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Running command: sens.spec(" + inputString + ")"); m->mothurOutEndLine();
+ m->mothurCalling = true;
+
+ Command* sensspecCommand = new SensSpecCommand(inputString);
+ sensspecCommand->execute();
+
+ map<string, vector<string> > filenames = sensspecCommand->getOutputFiles();
+
+ delete sensspecCommand;
+ m->mothurCalling = false;
+
+ string outputFileName = filenames["sensspec"][0];
+
+ outputTypes["sensspec"].push_back(outputFileName); outputNames.push_back(outputFileName);
+
+ m->mothurOut("/******************************************/"); m->mothurOutEndLine();
+ m->mothurOut("Done.\n\n"); m->mothurOutEndLine();
+
+ ifstream in;
+ m->openInputFile(outputFileName, in);
+
+ while(!in.eof()){
+ if (m->control_pressed) { break; }
+
+ m->mothurOut(m->getline(in)+"\n"); m->gobble(in);
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "ClusterSplitCommand", "runSensSpec");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
int ClusterSplitCommand::createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund){
try {
rabund->setLabel(list->getLabel());
@@ -1621,7 +1796,7 @@ string ClusterSplitCommand::readFile(vector< map<string, string> >& distName){
}
ListVector* listSingle;
- map<float, int> labelBins = completeListFile(listFileNames, singleton, listLabels, listSingle);
+ map<double, int> labelBins = completeListFile(listFileNames, singleton, listLabels, listSingle);
mergeLists(listFileNames, labelBins, listSingle);
@@ -1685,12 +1860,10 @@ bool ClusterSplitCommand::findVsearch(){
if (cutoffNotSet) { m->mothurOut("\nYou did not set a cutoff, using 0.03.\n"); cutoff = 0.03; }
- //look for uchime exe
- string path = m->argv;
- string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
-
+ //look for vsearch exe
+
+ string path = m->mothurProgramPath;
+
string vsearchCommand;
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
vsearchCommand = path + "vsearch"; // format the database, -o option gives us the ability
@@ -1705,25 +1878,25 @@ bool ClusterSplitCommand::findVsearch(){
delete newCommand;
}
#else
- vsearchCommand = path + "vsearch.exe";
+ vsearchCommand = path + "\\vsearch.exe";
#endif
- //test to make sure uchime exists
+ //test to make sure vsearch exists
ifstream in;
vsearchCommand = m->getFullPathName(vsearchCommand);
int ableToOpen = m->openInputFile(vsearchCommand, in, "no error"); in.close();
if(ableToOpen == 1) {
m->mothurOut(vsearchCommand + " file does not exist. Checking path... \n");
- //check to see if uchime is in the path??
-
- string uLocation = m->findProgramPath("vsearch");
-
+ //check to see if vsearch is in the path??
ifstream in2;
+ string uLocation = "";
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ uLocation = m->findProgramPath("vsearch");
ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
#else
- ableToOpen = m->openInputFile((uLocation + ".exe"), in2, "no error"); in2.close();
+ uLocation = m->findProgramPath("vsearch.exe");
+ ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close();
#endif
if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uLocation + " file does not exist. mothur requires the vsearch executable."); m->mothurOutEndLine(); abort = true; }
@@ -1732,9 +1905,7 @@ bool ClusterSplitCommand::findVsearch(){
vsearchLocation = m->getFullPathName(vsearchLocation);
- if (m->debug) {
- m->mothurOut("[DEBUG]: vsearch location using " + vsearchLocation + "\n");
- }
+ if (m->debug) { m->mothurOut("[DEBUG]: vsearch location using " + vsearchLocation + "\n"); }
if (!abort) { return true; }
diff --git a/source/commands/clustersplitcommand.h b/source/commands/clustersplitcommand.h
index 5396409..e7941d9 100644
--- a/source/commands/clustersplitcommand.h
+++ b/source/commands/clustersplitcommand.h
@@ -24,6 +24,8 @@
#include "inputdata.h"
#include "clustercommand.h"
#include "clusterclassic.h"
+#include "vsearchfileparser.h"
+#include "opticluster.h"
class ClusterSplitCommand : public Command {
@@ -48,20 +50,21 @@ private:
vector<int> processIDS; //processid
vector<string> outputNames;
- string file, method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, countfile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile, inputDir, vsearchLocation;
- double cutoff, splitcutoff;
- int precision, length, processors, taxLevelCutoff;
- bool print_start, abort, large, classic, runCluster, deleteFiles, isList, cutoffNotSet;
+ string file, method, fileroot, tag, outputDir, phylipfile, columnfile, namefile, countfile, distfile, format, showabund, timing, splitmethod, taxFile, fastafile, inputDir, vsearchLocation, metric, initialize;
+ double cutoff, splitcutoff, stableMetric;
+ int precision, length, processors, taxLevelCutoff, maxIters;
+ bool print_start, abort, large, classic, runCluster, deleteFiles, isList, cutoffNotSet, makeDist;
time_t start;
ofstream outList, outRabund, outSabund;
+ long long numSingletons;
void printData(ListVector*);
vector<string> createProcesses(vector< map<string, string> >, set<string>&);
vector<string> cluster(vector< map<string, string> >, set<string>&);
string clusterFile(string, string, set<string>&, double&);
string clusterClassicFile(string, string, set<string>&, double&);
- int mergeLists(vector<string>, map<float, int>, ListVector*);
- map<float, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
+ int mergeLists(vector<string>, map<double, int>, ListVector*);
+ map<double, int> completeListFile(vector<string>, string, set<string>&, ListVector*&);
int createMergedDistanceFile(vector< map<string, string> >);
int createRabund(CountTable*& ct, ListVector*& list, RAbundVector*& rabund);
string readFile(vector< map<string, string> >&);
@@ -70,6 +73,8 @@ private:
bool findVsearch();
int vsearchDriver(string, string, string, double);
string runVsearchCluster(string, string, set<string>&, double&);
+ string runOptiCluster(string, string, set<string>&, double&);
+ int runSensSpec();
};
/////////////////not working for Windows////////////////////////////////////////////////////////////
diff --git a/source/commands/createdatabasecommand.cpp b/source/commands/createdatabasecommand.cpp
index 23717ba..ed66a2e 100644
--- a/source/commands/createdatabasecommand.cpp
+++ b/source/commands/createdatabasecommand.cpp
@@ -12,9 +12,9 @@
//**********************************************************************************************************************
vector<string> CreateDatabaseCommand::setParameters(){
try {
- CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none","database",false,true,true); parameters.push_back(pfasta);
- CommandParameter pname("repname", "InputTypes", "", "", "NameCount", "NameCount", "none","",false,false,true); parameters.push_back(pname);
- CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "NameCount", "none","",false,false,true); parameters.push_back(pcount);
+ CommandParameter pfasta("repfasta", "InputTypes", "", "", "none", "none", "none","database",false,false,true); parameters.push_back(pfasta);
+ CommandParameter pname("repname", "InputTypes", "", "", "NameCount", "none", "none","",false,false,true); parameters.push_back(pname);
+ CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none","",false,false,true); parameters.push_back(pcount);
CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none","",false,false,true); parameters.push_back(pgroup);
CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pconstaxonomy);
CommandParameter plist("list", "InputTypes", "", "", "ListShared", "ListShared", "none","",false,false,true); parameters.push_back(plist);
@@ -37,8 +37,8 @@ vector<string> CreateDatabaseCommand::setParameters(){
string CreateDatabaseCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The create.database command reads a list file or a shared file, *.cons.taxonomy, *.rep.fasta, *.rep.names and optional groupfile, or count file and creates a database file.\n";
- helpString += "The create.database command parameters are repfasta, list, shared, repname, constaxonomy, group, count and label. List, repfasta, repnames or count, and constaxonomy are required.\n";
+ helpString += "The create.database command reads a list file or a shared file, *.cons.taxonomy, and optional *.rep.fasta, *.rep.names, groupfile, or count file and creates a database file.\n";
+ helpString += "The create.database command parameters are repfasta, list, shared, repname, constaxonomy, group, count and label. List or shared and constaxonomy are required.\n";
helpString += "The repfasta file is fasta file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
helpString += "The repname file is the name file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, name=yourNameFile).\n";
helpString += "The count file is the count file outputted by get.oturep(fasta=yourFastaFile, list=yourListfile, column=yourDistFile, count=yourCountFile). If it includes group info, mothur will give you the abundance breakdown by group. \n";
@@ -199,7 +199,7 @@ CreateDatabaseCommand::CreateDatabaseCommand(string option) {
sharedfile = m->getSharedFile();
if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
else {
- m->mothurOut("No valid current files. You must provide a shared or list file before you can use the create.database command."); m->mothurOutEndLine();
+ m->mothurOut("[ERROR]: No valid current files. You must provide a shared or list file before you can use the create.database command."); m->mothurOutEndLine();
abort = true;
}
}
@@ -216,30 +216,20 @@ CreateDatabaseCommand::CreateDatabaseCommand(string option) {
else if (contaxonomyfile == "not open") { contaxonomyfile = ""; abort = true; }
repfastafile = validParameter.validFile(parameters, "repfasta", true);
- if (repfastafile == "not found") { //if there is a current list file, use it
- repfastafile = ""; m->mothurOut("The repfasta parameter is required, aborting."); m->mothurOutEndLine(); abort = true;
- }
+ if (repfastafile == "not found") { repfastafile = ""; }
else if (repfastafile == "not open") { repfastafile = ""; abort = true; }
repnamesfile = validParameter.validFile(parameters, "repname", true);
if (repnamesfile == "not found") { repnamesfile = ""; }
else if (repnamesfile == "not open") { repnamesfile = ""; abort = true; }
+ if ((repnamesfile != "") && (repfastafile == "")) { m->mothurOut("[ERROR]: You must provide a repfasta file if you are using a repnames file."); m->mothurOutEndLine();
+ abort = true; }
+
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not found") { countfile = ""; }
else if (countfile == "not open") { countfile = ""; abort = true; }
- if ((countfile == "") && (repnamesfile == "")) {
- //if there is a current name file, use it, else look for current count file
- string repnamesfile = m->getNameFile();
- if (repnamesfile != "") { m->mothurOut("Using " + repnamesfile + " as input file for the repname parameter."); m->mothurOutEndLine(); }
- else {
- countfile = m->getCountTableFile();
- if (countfile != "") { m->mothurOut("Using " + countfile + " as input file for the count parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("[ERROR]: You must provide a count or repname file."); m->mothurOutEndLine(); abort = true; }
- }
- }
-
groupfile = validParameter.validFile(parameters, "group", true);
if (groupfile == "not open") { groupfile = ""; abort = true; }
else if (groupfile == "not found") { groupfile = ""; }
@@ -271,7 +261,8 @@ int CreateDatabaseCommand::execute(){
if (m->control_pressed) { return 0; }
vector<Sequence> seqs;
- vector<int> repOtusSizes = readFasta(seqs);
+ vector<int> repOtusSizes;
+ if (repfastafile != "") { repOtusSizes = readFasta(seqs); }
if (m->control_pressed) { return 0; }
@@ -280,7 +271,7 @@ int CreateDatabaseCommand::execute(){
map<string, int> nameMap;
int numUniqueNamesFile = 0;
CountTable ct;
- if (countfile == "") {
+ if (repnamesfile != "") {
numUniqueNamesFile = m->readNames(repnamesfile, repNames, 1);
//the repnames file does not have the same order as the list file bins so we need to sort and reassemble for the search below
map<string, string> tempRepNames;
@@ -298,26 +289,29 @@ int CreateDatabaseCommand::execute(){
repNames.erase(it++);
}
repNames = tempRepNames;
- }else {
+ }else if (countfile != ""){
ct.readTable(countfile, true, false);
numUniqueNamesFile = ct.getNumUniqueSeqs();
nameMap = ct.getNameMap();
}
- //are there the same number of otus in the fasta and name files
- if (repOtusSizes.size() != numUniqueNamesFile) { m->mothurOut("[ERROR]: you have " + toString(numUniqueNamesFile) + " unique seqs in your repname file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file. These should match.\n"); m->control_pressed = true; }
-
- if (m->control_pressed) { return 0; }
-
- //are there the same number of OTUs in the tax and fasta file
- if (classifyOtuSizes.size() != repOtusSizes.size()) { m->mothurOut("[ERROR]: you have " + toString(classifyOtuSizes.size()) + " taxonomies in your contaxonomy file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file. These should match.\n"); m->control_pressed = true; }
-
if (m->control_pressed) { return 0; }
- //at this point we have the same number of OTUs. Are the sizes we have found so far accurate?
- for (int i = 0; i < classifyOtuSizes.size(); i++) {
- if (classifyOtuSizes[i] != repOtusSizes[i]) {
- m->mothurOut("[ERROR]: OTU size info does not match for bin " + toString(i+1) + ". The contaxonomy file indicated the OTU represented " + toString(classifyOtuSizes[i]) + " sequences, but the repfasta file had " + toString(repOtusSizes[i]) + ". These should match. Make sure you are using files for the same distance.\n"); m->control_pressed = true;
+ if (repfastafile != "") {
+
+ //are there the same number of otus in the fasta and name files
+ if (repOtusSizes.size() != numUniqueNamesFile) { m->mothurOut("[ERROR]: you have " + toString(numUniqueNamesFile) + " unique seqs in your repname file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file. These should match.\n"); m->control_pressed = true; }
+
+ //are there the same number of OTUs in the tax and fasta file
+ if (classifyOtuSizes.size() != repOtusSizes.size()) { m->mothurOut("[ERROR]: you have " + toString(classifyOtuSizes.size()) + " taxonomies in your contaxonomy file, but " + toString(repOtusSizes.size()) + " seqs in your repfasta file. These should match.\n"); m->control_pressed = true; }
+
+ if (m->control_pressed) { return 0; }
+
+ //at this point we have the same number of OTUs. Are the sizes we have found so far accurate?
+ for (int i = 0; i < classifyOtuSizes.size(); i++) {
+ if (classifyOtuSizes[i] != repOtusSizes[i]) {
+ m->mothurOut("[ERROR]: OTU size info does not match for bin " + toString(i+1) + ". The contaxonomy file indicated the OTU represented " + toString(classifyOtuSizes[i]) + " sequences, but the repfasta file had " + toString(repOtusSizes[i]) + ". These should match. Make sure you are using files for the same distance.\n"); m->control_pressed = true;
+ }
}
}
@@ -362,7 +356,9 @@ int CreateDatabaseCommand::execute(){
for (int i = 0; i < ct.getNamesOfGroups().size(); i++) { header += '\t' + (ct.getNamesOfGroups())[i]; }
}
}
- header += "\trepSeqName\trepSeq\tOTUConTaxonomy";
+
+ if (repfastafile != "") { header += "\trepSeqName\trepSeq"; }
+ header += "\tOTUConTaxonomy";
out << header << endl;
vector<string> binLabels = list->getLabels();
@@ -380,9 +376,9 @@ int CreateDatabaseCommand::execute(){
m->splitAtComma(bin, binNames);
string seqRepName = "";
- int numSeqsRep = 0;
+ int numSeqsRep = binNames.size();
- if (countfile == "") {
+ if (repnamesfile != "") {
sort(binNames.begin(), binNames.end());
bin = "";
for (int j = 0; j < binNames.size()-1; j++) {
@@ -399,14 +395,14 @@ int CreateDatabaseCommand::execute(){
if (binNames.size() != classifyOtuSizes[index]) {
m->mothurOut("[ERROR: OTU " + otuLabels[index] + " contains " + toString(binNames.size()) + " sequence, but the rep and taxonomy files indicated this OTU should have " + toString(classifyOtuSizes[index]) + ". Make sure you are using files for the same distance.\n"); m->control_pressed = true; break;
}
- }else {
+ }else if ((countfile != "") && (repfastafile != "")) {
//find rep sequence in bin
for (int j = 0; j < binNames.size(); j++) {
map<string, int>::iterator itNameMap = nameMap.find(binNames[j]); //if you are in the counttable you must be the rep. because get.oturep with a countfile only includes the rep sequences in the rep.count file.
if (itNameMap != nameMap.end()) {
seqRepName = itNameMap->first;
numSeqsRep = itNameMap->second;
- j += binNames.size();
+ j += binNames.size(); //exit loop
}
}
@@ -440,15 +436,25 @@ int CreateDatabaseCommand::execute(){
for (int j = 0; j < groupmap->getNamesOfGroups().size(); j++) { out << '\t' << counts[(groupmap->getNamesOfGroups())[j]]; }
if (error) { m->control_pressed = true; }
- }else if (countfile != "") {
+ }else if ((countfile != "") && (repfastafile != "")) {
if (ct.hasGroupInfo()) {
vector<int> groupCounts = ct.getGroupCounts(seqRepName);
for (int j = 0; j < groupCounts.size(); j++) { out << '\t' << groupCounts[j]; }
}else { out << '\t' << numSeqsRep; }
+ }else if ((countfile != "") && (repfastafile == "")) {
+ if (ct.hasGroupInfo()) {
+ vector<int> groupTotals; groupTotals.resize(ct.getNumGroups(), 0);
+ for (int j = 0; j < binNames.size(); j++) {
+ vector<int> groupCounts = ct.getGroupCounts(binNames[j]);
+ for (int k = 0; k < groupCounts.size(); k++) { groupTotals[k] += groupCounts[k]; }
+ }
+ for (int j = 0; j < groupTotals.size(); j++) { out << '\t' << groupTotals[j]; }
+ }else { out << '\t' << numSeqsRep; }
}else { out << '\t' << numSeqsRep; }
//output repSeq
- out << '\t' << seqRepName << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
+ if (repfastafile != "") { out << '\t' << seqRepName << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl; }
+ else { out << '\t' << taxonomies[index] << endl; }
}
@@ -460,7 +466,8 @@ int CreateDatabaseCommand::execute(){
header = "OTUNumber";
for (int i = 0; i < lookup.size(); i++) { header += '\t' + lookup[i]->getGroup(); }
- header += "\trepSeqName\trepSeq\tOTUConTaxonomy";
+ if (repfastafile != "") { header += "\trepSeqName\trepSeq"; }
+ header += "\tOTUConTaxonomy";
out << header << endl;
for (int h = 0; h < lookup[0]->getNumBins(); h++) {
@@ -487,7 +494,8 @@ int CreateDatabaseCommand::execute(){
}
//output repSeq
- out << '\t' << seqs[index].getName() << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl;
+ if (repfastafile != "") { out << '\t' << seqs[index].getName() << '\t' << seqs[index].getAligned() << '\t' << taxonomies[index] << endl; }
+ else { out << '\t' << taxonomies[index] << endl; }
}
}
out.close();
@@ -539,7 +547,8 @@ vector<int> CreateDatabaseCommand::readTax(vector<string>& taxonomies, vector<st
string otu = ""; string tax = "unknown";
int size = 0;
- in >> otu >> size >> tax; m->gobble(in);
+ in >> otu >> size; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
sizes.push_back(size);
taxonomies.push_back(tax);
diff --git a/source/commands/distancecommand.cpp b/source/commands/distancecommand.cpp
index 67dca9b..58a4bae 100644
--- a/source/commands/distancecommand.cpp
+++ b/source/commands/distancecommand.cpp
@@ -240,7 +240,7 @@ int DistanceCommand::execute(){
if (m->control_pressed) { return 0; }
int numSeqs = alignDB.getNumSeqs();
- cutoff += 0.005;
+ //cutoff += 0.005;
if (!alignDB.sameLength()) { m->mothurOut("[ERROR]: your sequences are not the same length, aborting."); m->mothurOutEndLine(); return 0; }
diff --git a/source/commands/getcommandinfocommand.cpp b/source/commands/getcommandinfocommand.cpp
index c113956..16aece8 100644
--- a/source/commands/getcommandinfocommand.cpp
+++ b/source/commands/getcommandinfocommand.cpp
@@ -84,7 +84,7 @@ int GetCommandInfoCommand::execute(){
int numNonHidden = 0;
- out << "mothurLocation=" << m->getFullPathName(m->argv) << endl;
+ out << "mothurLocation=" << m->getFullPathName(m->mothurProgramPath) << endl;
out << "mothurVersion=" << m->getVersion() << endl;
map<string, string> commands = commandFactory->getListCommands();
diff --git a/source/commands/getcurrentcommand.cpp b/source/commands/getcurrentcommand.cpp
index 3473814..6388014 100644
--- a/source/commands/getcurrentcommand.cpp
+++ b/source/commands/getcurrentcommand.cpp
@@ -162,6 +162,8 @@ int GetCurrentCommand::execute(){
m->setAccnosFile("");
}else if (types[i] == "taxonomy") {
m->setTaxonomyFile("");
+ }else if (types[i] == "constaxonomy") {
+ m->setConsTaxonomyFile("");
}else if (types[i] == "flow") {
m->setFlowFile("");
}else if (types[i] == "biom") {
diff --git a/source/commands/getgroupscommand.cpp b/source/commands/getgroupscommand.cpp
index 61dfb97..600957a 100644
--- a/source/commands/getgroupscommand.cpp
+++ b/source/commands/getgroupscommand.cpp
@@ -992,8 +992,8 @@ int GetGroupsCommand::readTax(){
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; //read from first column
- in >> tax; //read from second column
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
//if this name is in the accnos file
if (names.count(name) != 0) {
@@ -1007,8 +1007,6 @@ int GetGroupsCommand::readTax(){
out << it->second << '\t' << tax << endl;
}
}
-
- m->gobble(in);
}
in.close();
out.close();
diff --git a/source/commands/getlineagecommand.cpp b/source/commands/getlineagecommand.cpp
index cc59fa6..80ef4b8 100644
--- a/source/commands/getlineagecommand.cpp
+++ b/source/commands/getlineagecommand.cpp
@@ -350,7 +350,7 @@ int GetLineageCommand::execute(){
m->mothurOut("\n[NOTE]: The count file should contain only unique names, so mothur assumes your fasta, list and taxonomy files also contain only uniques.\n\n");
}
}
-
+
//read through the correct file and output lines you want to keep
if (taxfile != "") {
readTax(); //fills the set of names to get
@@ -412,6 +412,12 @@ int GetLineageCommand::execute(){
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
+
+ //set constaxonomy file as new current constaxonomyfile
+ itTypes = outputTypes.find("constaxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setConsTaxonomyFile(current); }
+ }
}
return 0;
@@ -1081,8 +1087,8 @@ int GetLineageCommand::readTax(){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; //read from first column
- in >> tax; //read from second column
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
string noQuotesTax = m->removeQuotes(tax);
@@ -1178,8 +1184,6 @@ int GetLineageCommand::readTax(){
}
}
-
- m->gobble(in);
}
in.close();
out.close();
@@ -1239,7 +1243,7 @@ int GetLineageCommand::readConsTax(){
in >> otuLabel; m->gobble(in);
in >> numReps; m->gobble(in);
- in >> tax; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
string noQuotesTax = m->removeQuotes(tax);
diff --git a/source/commands/getotulabelscommand.cpp b/source/commands/getotulabelscommand.cpp
index d3856d9..3b3112f 100644
--- a/source/commands/getotulabelscommand.cpp
+++ b/source/commands/getotulabelscommand.cpp
@@ -268,6 +268,12 @@ int GetOtuLabelsCommand::execute(){
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
+ //set constaxonomy file as new current constaxonomyfile
+ itTypes = outputTypes.find("constaxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setConsTaxonomyFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
@@ -305,7 +311,8 @@ int GetOtuLabelsCommand::readClassifyOtu(){
string otu = ""; string tax = "unknown";
int size = 0;
- in >> otu >> size >> tax; m->gobble(in);
+ in >> otu >> size; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
if (m->debug) { m->mothurOut("Otu=" + otu + ", size=" + toString(size) + ", tax=" + tax + "\n"); }
diff --git a/source/commands/getotuscommand.cpp b/source/commands/getotuscommand.cpp
deleted file mode 100644
index e9f333f..0000000
--- a/source/commands/getotuscommand.cpp
+++ /dev/null
@@ -1,432 +0,0 @@
-/*
- * getotuscommand.cpp
- * Mothur
- *
- * Created by westcott on 11/10/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "getotuscommand.h"
-#include "inputdata.h"
-#include "sharedutilities.h"
-
-
-//**********************************************************************************************************************
-vector<string> GetOtusCommand::setParameters(){
- try {
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true, true); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true, true); parameters.push_back(plist);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
- CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string GetOtusCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The get.otus command selects otus containing sequences from a specfic group or set of groups.\n";
- helpString += "It outputs a new list file containing the otus containing sequences from in the those specified groups.\n";
- helpString += "The get.otus command parameters are accnos, group, list, label and groups. The group and list parameters are required, unless you have valid current files.\n";
- helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
- helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n";
- helpString += "The label parameter allows you to specify which distance you want to process.\n";
- helpString += "The get.otus command should be in the following format: get.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n";
- helpString += "Example get.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n";
- helpString += "or get.otus(groups=pasture, list=amazon.fn.list, amazon.groups, label=0.03).\n";
- helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string GetOtusCommand::getOutputPattern(string type) {
- try {
- string pattern = "";
-
- if (type == "group") { pattern = "[filename],[tag],pick,[extension]"; }
- else if (type == "list") { pattern = "[filename],[tag],pick,[extension]"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
-
- return pattern;
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "getOutputPattern");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetOtusCommand::GetOtusCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "GetOtusCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetOtusCommand::GetOtusCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
- map<string,string>::iterator it;
-
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
-
-
- //if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
- if (inputDir == "not found"){ inputDir = ""; }
- else {
- string path;
- it = parameters.find("accnos");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["accnos"] = inputDir + it->second; }
- }
-
- it = parameters.find("list");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["list"] = inputDir + it->second; }
- }
-
- it = parameters.find("group");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["group"] = inputDir + it->second; }
- }
- }
-
-
- //check for required parameters
- accnosfile = validParameter.validFile(parameters, "accnos", true);
- if (accnosfile == "not open") { abort = true; }
- else if (accnosfile == "not found") { accnosfile = ""; }
- else { m->setAccnosFile(accnosfile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") {
- groupfile = m->getGroupFile();
- if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setGroupFile(groupfile); }
-
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") {
- listfile = m->getListFile();
- if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setListFile(listfile); }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else {
- m->splitAtDash(groups, Groups);
- }
-
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
-
- if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "GetOtusCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetOtusCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
-
- //get groups you want to get
- if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
-
- //make sure groups are valid
- //takes care of user setting groupNames that are invalid or setting groups=all
- SharedUtil* util = new SharedUtil();
- vector<string> gNamesOfGroups = groupMap->getNamesOfGroups();
- util->setGroups(Groups, gNamesOfGroups);
- groupMap->setNamesOfGroups(gNamesOfGroups);
- delete util;
-
- if (m->control_pressed) { delete groupMap; return 0; }
-
- //read through the list file keeping any otus that contain any sequence from the groups selected
- readListGroup();
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- if (outputNames.size() != 0) {
- m->mothurOutEndLine();
- m->mothurOut("Output File names: "); m->mothurOutEndLine();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-
- //set list file as new current listfile
- string current = "";
- itTypes = outputTypes.find("group");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
- }
-
- itTypes = outputTypes.find("list");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
- }
- }
-
- return 0;
- }
-
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int GetOtusCommand::readListGroup(){
- try {
- InputData* input = new InputData(listfile, "list");
- ListVector* list = input->getListVector();
- string lastLabel = list->getLabel();
-
- //using first label seen if none is provided
- if (label == "") { label = lastLabel; }
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- map<string, string> variables;
- variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
- variables["[tag]"] = label;
- variables["[extension]"] = m->getExtension(listfile);
- string outputFileName = getOutputFileName("list", variables);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- string GroupOutputDir = outputDir;
- if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); }
- variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
- variables["[extension]"] = m->getExtension(groupfile);
- string outputGroupFileName = getOutputFileName("group", variables);
-
- ofstream outGroup;
- m->openOutputFile(outputGroupFileName, outGroup);
-
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> labels; labels.insert(label);
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- bool wroteSomething = false;
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((list != NULL) && (userLabels.size() != 0)) {
-
- if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName);return 0; }
-
- if(labels.count(list->getLabel()) == 1){
- processList(list, groupMap, out, outGroup, wroteSomething);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- }
-
- if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = list->getLabel();
-
- delete list;
-
- list = input->getListVector(lastLabel);
-
- processList(list, groupMap, out, outGroup, wroteSomething);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
-
- //restore real lastlabel to save below
- list->setLabel(saveLabel);
- }
-
- lastLabel = list->getLabel();
-
- delete list; list = NULL;
-
- //get next line to process
- list = input->getListVector();
- }
-
-
- if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName); return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (list != NULL) { delete list; }
-
- list = input->getListVector(lastLabel);
-
- processList(list, groupMap, out, outGroup, wroteSomething);
-
- delete list; list = NULL;
- }
-
- out.close();
- outGroup.close();
-
- if (wroteSomething == false) { m->mothurOut("At distance " + label + " your file does NOT contain any otus containing sequences from the groups you wish to get."); m->mothurOutEndLine(); }
- outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
- outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName);
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "readList");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int GetOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream& out, ofstream& outGroup, bool& wroteSomething){
- try {
-
- //make a new list vector
- ListVector newList;
- newList.setLabel(list->getLabel());
-
- int numOtus = 0;
- //for each bin
- vector<string> binLabels = list->getLabels();
- vector<string> newBinLabels;
- for (int i = 0; i < list->getNumBins(); i++) {
- if (m->control_pressed) { return 0; }
-
- //parse out names that are in accnos file
- string binnames = list->get(i);
-
- bool keepBin = false;
- string groupFileOutput = "";
-
- //parse names
- string individual = "";
- int length = binnames.length();
- for(int j=0;j<length;j++){
- if(binnames[j] == ','){
- string group = groupMap->getGroup(individual);
- if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (m->inUsersGroups(group, Groups)) { keepBin = true; }
- groupFileOutput += individual + "\t" + group + "\n";
- individual = "";
-
- }
- else{ individual += binnames[j]; }
- }
-
- string group = groupMap->getGroup(individual);
- if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (m->inUsersGroups(group, Groups)) { keepBin = true; }
- groupFileOutput += individual + "\t" + group + "\n";
-
- //if there are sequences from the groups we want in this bin add to new list, output to groupfile
- if (keepBin) {
- newList.push_back(binnames);
- newBinLabels.push_back(binLabels[i]);
- outGroup << groupFileOutput;
- numOtus++;
- }
- }
-
- //print new listvector
- if (newList.getNumBins() != 0) {
- wroteSomething = true;
- newList.setLabels(newBinLabels);
- newList.printHeaders(out);
- newList.print(out);
- }
-
- m->mothurOut(newList.getLabel() + " - selected " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "GetOtusCommand", "processList");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
diff --git a/source/commands/getotuscommand.h b/source/commands/getotuscommand.h
deleted file mode 100644
index c71ab06..0000000
--- a/source/commands/getotuscommand.h
+++ /dev/null
@@ -1,55 +0,0 @@
-#ifndef GETOTUSCOMMAND_H
-#define GETOTUSCOMMAND_H
-
-/*
- * getotuscommand.h
- * Mothur
- *
- * Created by westcott on 11/10/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-
-
-#include "command.hpp"
-#include "groupmap.h"
-#include "listvector.hpp"
-
-class GetOtusCommand : public Command {
-
-public:
-
- GetOtusCommand(string);
- GetOtusCommand();
- ~GetOtusCommand(){}
-
- vector<string> setParameters();
- string getCommandName() { return "get.otus"; }
- string getCommandCategory() { return "OTU-Based Approaches"; }
-
- string getHelpString();
- string getOutputPattern(string);
- string getCitation() { return "http://www.mothur.org/wiki/Get.otus"; }
- string getDescription() { return "outputs a new list file containing the otus containing sequences from the groups specified"; }
-
-
- int execute();
- void help() { m->mothurOut(getHelpString()); }
-
-
-private:
- string accnosfile, groupfile, listfile, outputDir, groups, label;
- bool abort;
- vector<string> outputNames, Groups;
- GroupMap* groupMap;
-
- int readListGroup();
- int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
-
-};
-
-#endif
-
-
-
diff --git a/source/commands/getseqscommand.cpp b/source/commands/getseqscommand.cpp
index a1b1b75..53e43e1 100644
--- a/source/commands/getseqscommand.cpp
+++ b/source/commands/getseqscommand.cpp
@@ -968,7 +968,7 @@ int GetSeqsCommand::readGroup(){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; //read from first column
+ in >> name; m->gobble(in); //read from first column
in >> group; //read from second column
@@ -1031,8 +1031,8 @@ int GetSeqsCommand::readTax(){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; //read from first column
- in >> tax; //read from second column
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
@@ -1053,8 +1053,6 @@ int GetSeqsCommand::readTax(){
m->mothurOut("[WARNING]: " + name + " is in your taxonomy file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}
-
- m->gobble(in);
}
in.close();
out.close();
diff --git a/source/commands/listseqscommand.cpp b/source/commands/listseqscommand.cpp
index ac90705..b44995d 100644
--- a/source/commands/listseqscommand.cpp
+++ b/source/commands/listseqscommand.cpp
@@ -540,13 +540,10 @@ int ListSeqsCommand::readTax(){
if (m->control_pressed) { in.close(); return 0; }
- in >> firstCol;
- in >> secondCol;
+ in >> firstCol; m->gobble(in);
+ secondCol = m->getline(in); m->gobble(in);
names.push_back(firstCol);
-
- m->gobble(in);
-
}
in.close();
diff --git a/source/commands/makebiomcommand.cpp b/source/commands/makebiomcommand.cpp
index bb5d252..30f5c75 100644
--- a/source/commands/makebiomcommand.cpp
+++ b/source/commands/makebiomcommand.cpp
@@ -805,7 +805,9 @@ vector<string> MakeBiomCommand::getMetaData(vector<SharedRAbundVector*>& lookup)
if (m->control_pressed) { in.close(); return metadata; }
- in >> otuLabel >> size >> tax; m->gobble(in);
+ in >> otuLabel; m->gobble(in);
+ in >> size; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
otuLabels.push_back(otuLabel);
taxs.push_back(tax);
@@ -920,7 +922,9 @@ vector<string> MakeBiomCommand::getMetaData(vector<SharedRAbundFloatVector*>& lo
if (m->control_pressed) { in.close(); return metadata; }
- in >> otuLabel >> size >> tax; m->gobble(in);
+ in >> otuLabel; m->gobble(in);
+ in >> size; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
otuLabels.push_back(otuLabel);
taxs.push_back(tax);
diff --git a/source/commands/makecontigscommand.cpp b/source/commands/makecontigscommand.cpp
index 68f449e..858c5e8 100644
--- a/source/commands/makecontigscommand.cpp
+++ b/source/commands/makecontigscommand.cpp
@@ -2512,8 +2512,48 @@ int MakeContigsCommand::setNameType(string forward, string reverse) {
if (pos2 != string::npos) { tempReverse = reverse.substr(0, pos2); }
if (tempForward == tempReverse) { type = poundMatch; }
+ else {
+ char delim = ':';
+ if (m->changedSeqNames) { delim = '_'; }
+
+ int pos = forward.find_last_of(delim);
+ string tempForward = forward;
+ string tempForwardEnd = forward;
+ if (pos != string::npos) {
+ tempForwardEnd = forward.substr(pos+1);
+ }
+
+ int pos2 = reverse.find_last_of(delim);
+ string tempReverse = reverse;
+ string tempReverseEnd = reverse;
+ if (pos2 != string::npos) {
+ tempReverseEnd = reverse.substr(pos2+1);
+ }
+
+ if (tempForwardEnd == tempReverseEnd) {
+ if ((m->isAllAlphas(tempForwardEnd)) && (m->isAllAlphas(tempReverseEnd))) {
+ //check for off by one on rest of name
+ if (tempForward.length() == tempReverse.length()) {
+ int numDiffs = 0;
+ char forwardDiff = ' '; char reverseDiff = ' '; int spot = 0;
+ for (int i = 0; i < tempForward.length(); i++) {
+ if (tempForward[i] != tempReverse[i]) {
+ numDiffs++;
+ forwardDiff = tempForward[i];
+ reverseDiff = tempReverse[i];
+ spot = i;
+ }
+ }
+ if (numDiffs == 1) {
+ if ((forwardDiff == '1') && (reverseDiff == '2')) { type = offByOne; offByOneTrimLength = tempForward.length()-spot+1; }
+ }
+ //cout << tempReverse.substr(0, (tempReverse.length()-offByOneTrimLength)) << endl;
+ }
+ }
+ }
+ }
}
-
+
return type;
}
catch(exception& e) {
@@ -2981,10 +3021,10 @@ vector< vector<string> > MakeContigsCommand::readFileNames(string filename){
}
//look for mothur exe
- string mpath = m->argv;
- string tempPath = mpath;
- for (int i = 0; i < mpath.length(); i++) { tempPath[i] = tolower(mpath[i]); }
- mpath = mpath.substr(0, (tempPath.find_last_of('m')));
+ string mpath = m->mothurProgramPath;
+ //string tempPath = mpath;
+ //for (int i = 0; i < mpath.length(); i++) { tempPath[i] = tolower(mpath[i]); }
+ //mpath = mpath.substr(0, (tempPath.find_last_of('m')));
//check to make sure both are able to be opened
ifstream in2;
@@ -3355,7 +3395,11 @@ bool MakeContigsCommand::fixName(string& forward){
int pos = forward.find_last_of('#');
if (pos != string::npos) { forward = forward.substr(0, pos); }
}else if (nameType == perfectMatch) { match = true; }
-
+ else if (nameType == offByOne) {
+ match = true;
+ forward = forward.substr(0, (forward.length()-offByOneTrimLength));
+ }
+
return match;
}
catch(exception& e) {
@@ -3372,12 +3416,12 @@ bool MakeContigsCommand::checkName(FastqRead& forward, FastqRead& reverse){
try {
bool match = false;
+ string forwardName = forward.getName();
+ string reverseName = reverse.getName();
+
if (nameType == poundMatch) {
match = true;
-
- string forwardName = forward.getName();
- string reverseName = reverse.getName();
-
+
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -3391,7 +3435,23 @@ bool MakeContigsCommand::checkName(FastqRead& forward, FastqRead& reverse){
match = false;
}
- }else if (nameType == perfectMatch) { match = true; }
+ }else if (nameType == perfectMatch) {
+ if (forwardName == reverseName) { match = true; }
+ }
+ else if (nameType == offByOne) {
+
+ match = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ forward.setName(forwardName);
+ reverse.setName(reverseName);
+ }else{
+ match = false;
+ }
+ }
return match;
}
@@ -3407,12 +3467,12 @@ bool MakeContigsCommand::checkName(FastqRead& forward, FastqRead& reverse){
bool MakeContigsCommand::checkName(Sequence& forward, Sequence& reverse){
try {
bool match = false;
+ string forwardName = forward.getName();
+ string reverseName = reverse.getName();
if (nameType == poundMatch) {
match = true;
- string forwardName = forward.getName();
- string reverseName = reverse.getName();
-
+
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -3425,8 +3485,22 @@ bool MakeContigsCommand::checkName(Sequence& forward, Sequence& reverse){
}else{
match = false;
}
- }else if (nameType == perfectMatch) { match = true; }
-
+ }else if (nameType == perfectMatch) { if (forwardName == reverseName) { match = true; } }
+ else if (nameType == offByOne) {
+
+ match = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ forward.setName(forwardName);
+ reverse.setName(reverseName);
+ }else{
+ match = false;
+ }
+ }
+
return match;
}
catch(exception& e) {
@@ -3441,13 +3515,12 @@ bool MakeContigsCommand::checkName(Sequence& forward, Sequence& reverse){
bool MakeContigsCommand::checkName(QualityScores& forward, QualityScores& reverse){
try {
bool match = false;
-
+ string forwardName = forward.getName();
+ string reverseName = reverse.getName();
+
if (nameType == poundMatch) {
match = true;
- string forwardName = forward.getName();
- string reverseName = reverse.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -3461,7 +3534,22 @@ bool MakeContigsCommand::checkName(QualityScores& forward, QualityScores& revers
match = false;
}
- }else if (nameType == perfectMatch) { match = true; }
+ }else if (nameType == perfectMatch) { if (forwardName == reverseName) { match = true; } }
+ else if (nameType == offByOne) {
+
+ match = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ forward.setName(forwardName);
+ reverse.setName(reverseName);
+ }else{
+ match = false;
+ }
+ }
+
return match;
@@ -3479,6 +3567,8 @@ bool MakeContigsCommand::checkName(QualityScores& forward, QualityScores& revers
bool MakeContigsCommand::checkName(Sequence& forward, QualityScores& reverse){
try {
bool match = false;
+ string forwardName = forward.getName();
+ string reverseName = reverse.getName();
if (nameType == poundMatch) {
match = true;
@@ -3499,8 +3589,22 @@ bool MakeContigsCommand::checkName(Sequence& forward, QualityScores& reverse){
match = false;
}
- }else if (nameType == perfectMatch) { match = true; }
-
+ }else if (nameType == perfectMatch) { if (forwardName == reverseName) { match = true; } }
+ else if (nameType == offByOne) {
+
+ match = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ forward.setName(forwardName);
+ reverse.setName(reverseName);
+ }else{
+ match = false;
+ }
+ }
+
return match;
}
catch(exception& e) {
diff --git a/source/commands/makecontigscommand.h b/source/commands/makecontigscommand.h
index 146d25b..888b824 100644
--- a/source/commands/makecontigscommand.h
+++ b/source/commands/makecontigscommand.h
@@ -62,13 +62,14 @@ private:
#define perfectMatch 2
#define poundMatch 1
+#define offByOne 3
char delim;
bool abort, allFiles, trimOverlap, createFileGroup, createOligosGroup, makeCount, noneOk, reorient, gz, renameSeq;
string outputDir, ffastqfile, rfastqfile, align, oligosfile, rfastafile, ffastafile, rqualfile, fqualfile, findexfile, rindexfile, file, format, inputDir;
string outFastaFile, outQualFile, outScrapFastaFile, outScrapQualFile, outMisMatchFile, outputGroupFileName, group;
float match, misMatch, gapOpen, gapExtend;
- int processors, longestBase, insert, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, deltaq, kmerSize, numBarcodes, numFPrimers, numLinkers, numSpacers, numRPrimers, nameType;
+ int processors, longestBase, insert, tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, deltaq, kmerSize, numBarcodes, numFPrimers, numLinkers, numSpacers, numRPrimers, nameType, offByOneTrimLength;
vector<string> outputNames;
Oligos* oligos;
@@ -121,7 +122,7 @@ struct contigsData {
vector<vector<string> > fastaFileNames, qualFileNames;
MothurOut* m;
float match, misMatch, gapOpen, gapExtend;
- int count, insert, threadID, pdiffs, bdiffs, tdiffs, deltaq, kmerSize, nameType;
+ int count, insert, threadID, pdiffs, bdiffs, tdiffs, deltaq, kmerSize, nameType, offByOneTrimLength;
bool allFiles, createOligosGroup, createFileGroup, done, trimOverlap, reorient, gz, renameSeqs;
map<string, int> groupCounts;
map<string, string> groupMap;
@@ -277,6 +278,46 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pos2 != string::npos) { tempReverse = reverse.substr(0, pos2); }
if (tempForward == tempReverse) { type = poundMatch; }
+ else {
+ char delim = ':';
+ if (pDataArray->m->changedSeqNames) { delim = '_'; }
+
+ int pos = forward.find_last_of(delim);
+ string tempForward = forward;
+ string tempForwardEnd = forward;
+ if (pos != string::npos) {
+ tempForwardEnd = forward.substr(pos+1);
+ }
+
+ int pos2 = reverse.find_last_of(delim);
+ string tempReverse = reverse;
+ string tempReverseEnd = reverse;
+ if (pos2 != string::npos) {
+ tempReverseEnd = reverse.substr(pos2+1);
+ }
+
+ if (tempForwardEnd == tempReverseEnd) {
+ if ((pDataArray->m->isAllAlphas(tempForwardEnd)) && (pDataArray->m->isAllAlphas(tempReverseEnd))) {
+ //check for off by one on rest of name
+ if (tempForward.length() == tempReverse.length()) {
+ int numDiffs = 0;
+ char forwardDiff = ' '; char reverseDiff = ' '; int spot = 0;
+ for (int i = 0; i < tempForward.length(); i++) {
+ if (tempForward[i] != tempReverse[i]) {
+ numDiffs++;
+ forwardDiff = tempForward[i];
+ reverseDiff = tempReverse[i];
+ spot = i;
+ }
+ }
+ if (numDiffs == 1) {
+ if ((forwardDiff == '1') && (reverseDiff == '2')) { type = offByOne; pDataArray->offByOneTrimLength = tempForward.length()-spot+1; }
+ }
+ //cout << tempReverse.substr(0, (tempReverse.length()-offByOneTrimLength)) << endl;
+ }
+ }
+ }
+ }
}
pDataArray->nameType = type;
@@ -660,15 +701,15 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
FastqRead fread(inFFasta, tignore, pDataArray->format); pDataArray->m->gobble(inFFasta);
FastqRead rread(inRFasta, ignore, pDataArray->format); pDataArray->m->gobble(inRFasta);
+ string forwardName = fread.getName();
+ string reverseName = rread.getName();
+
///bool fixed = checkName(fread, rread);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
-
- string forwardName = fread.getName();
- string reverseName = rread.getName();
-
+
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -682,20 +723,33 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
+
/////////////////////////////////////////////////////////////
if (!fixed) {
FastqRead f2read(inFFasta, tignore, pDataArray->format); pDataArray->m->gobble(inFFasta);
+ string forwardName = f2read.getName();
+ string reverseName = rread.getName();
///bool fixed = checkName(f2read, rread);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
-
- string forwardName = f2read.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -709,20 +763,32 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ f2read.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) {
FastqRead r2read(inRFasta, ignore, pDataArray->format); pDataArray->m->gobble(inRFasta);
+
+ string forwardName = fread.getName();
+ string reverseName = r2read.getName();
///bool fixed = checkName(fread, r2read);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
-
- string forwardName = fread.getName();
- string reverseName = r2read.getName();
-
- int pos = forwardName.find_last_of('#');
+ int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
int pos2 = reverseName.find_last_of('#');
@@ -735,7 +801,20 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ r2read.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
else { rread = r2read; }
@@ -755,16 +834,16 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
FastqRead firead(inFQualIndex, tignore, pDataArray->format); pDataArray->m->gobble(inFQualIndex);
if (tignore) { ignore=true; }
findexBarcode.setAligned(firead.getSeq());
+
+ string forwardName = fread.getName();
+ string reverseName = firead.getName();
+
///bool fixed = checkName(fread, firead);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
-
- string forwardName = fread.getName();
- string reverseName = firead.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -778,19 +857,32 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ firead.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
FastqRead f2iread(inFQualIndex, tignore, pDataArray->format); pDataArray->m->gobble(inFQualIndex);
+ string forwardName = fread.getName();
+ string reverseName = f2iread.getName();
+
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
-
- string forwardName = fread.getName();
- string reverseName = f2iread.getName();
-
+
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -804,7 +896,20 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ f2iread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
pDataArray->m->mothurOut("[WARNING]: name mismatch in forward index file. Ignoring, " + fread.getName() + ".\n"); ignore = true;
@@ -813,6 +918,10 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}
if (thisrqualindexfile != "") { //reverse index file
FastqRead riread(inRQualIndex, tignore, pDataArray->format); pDataArray->m->gobble(inRQualIndex);
+
+ string forwardName = fread.getName();
+ string reverseName = riread.getName();
+
if (tignore) { ignore=true; }
rindexBarcode.setAligned(riread.getSeq());
///bool fixed = checkName(fread, riread);
@@ -822,9 +931,6 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = poundMatch;
//we know the location of the # matches in the forward and reverse
- string forwardName = fread.getName();
- string reverseName = riread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -838,19 +944,30 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ riread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
FastqRead r2iread(inRQualIndex, tignore, pDataArray->format); pDataArray->m->gobble(inRQualIndex);
+
+ string forwardName = fread.getName();
+ string reverseName = r2iread.getName();
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
-
- string forwardName = fread.getName();
- string reverseName = r2iread.getName();
-
+
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -864,7 +981,20 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ r2iread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
pDataArray->m->mothurOut("[WARNING]: name mismatch in reverse index file. Ignoring, " + fread.getName() + ".\n"); ignore = true;
@@ -875,16 +1005,14 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else { //reading fasta and maybe qual
Sequence fread(inFFasta); pDataArray->m->gobble(inFFasta);
Sequence rread(inRFasta); pDataArray->m->gobble(inRFasta);
+ string forwardName = fread.getName();
+ string reverseName = rread.getName();
///bool fixed = checkName(fread, rread);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
- string forwardName = fread.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -898,20 +1026,30 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
Sequence f2read(inFFasta); pDataArray->m->gobble(inFFasta);
+ string forwardName = f2read.getName();
+ string reverseName = rread.getName();
///bool fixed = checkName(f2read, rread);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
-
- string forwardName = f2read.getName();
- string reverseName = rread.getName();
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -926,20 +1064,30 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ f2read.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) {
Sequence r2read(inRFasta); pDataArray->m->gobble(inRFasta);
+ string forwardName = fread.getName();
+ string reverseName = r2read.getName();
///bool fixed = checkName(fread, r2read);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- //we know the location of the # matches in the forward and reverse
-
- string forwardName = fread.getName();
- string reverseName = r2read.getName();
-
+
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -953,8 +1101,20 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ r2read.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
else { rread = r2read; }
@@ -969,6 +1129,10 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (thisfqualindexfile != "") {
fQual = new QualityScores(inFQualIndex); pDataArray->m->gobble(inFQualIndex);
rQual = new QualityScores(inRQualIndex); pDataArray->m->gobble(inRQualIndex);
+
+ string forwardName = fread.getName();
+ string reverseName = rread.getName();
+
if (fQual->getName() != rQual->getName()) {
///bool fixed = checkName(fread, rread);
//////////////////////////////////////////////////////////////
@@ -976,9 +1140,6 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -992,8 +1153,20 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse qfile file. Ignoring, " + fQual->getName() + ".\n"); ignore = true; }
@@ -1013,15 +1186,15 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
FastqRead fread(inFF, tignore, pDataArray->format);
FastqRead rread(inRF, ignore, pDataArray->format);
+ string forwardName = fread.getName();
+ string reverseName = rread.getName();
+
///bool fixed = checkName(fread, rread);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1035,20 +1208,30 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
FastqRead f2read(inFF, tignore, pDataArray->format);
+ string forwardName = f2read.getName();
+ string reverseName = rread.getName();
///bool fixed = checkName(f2read, rread);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
-
- string forwardName = f2read.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1062,19 +1245,31 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ f2read.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) {
FastqRead r2read(inRF, ignore, pDataArray->format);
+
+ string forwardName = fread.getName();
+ string reverseName = r2read.getName();
+
///bool fixed = checkName(fread, r2read);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
-
- string forwardName = fread.getName();
- string reverseName = r2read.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1088,8 +1283,20 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ r2read.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
else { rread = r2read; }
@@ -1109,15 +1316,15 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
FastqRead firead(inFQ, tignore, pDataArray->format);
if (tignore) { ignore=true; }
findexBarcode.setAligned(firead.getSeq());
+ string forwardName = fread.getName();
+ string reverseName = firead.getName();
+
///bool fixed = checkName(fread, firead);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = firead.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1131,16 +1338,28 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ firead.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
FastqRead f2iread(inFQ, tignore, pDataArray->format);
+ string forwardName = fread.getName();
+ string reverseName = f2iread.getName();
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = f2iread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1154,7 +1373,20 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ f2iread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
pDataArray->m->mothurOut("[WARNING]: name mismatch in forward index file. Ignoring, " + fread.getName() + ".\n"); ignore = true;
@@ -1165,15 +1397,14 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
FastqRead riread(inRQ, tignore, pDataArray->format);
if (tignore) { ignore=true; }
rindexBarcode.setAligned(riread.getSeq());
+ string forwardName = fread.getName();
+ string reverseName = riread.getName();
///bool fixed = checkName(fread, riread);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = riread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1187,16 +1418,30 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ riread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
FastqRead r2iread(inRQ, tignore, pDataArray->format);
+
+ string forwardName = fread.getName();
+ string reverseName = r2iread.getName();
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
-
- string forwardName = fread.getName();
- string reverseName = r2iread.getName();
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1211,8 +1456,21 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ r2iread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
pDataArray->m->mothurOut("[WARNING]: name mismatch in forward index file. Ignoring, " + fread.getName() + ".\n"); ignore = true;
@@ -1223,15 +1481,15 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
}else { //reading fasta and maybe qual
Sequence tfSeq(inFF);
Sequence trSeq(inRF);
+ string forwardName = fread.getName();
+ string reverseName = rread.getName();
+
///bool fixed = checkName(fread, rread);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1245,19 +1503,32 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
Sequence tf2Seq(inFF);
+ string forwardName = f2read.getName();
+ string reverseName = rread.getName();
///bool fixed = checkName(f2read, rread);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
-
- string forwardName = f2read.getName();
- string reverseName = rread.getName();
-
+
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1271,19 +1542,32 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ f2read.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) {
Sequence tr2Seq(inRF);
+ string forwardName = fread.getName();
+ string reverseName = r2read.getName();
+
+
///bool fixed = checkName(fread, r2read);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = r2read.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1297,8 +1581,20 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ r2read.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + tfSeq.getName() + ".\n"); ignore = true; }
else { trSeq = tr2Seq; }
@@ -1313,6 +1609,9 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (thisfqualindexfile != "") {
fQual = new QualityScores(inFQ);
rQual = new QualityScores(inRQ);
+
+ string forwardName = fread.getName();
+ string reverseName = rread.getName();
if (fQual->getName() != rQual->getName()) {
///bool fixed = checkName(fread, rread);
//////////////////////////////////////////////////////////////
@@ -1320,8 +1619,6 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = rread.getName();
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -1336,8 +1633,21 @@ static DWORD WINAPI MyGroupContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse qfile file. Ignoring, " + fQual->getName() + ".\n"); ignore = true; }
@@ -2204,14 +2514,14 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
FastqRead fread(inFFasta, tignore, pDataArray->format); pDataArray->m->gobble(inFFasta);
FastqRead rread(inRFasta, ignore, pDataArray->format); pDataArray->m->gobble(inRFasta);
+ string forwardName = fread.getName();
+ string reverseName = rread.getName();
///bool fixed = checkName(fread, rread);
bool fixed = false;
//////////////////////////////////////////////////////////////
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = rread.getName();
-
+
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2225,19 +2535,31 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
FastqRead f2read(inFFasta, tignore, pDataArray->format); pDataArray->m->gobble(inFFasta);
- ///bool fixed = checkName(f2read, rread);
+
+ string forwardName = f2read.getName();
+ string reverseName = rread.getName();
+ ///bool fixed = checkName(f2read, rread);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
-
- string forwardName = f2read.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2251,18 +2573,32 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ f2read.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) {
FastqRead r2read(inRFasta, ignore, pDataArray->format); pDataArray->m->gobble(inRFasta);
+
+ string forwardName = fread.getName();
+ string reverseName = r2read.getName();
///bool fixed = checkName(fread, r2read);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = r2read.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2276,8 +2612,20 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ r2read.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
else { rread = r2read; }
@@ -2297,15 +2645,16 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
FastqRead firead(inFQualIndex, tignore, pDataArray->format); pDataArray->m->gobble(inFQualIndex);
if (tignore) { ignore=true; }
findexBarcode.setAligned(firead.getSeq());
+
+ string forwardName = fread.getName();
+ string reverseName = firead.getName();
+
///bool fixed = checkName(fread, firead);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = firead.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2319,19 +2668,34 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ firead.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
FastqRead f2iread(inFQualIndex, tignore, pDataArray->format); pDataArray->m->gobble(inFQualIndex);
+
+ string forwardName = fread.getName();
+ string reverseName = f2iread.getName();
+
if (tignore) { ignore=true; }
///bool fixed = checkName(fread, f2iread);
/////////////////////////////////////////////////////////////
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = f2iread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2345,7 +2709,21 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ f2iread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
pDataArray->m->mothurOut("[WARNING]: name mismatch in forward index file. Ignoring, " + fread.getName() + ".\n"); ignore = true;
@@ -2357,15 +2735,16 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
FastqRead riread(inRQualIndex, tignore, pDataArray->format); pDataArray->m->gobble(inRQualIndex);
if (tignore) { ignore=true; }
rindexBarcode.setAligned(riread.getSeq());
+
+ string forwardName = fread.getName();
+ string reverseName = riread.getName();
+
///bool fixed = checkName(fread, riread);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = riread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2379,20 +2758,33 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ riread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
FastqRead r2iread(inRQualIndex, tignore, pDataArray->format); pDataArray->m->gobble(inRQualIndex);
+
+ string forwardName = fread.getName();
+ string reverseName = r2iread.getName();
+
///bool fixed = checkName(fread, r2iread);
/////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = r2iread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2406,7 +2798,21 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ r2iread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
pDataArray->m->mothurOut("[WARNING]: name mismatch in reverse index file. Ignoring, " + fread.getName() + ".\n"); ignore = true;
@@ -2418,15 +2824,16 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
}else { //reading fasta and maybe qual
Sequence fread(inFFasta); pDataArray->m->gobble(inFFasta);
Sequence rread(inRFasta); pDataArray->m->gobble(inRFasta);
+ string forwardName = fread.getName();
+ string reverseName = rread.getName();
+
+
///bool fixed = checkName(fread, rread);
//////////////////////////////////////////////////////////////
bool fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2440,19 +2847,33 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
Sequence f2read(inFFasta); pDataArray->m->gobble(inFFasta);
+
+ string forwardName = f2read.getName();
+ string reverseName = rread.getName();
+
///bool fixed = checkName(f2read, rread);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = f2read.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2466,19 +2887,32 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ f2read.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) {
Sequence r2read(inRFasta); pDataArray->m->gobble(inRFasta);
+
+ string forwardName = fread.getName();
+ string reverseName = r2read.getName();
///bool fixed = checkName(fread, r2read);
//////////////////////////////////////////////////////////////
fixed = false;
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = r2read.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2492,8 +2926,21 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
-
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ r2read.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
if (!fixed) { pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse fastq file. Ignoring, " + fread.getName() + ".\n"); ignore = true; }
else { rread = r2read; }
@@ -2508,6 +2955,9 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
if (thisfqualindexfile != "") {
fQual = new QualityScores(inFQualIndex); pDataArray->m->gobble(inFQualIndex);
rQual = new QualityScores(inRQualIndex); pDataArray->m->gobble(inRQualIndex);
+
+ string forwardName = fread.getName();
+ string reverseName = rread.getName();
if (fQual->getName() != rQual->getName()) {
///bool fixed = checkName(fread, rread);
//////////////////////////////////////////////////////////////
@@ -2515,9 +2965,6 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
if (pDataArray->nameType == poundMatch) {
fixed = poundMatch;
- string forwardName = fread.getName();
- string reverseName = rread.getName();
-
int pos = forwardName.find_last_of('#');
if (pos != string::npos) { forwardName = forwardName.substr(0, pos); }
@@ -2531,7 +2978,20 @@ static DWORD WINAPI MyContigsThreadFunction(LPVOID lpParam){
fixed = false;
}
- }else if (pDataArray->nameType == perfectMatch) { fixed = true; }
+ }else if (pDataArray->nameType == perfectMatch) { if (forwardName == reverseName) { fixed = true; } }
+ else if (pDataArray->nameType == offByOne) {
+
+ fixed = true;
+ reverseName = reverseName.substr(0, (reverseName.length()-pDataArray->offByOneTrimLength));
+ forwardName = forwardName.substr(0, (forwardName.length()-pDataArray->offByOneTrimLength));
+
+ if (forwardName == reverseName) {
+ fread.setName(forwardName);
+ rread.setName(reverseName);
+ }else{
+ fixed = false;
+ }
+ }
/////////////////////////////////////////////////////////////
if (!fixed) {
pDataArray->m->mothurOut("[WARNING]: name mismatch in forward and reverse qfile file. Ignoring, " + fQual->getName() + ".\n"); ignore = true; }
diff --git a/source/commands/makefilecommand.cpp b/source/commands/makefilecommand.cpp
index 92f580f..591e8f8 100644
--- a/source/commands/makefilecommand.cpp
+++ b/source/commands/makefilecommand.cpp
@@ -145,9 +145,7 @@ int MakeFileCommand::execute(){
//find all .fastq files
string tempFile = inputDir + "fileList.temp";
- string findCommand = "find \"" + inputDir.substr(0, inputDir.length()-1) + "\" -maxdepth 1 -name \"*." + typeFile + "\" > \"" + tempFile + "\"";
- if (m->debug) { m->mothurOut(findCommand + "\n"); }
- system(findCommand.c_str());
+ fillAccnosFile(tempFile);
//read in list of files
vector<string> fastqFiles;
@@ -162,6 +160,7 @@ int MakeFileCommand::execute(){
vector< vector<string> > paired;
vector<string> singles;
+ set<string> groups;
string lastFile = "";
for (int i = 0; i < fastqFiles.size()-1; i++) {
@@ -182,13 +181,6 @@ int MakeFileCommand::execute(){
if (numDiffs > 1) { singles.push_back(fastqFiles[i]); lastFile = fastqFiles[i]; }
else { //only one diff = paired files
vector<string> temp;
- if (numCols == 3) {
- string groupName = "noGroup"+toString(i);
- int posUnderscore = fastqFiles[i].find_first_of('_');
- if (posUnderscore == string::npos) { groupName = m->getSimpleName(m->getRootName(fastqFiles[i])); }
- else{ groupName = m->getSimpleName(fastqFiles[i].substr(0, posUnderscore)); }
- temp.push_back(groupName);
- }
temp.push_back(fastqFiles[i]); temp.push_back(fastqFiles[i+1]); lastFile = fastqFiles[i+1];
paired.push_back(temp);
i++;
@@ -215,6 +207,9 @@ int MakeFileCommand::execute(){
out.close();
}
+ //generates unique group names
+ if (numCols == 3) { paired = findGroupNames(paired); }
+
if (paired.size() != 0) {
map<string, string> variables;
variables["[filename]"] = outputDir + prefix + ".";
@@ -250,5 +245,119 @@ int MakeFileCommand::execute(){
}
}
//**********************************************************************************************************************
+//groupName defaults to "noGroup"+toString(i);
+vector< vector<string> > MakeFileCommand::findGroupNames(vector< vector<string> > paired){
+ try {
+
+ //remove any "words" in filenames that is the same in all filenames separated by delim(_ .)
+ //MI.M00833_0261.001.FLD0207.TRIN-META_16S_R2.fastq
+ //MI.M00833_0261.001.FLD0223.ERIFF-META_16S_R2.fastq
+ //would become...
+ //FLD0207.TRIN-META
+ //FLD0223.ERIFF-META
+
+ //split all forward names into pieces
+ vector<vector<string> > words; words.resize(paired.size());
+ map<int, set<string> > posToWord;
+
+ for (int i = 0; i < paired.size(); i++) {
+ if (m->control_pressed) { break; }
+
+ string filename = m->getRootName(m->getSimpleName(paired[i][0]));
+
+ int pos = 0;
+ string individual = "";
+ for(int j=0;j<filename.length();j++){
+ if((filename[j] == '.') || (filename[j] == '_')){
+ words[i].push_back(individual);
+
+ map<int, set<string> >::iterator it = posToWord.find(pos);
+ if (it != posToWord.end()) { posToWord[pos].insert(individual); }
+ else {
+ set<string> temp; temp.insert(individual);
+ posToWord[pos] = temp;
+ }
+ individual = "";
+ pos++;
+ }
+ else{
+ individual += filename[j];
+ }
+ }
+ if (!m->allSpaces(individual)) {
+ words[i].push_back(individual);
+ map<int, set<string> >::iterator it = posToWord.find(pos);
+ if (it != posToWord.end()) { posToWord[pos].insert(individual); }
+ else {
+ set<string> temp; temp.insert(individual);
+ posToWord[pos] = temp;
+ }
+ }
+ }
+
+ //remove duplicate pieces
+ set<int> goodIndexes;
+ for (map<int, set<string> >::iterator it = posToWord.begin(); it != posToWord.end(); it++) {
+ set<string> w = it->second;;
+ if (w.size() != 1) { goodIndexes.insert(it->first); }
+ }
+
+ set<string> groups;
+ vector< vector<string> > results; results.resize(paired.size());
+ for (int i = 0; i < words.size(); i++) {
+
+ //assemble groupNames
+ string groupName = "";
+ for (int j = 0; j < words[i].size(); j++) {
+ //include word
+ if (goodIndexes.count(j) != 0) { groupName += words[i][j] + "_"; }
+ }
+
+ if (groupName != "") { groupName = groupName.substr(0, groupName.length()-1); }
+
+ //is this name unique
+ if (groups.count(groupName) == 0) { groups.insert(groupName); }
+ else { groupName = "Group_"+ toString(i); groups.insert(groupName); }
+
+ results[i].push_back(groupName); results[i].push_back(paired[i][0]); results[i].push_back(paired[i][1]);
+ }
+
+ return results;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeFileCommand", "findGroupName");
+ exit(1);
+ }
+}
+
+//**********************************************************************************************************************
+
+int MakeFileCommand::fillAccnosFile(string tempFile){
+ try {
+
+ string findCommand = "";
+ tempFile = "\"" + tempFile + "\"";
+
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+
+ findCommand = "find \"" + inputDir.substr(0, inputDir.length()-1) + "\" -maxdepth 1 -name \"*." + typeFile + "\" > " + tempFile;
+ if (m->debug) { m->mothurOut(findCommand + "\n"); }
+ system(findCommand.c_str());
+#else
+ //use ls command
+
+ findCommand = "ls *." + typeFile + " > " + tempFile;
+ if (m->debug) { m->mothurOut(findCommand + "\n"); }
+ system(findCommand.c_str());
+#endif
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "MakeFileCommand", "fillAccnosFile");
+ exit(1);
+ }
+}
+//**********************************************************************************************************************
diff --git a/source/commands/makefilecommand.h b/source/commands/makefilecommand.h
index eb6a7bf..fcdd2a6 100644
--- a/source/commands/makefilecommand.h
+++ b/source/commands/makefilecommand.h
@@ -36,6 +36,9 @@ private:
vector<string> outputNames;
int numCols;
bool abort;
+
+ vector< vector<string> > findGroupNames(vector< vector<string> > paired);
+ int fillAccnosFile(string tempFile);
};
diff --git a/source/commands/mergetaxsummarycommand.cpp b/source/commands/mergetaxsummarycommand.cpp
index bb2b5ed..5e0841d 100644
--- a/source/commands/mergetaxsummarycommand.cpp
+++ b/source/commands/mergetaxsummarycommand.cpp
@@ -186,14 +186,30 @@ int MergeTaxSummaryCommand::execute(){
int level, daugterLevels, total;
float totalFloat;
- string rankId, tax;
+ string rankId, tax; tax = "";
map<int, int> levelToCurrentNode;
levelToCurrentNode[0] = 0;
while (!in.eof()) {
if (m->control_pressed) { return 0; }
- in >> level >> rankId >> tax >> daugterLevels >> totalFloat; m->gobble(in);
+ in >> level >> rankId; m->gobble(in);
+ string rest = m->getline(in); m->gobble(in);
+ vector<string> pieces = m->splitWhiteSpaceWithQuotes(rest);
+
+ map<string, int> groupCounts;
+ int pcount = pieces.size()-1;
+ if (thisFilesGroups.size() != 0) {
+ for (int j = thisFilesGroups.size()-1; j >= 0; j--) {
+ int tempNum;
+ m->mothurConvert(pieces[pcount], tempNum);
+ groupCounts[thisFilesGroups[j]] = tempNum;
+ pcount--;
+ }
+ }
+
+ //column 5
+ m->mothurConvert(pieces[pcount], totalFloat); pcount--;
if ((totalFloat < 1) && (totalFloat > 0)) {
m->mothurOut("[ERROR]: cannot merge tax.summary files with relative abundances.\n"); m->control_pressed = true; in.close(); return 0;
@@ -201,19 +217,18 @@ int MergeTaxSummaryCommand::execute(){
total = int(totalFloat);
}
- map<string, int> groupCounts;
- if (thisFilesGroups.size() != 0) {
- for (int j = 0; j < thisFilesGroups.size(); j++) {
- int tempNum; in >> tempNum; m->gobble(in);
- groupCounts[thisFilesGroups[j]] = tempNum;
- }
- }
+ //column 4
+ m->mothurConvert(pieces[pcount], daugterLevels);
+
+ //assemble tax - this is done in case taxonomy contains spaces
+ tax = "";
+ for (int k = 0; k < pcount; k++) { tax += pieces[k] + " "; }
if (level == 0) {}
else {
map<int, int>::iterator itParent = levelToCurrentNode.find(level-1);
int parent = 0;
- if (itParent == levelToCurrentNode.end()) { m->mothurOut("[ERROR]: situation I didnt expect.\n"); }
+ if (itParent == levelToCurrentNode.end()) { m->mothurOut("[ERROR]: situation I didn't expect.\n"); }
else { parent = itParent->second; }
levelToCurrentNode[level] = addTaxToTree(tree, level, parent, tax, total, groupCounts);
diff --git a/source/commands/mgclustercommand.cpp b/source/commands/mgclustercommand.cpp
index bd2a472..7ad4dcb 100644
--- a/source/commands/mgclustercommand.cpp
+++ b/source/commands/mgclustercommand.cpp
@@ -20,7 +20,6 @@ vector<string> MGClusterCommand::setParameters(){
CommandParameter pcutoff("cutoff", "Number", "", "0.70", "", "", "","",false,false,true); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
CommandParameter pmethod("method", "Multiple", "furthest-nearest-average", "average", "", "", "","",false,false); parameters.push_back(pmethod);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
CommandParameter pmin("min", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmin);
CommandParameter pmerge("merge", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmerge);
CommandParameter padjust("adjust", "String", "", "F", "", "", "","",false,false); parameters.push_back(padjust);
@@ -42,7 +41,7 @@ vector<string> MGClusterCommand::setParameters(){
string MGClusterCommand::getHelpString(){
try {
string helpString = "";
- helpString += "The mgcluster command parameter options are blast, name, cutoff, precision, hard, method, merge, min, length, penalty and adjust. The blast parameter is required.\n";
+ helpString += "The mgcluster command parameter options are blast, name, cutoff, precision, method, merge, min, length, penalty and adjust. The blast parameter is required.\n";
helpString += "The mgcluster command reads a blast and name file and clusters the sequences into OPF units similar to the OTUs.\n";
helpString += "This command outputs a .list, .rabund and .sabund file that can be used with mothur other commands to estimate richness.\n";
helpString += "The cutoff parameter is used to specify the maximum distance you would like to cluster to. The default is 0.70.\n";
@@ -190,8 +189,7 @@ MGClusterCommand::MGClusterCommand(string option) {
temp = validParameter.validFile(parameters, "cutoff", false);
if (temp == "not found") { temp = "0.70"; }
else { cutoffSet = true; }
- m->mothurConvert(temp, cutoff);
- cutoff += (5 / (precision * 10.0));
+ m->mothurConvert(temp, cutoff);
method = validParameter.validFile(parameters, "method", false);
if (method == "not found") { method = "average"; }
@@ -210,9 +208,6 @@ MGClusterCommand::MGClusterCommand(string option) {
temp = validParameter.validFile(parameters, "merge", false); if (temp == "not found") { temp = "true"; }
merge = m->isTrue(temp);
-
- temp = validParameter.validFile(parameters, "hard", false); if (temp == "not found") { temp = "T"; }
- hard = m->isTrue(temp);
temp = validParameter.validFile(parameters, "adjust", false); if (temp == "not found") { if (cutoffSet) { temp = "F"; }else { temp="T"; } }
if (m->isNumeric1(temp)) { m->mothurConvert(temp, adjust); }
@@ -342,12 +337,7 @@ int MGClusterCommand::execute(){
}
float dist = distMatrix->getSmallDist();
- float rndDist;
- if (hard) {
- rndDist = m->ceilDist(dist, precision);
- }else{
- rndDist = m->roundDist(dist, precision);
- }
+ float rndDist = m->ceilDist(dist, precision);
if(previousDist <= 0.0000 && dist != previousDist){
oldList.setLabel("unique");
@@ -433,9 +423,7 @@ int MGClusterCommand::execute(){
m->mothurOutEndLine();
if (saveCutoff != cutoff) {
- if (hard) { saveCutoff = m->ceilDist(saveCutoff, precision); }
- else { saveCutoff = m->roundDist(saveCutoff, precision); }
-
+ saveCutoff = m->ceilDist(saveCutoff, precision);
m->mothurOut("changed cutoff to " + toString(cutoff)); m->mothurOutEndLine();
}
diff --git a/source/commands/mgclustercommand.h b/source/commands/mgclustercommand.h
index d477143..55ad90a 100644
--- a/source/commands/mgclustercommand.h
+++ b/source/commands/mgclustercommand.h
@@ -56,7 +56,7 @@ private:
double cutoff;
float penalty, adjust;
int precision, length, precisionLength;
- bool abort, minWanted, hclusterWanted, merge, hard, cutoffSet;
+ bool abort, minWanted, hclusterWanted, merge, cutoffSet;
void printData(ListVector*, map<string, int>&);
ListVector* mergeOPFs(map<string, int>, float);
diff --git a/source/commands/pcrseqscommand.cpp b/source/commands/pcrseqscommand.cpp
index 0bb15bd..44abbcc 100644
--- a/source/commands/pcrseqscommand.cpp
+++ b/source/commands/pcrseqscommand.cpp
@@ -1211,8 +1211,8 @@ int PcrSeqsCommand::readTax(set<string> names){
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; //read from first column
- in >> tax; //read from second column
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
//if this name is in the accnos file
if (names.count(name) == 0) {
@@ -1220,8 +1220,7 @@ int PcrSeqsCommand::readTax(set<string> names){
out << name << '\t' << tax << endl;
}else { removedCount++; }
- m->gobble(in);
- }
+ }
in.close();
out.close();
diff --git a/source/commands/phylotypecommand.cpp b/source/commands/phylotypecommand.cpp
index 4ffcc42..7666b9c 100644
--- a/source/commands/phylotypecommand.cpp
+++ b/source/commands/phylotypecommand.cpp
@@ -161,7 +161,7 @@ PhylotypeCommand::PhylotypeCommand(string option) {
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { namefile = ""; abort = true; }
else if (namefile == "not found") { namefile = ""; }
- else { readNamesFile(); m->setNameFile(namefile); }
+ else { m->readNames(namefile, namemap); m->setNameFile(namefile); }
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { abort = true; countfile = ""; }
@@ -384,32 +384,4 @@ int PhylotypeCommand::execute(){
exit(1);
}
}
-/*****************************************************************/
-int PhylotypeCommand::readNamesFile() {
- try {
-
- ifstream in;
- m->openInputFile(namefile, in);
-
- string first, second;
- map<string, string>::iterator itNames;
-
- while(!in.eof()) {
- in >> first >> second; m->gobble(in);
-
- itNames = namemap.find(first);
- if (itNames == namemap.end()) {
- namemap[first] = second;
- }else { m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); namemap.clear(); namefile = ""; return 1; }
- }
- in.close();
-
- return 0;
- }
- catch(exception& e) {
- m->errorOut(e, "PhylotypeCommand", "readNamesFile");
- exit(1);
- }
-}
-
/**********************************************************************************************************************/
diff --git a/source/commands/phylotypecommand.h b/source/commands/phylotypecommand.h
index ef8b8f1..0d4e088 100644
--- a/source/commands/phylotypecommand.h
+++ b/source/commands/phylotypecommand.h
@@ -47,8 +47,6 @@ private:
map<int, int> parentNodes;
map<int, int>::iterator itCurrent;
- int readNamesFile();
-
};
diff --git a/source/commands/preclustercommand.cpp b/source/commands/preclustercommand.cpp
index b8ad077..0f17144 100644
--- a/source/commands/preclustercommand.cpp
+++ b/source/commands/preclustercommand.cpp
@@ -10,6 +10,7 @@
#include "preclustercommand.h"
#include "deconvolutecommand.h"
+
//**********************************************************************************************************************
vector<string> PreClusterCommand::setParameters(){
try {
@@ -298,25 +299,11 @@ int PreClusterCommand::execute(){
ofstream outNames; m->openOutputFile(newNamesFile, outNames); outNames.close();
newMapFile = fileroot + "precluster.";
- //parse fasta and name file by group
- vector<string> groups;
- if (countfile != "") {
- cparser = new SequenceCountParser(countfile, fastafile);
- groups = cparser->getNamesOfGroups();
- }else {
- if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile); }
- else { parser = new SequenceParser(groupfile, fastafile); }
- groups = parser->getNamesOfGroups();
- }
-
- if(processors == 1) { driverGroups(newFastaFile, newNamesFile, newMapFile, 0, groups.size(), groups); }
- else { createProcessesGroups(newFastaFile, newNamesFile, newMapFile, groups); }
+ createProcessesGroups(newFastaFile, newNamesFile, newMapFile);
if (countfile != "") {
mergeGroupCounts(newCountFile, newNamesFile, newFastaFile);
- delete cparser;
- }else {
- delete parser;
+ }else {
//run unique.seqs for deconvolute results
string inputString = "fasta=" + newFastaFile;
if (namefile != "") { inputString += ", name=" + newNamesFile; }
@@ -342,7 +329,6 @@ int PreClusterCommand::execute(){
}else {
if (processors != 1) { m->mothurOut("When using running without group information mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; }
- if (namefile != "") { readNameFile(); }
//reads fasta file and return number of seqs
int numSeqs = readFASTA(); //fills alignSeqs and makes all seqs active
@@ -400,7 +386,7 @@ int PreClusterCommand::execute(){
}
}
/**************************************************************************************************/
-int PreClusterCommand::createProcessesGroups(string newFName, string newNName, string newMFile, vector<string> groups) {
+int PreClusterCommand::createProcessesGroups(string newFName, string newNName, string newMFile) {
try {
vector<int> processIDS;
@@ -408,6 +394,11 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s
int num = 0;
bool recalc = false;
+ //parse fasta and name file by group
+ vector<string> groups;
+ if (countfile != "") { CountTable ct; ct.testGroups(countfile, groups); }
+ else { GroupMap gp; gp.readMap(groupfile); groups = gp.getNamesOfGroups(); }
+
//sanity check
if (groups.size() < processors) { processors = groups.size(); }
@@ -603,7 +594,17 @@ int PreClusterCommand::createProcessesGroups(string newFName, string newNName, s
/**************************************************************************************************/
int PreClusterCommand::driverGroups(string newFFile, string newNFile, string newMFile, int start, int end, vector<string> groups){
try {
-
+ vector<string> subsetGroups;
+ for (int i = start; i < end; i++) { subsetGroups.push_back(groups[i]); }
+
+ //parse fasta and name file by group
+ if (countfile != "") {
+ cparser = new SequenceCountParser(countfile, fastafile, subsetGroups);
+ }else {
+ if (namefile != "") { parser = new SequenceParser(groupfile, fastafile, namefile, subsetGroups); }
+ else { parser = new SequenceParser(groupfile, fastafile, subsetGroups); }
+ }
+
int numSeqs = 0;
//precluster each group
@@ -611,7 +612,7 @@ int PreClusterCommand::driverGroups(string newFFile, string newNFile, string new
start = time(NULL);
- if (m->control_pressed) { return 0; }
+ if (m->control_pressed) { if (countfile != "") { delete cparser; }else { delete parser; } return 0; }
m->mothurOutEndLine(); m->mothurOut("Processing group " + groups[i] + ":"); m->mothurOutEndLine();
@@ -640,10 +641,11 @@ int PreClusterCommand::driverGroups(string newFFile, string newNFile, string new
m->mothurOut("pre.cluster removed " + toString(count) + " sequences."); m->mothurOutEndLine(); m->mothurOutEndLine();
printData(newFFile, newNFile, groups[i]);
- m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
-
+ m->mothurOut("It took " + toString(time(NULL) - start) + " secs to cluster " + toString(numSeqs) + " sequences."); m->mothurOutEndLine();
}
+ if (countfile != "") { delete cparser; }else { delete parser; }
+
return numSeqs;
}
catch(exception& e) {
@@ -679,7 +681,9 @@ int PreClusterCommand::process(string newMapFile){
if (alignSeqs[j].active) { //this sequence has not been merged yet
//are you within "diff" bases
- int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
+ int mismatch = length;
+ if (method == "unaligned") { mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned()); }
+ else { mismatch = calcMisMatches(alignSeqs[i].filteredSeq, alignSeqs[j].filteredSeq); }
if (mismatch <= diffs) {
//merge
@@ -720,7 +724,9 @@ int PreClusterCommand::process(string newMapFile){
if (originalCount[j] > originalCount[i]) { //this sequence is more abundant than I am
//are you within "diff" bases
- int mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned());
+ int mismatch = length;
+ if (method == "unaligned") { mismatch = calcMisMatches(alignSeqs[i].seq.getAligned(), alignSeqs[j].seq.getAligned()); }
+ else { mismatch = calcMisMatches(alignSeqs[i].filteredSeq, alignSeqs[j].filteredSeq); }
if (mismatch <= diffs) {
//merge
@@ -762,7 +768,10 @@ int PreClusterCommand::process(string newMapFile){
/**************************************************************************************************/
int PreClusterCommand::readFASTA(){
try {
- //ifstream inNames;
+ map<string, string> nameMap;
+ map<string, string>::iterator it;
+ if (namefile != "") { m->readNames(namefile, nameMap); }
+
ifstream inFasta;
m->openInputFile(fastafile, inFasta);
@@ -776,11 +785,12 @@ int PreClusterCommand::readFASTA(){
if (seq.getName() != "") { //can get "" if commented line is at end of fasta file
if (namefile != "") {
- itSize = sizes.find(seq.getName());
+ it = nameMap.find(seq.getName());
- if (itSize == sizes.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
+ if (it == nameMap.end()) { m->mothurOut(seq.getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); exit(1); }
else{
- seqPNode tempNode(itSize->second, seq, names[seq.getName()]);
+ string second = it->second;
+ seqPNode tempNode(m->getNumNames(second), seq, second);
alignSeqs.push_back(tempNode);
lengths.insert(seq.getAligned().length());
}
@@ -796,7 +806,7 @@ int PreClusterCommand::readFASTA(){
inFasta.close();
if (lengths.size() > 1) { method = "unaligned"; }
- else if (lengths.size() == 1) { method = "aligned"; }
+ else if (lengths.size() == 1) { method = "aligned"; filterSeqs(); }
length = *(lengths.begin());
@@ -813,7 +823,6 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
try {
set<int> lengths;
alignSeqs.clear();
- map<string, string>::iterator it;
bool error = false;
map<string, int> thisCount;
if (countfile != "") { thisCount = cparser->getCountTable(group); }
@@ -823,7 +832,7 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
if (m->control_pressed) { return 0; }
if (namefile != "") {
- it = thisName.find(thisSeqs[i].getName());
+ map<string, string>::iterator it = thisName.find(thisSeqs[i].getName());
//should never be true since parser checks for this
if (it == thisName.end()) { m->mothurOut(thisSeqs[i].getName() + " is not in your names file, please correct."); m->mothurOutEndLine(); error = true; }
@@ -853,16 +862,16 @@ int PreClusterCommand::loadSeqs(map<string, string>& thisName, vector<Sequence>&
}
}
- if (lengths.size() > 1) { method = "unaligned"; }
- else if (lengths.size() == 1) { method = "aligned"; }
-
length = *(lengths.begin());
+ if (lengths.size() > 1) { method = "unaligned"; }
+ else if (lengths.size() == 1) { method = "aligned"; filterSeqs(); }
+
//sanity check
if (error) { m->control_pressed = true; }
thisSeqs.clear();
-
+
return alignSeqs.size();
}
@@ -1006,15 +1015,33 @@ void PreClusterCommand::printData(string newfasta, string newname, string group)
}
if ((countfile != "") && (group == "")) { outNames << "Representative_Sequence\ttotal\n"; }
- for (int i = 0; i < alignSeqs.size(); i++) {
- if (alignSeqs[i].numIdentical != 0) {
- alignSeqs[i].seq.printSequence(outFasta);
- if (countfile != "") {
- if (group != "") { outNames << group << '\t' << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; }
- else { outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].numIdentical << endl; }
- }else { outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl; }
- }
- }
+
+ if (countfile != "") {
+ if (group != "") {
+ for (int i = 0; i < alignSeqs.size(); i++) {
+ if (alignSeqs[i].numIdentical != 0) {
+ alignSeqs[i].seq.printSequence(outFasta);
+ outNames << group << '\t' << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
+ }
+ }
+ }
+ else {
+ for (int i = 0; i < alignSeqs.size(); i++) {
+ if (alignSeqs[i].numIdentical != 0) {
+ alignSeqs[i].seq.printSequence(outFasta);
+ outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].numIdentical << endl;
+ }
+ }
+ }
+ }else {
+ for (int i = 0; i < alignSeqs.size(); i++) {
+ if (alignSeqs[i].numIdentical != 0) {
+ alignSeqs[i].seq.printSequence(outFasta);
+ outNames << alignSeqs[i].seq.getName() << '\t' << alignSeqs[i].names << endl;
+ }
+ }
+ }
+
outFasta.close();
outNames.close();
@@ -1027,30 +1054,39 @@ void PreClusterCommand::printData(string newfasta, string newname, string group)
}
/**************************************************************************************************/
-void PreClusterCommand::readNameFile(){
- try {
- ifstream in;
- m->openInputFile(namefile, in);
- string firstCol, secondCol;
-
- while (!in.eof()) {
- in >> firstCol >> secondCol; m->gobble(in);
-
- m->checkName(firstCol);
- m->checkName(secondCol);
- int size = m->getNumNames(secondCol);
-
- names[firstCol] = secondCol;
- sizes[firstCol] = size;
- }
- in.close();
- }
- catch(exception& e) {
- m->errorOut(e, "PreClusterCommand", "readNameFile");
- exit(1);
- }
+int PreClusterCommand::filterSeqs(){
+ try {
+ string filterString = "";
+ Filters F;
+
+ F.setLength(length);
+ F.initialize();
+ F.setFilter(string(length, '1'));
+
+ for (int i = 0; i < alignSeqs.size(); i++) {
+ F.getFreqs(alignSeqs[i].seq);
+ }
+
+ F.setNumSeqs(alignSeqs.size());
+ F.doVerticalAllBases();
+ filterString = F.getFilter();
+
+ //run filter
+ for (int i = 0; i < alignSeqs.size(); i++) {
+ alignSeqs[i].filteredSeq = "";
+ string align = alignSeqs[i].seq.getAligned();
+ for(int j=0;j<length;j++){
+ if(filterString[j] == '1'){ alignSeqs[i].filteredSeq += align[j]; }
+ }
+ }
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PreClusterCommand", "filterSeqs");
+ exit(1);
+ }
}
-
/**************************************************************************************************/
diff --git a/source/commands/preclustercommand.h b/source/commands/preclustercommand.h
index afe49b3..86d3163 100644
--- a/source/commands/preclustercommand.h
+++ b/source/commands/preclustercommand.h
@@ -21,33 +21,35 @@
#include "needlemanoverlap.hpp"
#include "blastalign.hpp"
#include "noalign.hpp"
-
+#include "filters.h"
/************************************************************/
struct seqPNode {
int numIdentical;
Sequence seq;
+ string filteredSeq;
string names;
bool active;
int diffs;
seqPNode() {}
- seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) { diffs = 0; }
+ seqPNode(int n, Sequence s, string nm) : numIdentical(n), seq(s), names(nm), active(1) { diffs = 0; filteredSeq = "";}
~seqPNode() {}
};
/************************************************************/
inline bool comparePriorityTopDown(seqPNode first, seqPNode second) {
if (first.numIdentical > second.numIdentical) { return true; }
- else if (first.numIdentical == second.numIdentical) {
- if (first.seq.getName() > second.seq.getName()) { return true; }
- }
+ //else if (first.numIdentical == second.numIdentical) {
+ //if (first.seq.getName() > second.seq.getName()) { return true; }
+ //}
+
return false;
}
/************************************************************/
inline bool comparePriorityDownTop(seqPNode first, seqPNode second) {
if (first.numIdentical < second.numIdentical) { return true; }
- else if (first.numIdentical == second.numIdentical) {
- if (first.seq.getName() > second.seq.getName()) { return true; }
- }
+ //else if (first.numIdentical == second.numIdentical) {
+ //if (first.seq.getName() > second.seq.getName()) { return true; }
+ //}
return false;
}
//************************************************************/
@@ -83,22 +85,17 @@ private:
bool abort, bygroup, topdown;
string fastafile, namefile, outputDir, groupfile, countfile, method, align;
vector<seqPNode> alignSeqs; //maps the number of identical seqs to a sequence
- map<string, string> names; //represents the names file first column maps to second column
- map<string, int> sizes; //this map a seq name to the number of identical seqs in the names file
- map<string, int>::iterator itSize;
-// map<string, bool> active; //maps sequence name to whether it has already been merged or not.
vector<string> outputNames;
int readFASTA();
- void readNameFile();
- //int readNamesFASTA();
int calcMisMatches(string, string);
void printData(string, string, string); //fasta filename, names file name
int process(string);
int loadSeqs(map<string, string>&, vector<Sequence>&, string);
- int driverGroups(string, string, string, int, int, vector<string> groups);
- int createProcessesGroups(string, string, string, vector<string>);
+ int driverGroups(string, string, string, int, int, vector<string>);
+ int createProcessesGroups(string, string, string);
int mergeGroupCounts(string, string, string);
+ int filterSeqs();
};
/**************************************************************************************************/
@@ -166,14 +163,17 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
alignment = new NeedlemanOverlap(pDataArray->gapOpen, pDataArray->match, pDataArray->misMatch, 1000);
}
- //parse fasta and name file by group
- SequenceParser* parser;
+ vector<string> subsetGroups;
+ for (int i = pDataArray->start; i < pDataArray->end; i++) { subsetGroups.push_back(pDataArray->groups[i]); }
+
+ //parse fasta and name file by group
SequenceCountParser* cparser;
+ SequenceParser* parser;
if (pDataArray->countfile != "") {
- cparser = new SequenceCountParser(pDataArray->countfile, pDataArray->fastafile);
+ cparser = new SequenceCountParser(pDataArray->countfile, pDataArray->fastafile, subsetGroups);
}else {
- if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile); }
- else { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile); }
+ if (pDataArray->namefile != "") { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile, subsetGroups); }
+ else { parser = new SequenceParser(pDataArray->groupfile, pDataArray->fastafile, subsetGroups); }
}
int numSeqs = 0;
@@ -189,7 +189,7 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
int start = time(NULL);
- if (pDataArray->m->control_pressed) { delete parser; delete alignment;return 0; }
+ if (pDataArray->m->control_pressed) { if (pDataArray->countfile != "") { delete cparser; } else { delete parser; } delete alignment;return 0; }
pDataArray->m->mothurOutEndLine(); pDataArray->m->mothurOut("Processing group " + pDataArray->groups[k] + ":"); pDataArray->m->mothurOutEndLine();
@@ -250,10 +250,38 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
}
}
+ length = *(lengths.begin());
+
if (lengths.size() > 1) { pDataArray->method = "unaligned"; }
- else if (lengths.size() == 1) { pDataArray->method = "aligned"; }
+ else if (lengths.size() == 1) {
+ pDataArray->method = "aligned";
+ ////////////////////////////////////////////////////
+ //filterSeqs();
+
+ string filterString = "";
+ Filters F;
+
+ F.setLength(length);
+ F.initialize();
+ F.setFilter(string(length, '1'));
+
+ for (int i = 0; i < alignSeqs.size(); i++) { F.getFreqs(alignSeqs[i].seq);}
+
+ F.setNumSeqs(alignSeqs.size());
+ F.doVerticalAllBases();
+ filterString = F.getFilter();
+
+ //run filter
+ for (int i = 0; i < alignSeqs.size(); i++) {
+ alignSeqs[i].filteredSeq = "";
+ string align = alignSeqs[i].seq.getAligned();
+ for(int j=0;j<length;j++){
+ if(filterString[j] == '1'){ alignSeqs[i].filteredSeq += align[j]; }
+ }
+ }
+ ////////////////////////////////////////////////////
+ }
- length = *(lengths.begin());
//sanity check
if (error) { pDataArray->m->control_pressed = true; }
@@ -323,9 +351,9 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
if (mismatch > pDataArray->diffs) { mismatch = length; break; } //to far to cluster
}
}else {
- for (int k = 0; k < alignSeqs[i].seq.getAligned().length(); k++) {
+ for (int k = 0; k < alignSeqs[i].filteredSeq.length(); k++) {
//do they match
- if (alignSeqs[i].seq.getAligned()[k] != alignSeqs[j].seq.getAligned()[k]) { mismatch++; }
+ if (alignSeqs[i].filteredSeq[k] != alignSeqs[j].filteredSeq[k]) { mismatch++; }
if (mismatch > pDataArray->diffs) { mismatch = length; break; } //to far to cluster
}
}
@@ -396,9 +424,9 @@ static DWORD WINAPI MyPreclusterThreadFunction(LPVOID lpParam){
}
}else {
- for (int k = 0; k < alignSeqs[i].seq.getAligned().length(); k++) {
+ for (int k = 0; k < alignSeqs[i].filteredSeq.length(); k++) {
//do they match
- if (alignSeqs[i].seq.getAligned()[k] != alignSeqs[j].seq.getAligned()[k]) { mismatch++; }
+ if (alignSeqs[i].filteredSeq[k] != alignSeqs[j].filteredSeq[k]) { mismatch++; }
if (mismatch > pDataArray->diffs) { mismatch = length; break; } //to far to cluster
}
}
diff --git a/source/commands/removegroupscommand.cpp b/source/commands/removegroupscommand.cpp
index ebe0dc7..8788ef5 100644
--- a/source/commands/removegroupscommand.cpp
+++ b/source/commands/removegroupscommand.cpp
@@ -1049,8 +1049,8 @@ int RemoveGroupsCommand::readTax(){
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; //read from first column
- in >> tax; //read from second column
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
//if this name is in the accnos file
if (names.count(name) == 0) {
@@ -1062,8 +1062,6 @@ int RemoveGroupsCommand::readTax(){
wroteSomething = true;
out << it->second << '\t' << tax << endl;
}else { removedCount++; } }
-
- m->gobble(in);
}
in.close();
out.close();
diff --git a/source/commands/removelineagecommand.cpp b/source/commands/removelineagecommand.cpp
index 8ccdae1..9bcafc9 100644
--- a/source/commands/removelineagecommand.cpp
+++ b/source/commands/removelineagecommand.cpp
@@ -416,6 +416,12 @@ int RemoveLineageCommand::execute(){
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setCountTableFile(current); }
}
+
+ //set constaxonomy file as new current constaxonomyfile
+ itTypes = outputTypes.find("constaxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setConsTaxonomyFile(current); }
+ }
}
return 0;
@@ -1070,9 +1076,9 @@ int RemoveLineageCommand::readTax(){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; //read from first column
- in >> tax; //read from second column
-
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
+
bool remove = false;
string noQuotesTax = m->removeQuotes(tax);
@@ -1176,7 +1182,6 @@ int RemoveLineageCommand::readTax(){
}
if (!remove) { wroteSomething = true; out << name << '\t' << tax << endl; }
- m->gobble(in);
}
in.close();
out.close();
@@ -1237,7 +1242,7 @@ int RemoveLineageCommand::readConsTax(){
in >> otuLabel; m->gobble(in);
in >> numReps; m->gobble(in);
- in >> tax; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
bool remove = false;
diff --git a/source/commands/removeotulabelscommand.cpp b/source/commands/removeotulabelscommand.cpp
index d3e4217..af1b610 100644
--- a/source/commands/removeotulabelscommand.cpp
+++ b/source/commands/removeotulabelscommand.cpp
@@ -270,6 +270,12 @@ int RemoveOtuLabelsCommand::execute(){
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setSharedFile(current); }
}
+ //set constaxonomy file as new current constaxonomyfile
+ itTypes = outputTypes.find("constaxonomy");
+ if (itTypes != outputTypes.end()) {
+ if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setConsTaxonomyFile(current); }
+ }
+
return 0;
}
catch(exception& e) {
@@ -306,7 +312,8 @@ int RemoveOtuLabelsCommand::readClassifyOtu(){
string otu = ""; string tax = "unknown";
int size = 0;
- in >> otu >> size >> tax; m->gobble(in);
+ in >> otu >> size; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
if (m->debug) { m->mothurOut("[DEBUG]: " + otu + toString(size) + tax + "\n"); }
diff --git a/source/commands/removeotuscommand.cpp b/source/commands/removeotuscommand.cpp
deleted file mode 100644
index 87f306b..0000000
--- a/source/commands/removeotuscommand.cpp
+++ /dev/null
@@ -1,439 +0,0 @@
-/*
- * removeotuscommand.cpp
- * Mothur
- *
- * Created by westcott on 11/12/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "removeotuscommand.h"
-#include "inputdata.h"
-#include "sharedutilities.h"
-
-//**********************************************************************************************************************
-vector<string> RemoveOtusCommand::setParameters(){
- try {
- CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","group",false,true,true); parameters.push_back(pgroup);
- CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","list",false,true,true); parameters.push_back(plist);
- CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
- CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
- CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
- CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string RemoveOtusCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The remove.otus command removes otus containing sequences from a specfic group or set of groups.\n";
- helpString += "It outputs a new list file containing the otus containing sequences NOT from in the those specified groups.\n";
- helpString += "The remove.otus command parameters are accnos, group, list, label and groups. The group and list parameters are required, unless you have valid current files.\n";
- helpString += "You must also provide an accnos containing the list of groups to get or set the groups parameter to the groups you wish to select.\n";
- helpString += "The groups parameter allows you to specify which of the groups in your groupfile you would like. You can separate group names with dashes.\n";
- helpString += "The label parameter allows you to specify which distance you want to process.\n";
- helpString += "The remove.otus command should be in the following format: remove.otus(accnos=yourAccnos, list=yourListFile, group=yourGroupFile, label=yourLabel).\n";
- helpString += "Example remove.otus(accnos=amazon.accnos, list=amazon.fn.list, group=amazon.groups, label=0.03).\n";
- helpString += "or remove.otus(groups=pasture, list=amazon.fn.list, amazon.groups, label=0.03).\n";
- helpString += "Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListFile).\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string RemoveOtusCommand::getOutputPattern(string type) {
- try {
- string pattern = "";
-
- if (type == "group") { pattern = "[filename],[tag],pick,[extension]"; }
- else if (type == "list") { pattern = "[filename],[tag],pick,[extension]"; }
- else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
-
- return pattern;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "getOutputPattern");
- exit(1);
- }
-}
-///**********************************************************************************************************************
-RemoveOtusCommand::RemoveOtusCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "RemoveOtusCommand");
- exit(1);
- }
-}
-
-//**********************************************************************************************************************
-RemoveOtusCommand::RemoveOtusCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
-
- ValidParameters validParameter;
- map<string,string>::iterator it;
-
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["group"] = tempOutNames;
- outputTypes["list"] = tempOutNames;
-
-
- //if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
- if (inputDir == "not found"){ inputDir = ""; }
- else {
- string path;
- it = parameters.find("accnos");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["accnos"] = inputDir + it->second; }
- }
-
- it = parameters.find("list");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["list"] = inputDir + it->second; }
- }
-
- it = parameters.find("group");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["group"] = inputDir + it->second; }
- }
- }
-
-
- //check for required parameters
- accnosfile = validParameter.validFile(parameters, "accnos", true);
- if (accnosfile == "not open") { abort = true; }
- else if (accnosfile == "not found") { accnosfile = ""; }
- else { m->setAccnosFile(accnosfile); }
-
- groupfile = validParameter.validFile(parameters, "group", true);
- if (groupfile == "not open") { abort = true; }
- else if (groupfile == "not found") {
- groupfile = m->getGroupFile();
- if (groupfile != "") { m->mothurOut("Using " + groupfile + " as input file for the group parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current group file and the group parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setGroupFile(groupfile); }
-
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { abort = true; }
- else if (listfile == "not found") {
- listfile = m->getListFile();
- if (listfile != "") { m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current list file and the list parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setListFile(listfile); }
-
- groups = validParameter.validFile(parameters, "groups", false);
- if (groups == "not found") { groups = ""; }
- else {
- m->splitAtDash(groups, Groups);
- }
-
- label = validParameter.validFile(parameters, "label", false);
- if (label == "not found") { label = ""; m->mothurOut("You did not provide a label, I will use the first label in your inputfile."); m->mothurOutEndLine(); label=""; }
-
- if ((accnosfile == "") && (Groups.size() == 0)) { m->mothurOut("You must provide an accnos file or specify groups using the groups parameter."); m->mothurOutEndLine(); abort = true; }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "RemoveOtusCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int RemoveOtusCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- groupMap = new GroupMap(groupfile);
- groupMap->readMap();
-
- //get groups you want to remove
- if (accnosfile != "") { m->readAccnos(accnosfile, Groups); m->setGroups(Groups); }
-
- //make sure groups are valid
- //takes care of user setting groupNames that are invalid or setting groups=all
- SharedUtil* util = new SharedUtil();
- vector<string> allGroups = groupMap->getNamesOfGroups();
- util->setGroups(Groups, allGroups);
- delete util;
-
- if (m->control_pressed) { delete groupMap; return 0; }
-
- //read through the list file keeping any otus that contain any sequence from the groups selected
- readListGroup();
-
- if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
-
- if (outputNames.size() != 0) {
- m->mothurOutEndLine();
- m->mothurOut("Output File names: "); m->mothurOutEndLine();
- for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
- m->mothurOutEndLine();
-
- //set fasta file as new current fastafile
- string current = "";
- itTypes = outputTypes.find("group");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
- }
-
- itTypes = outputTypes.find("list");
- if (itTypes != outputTypes.end()) {
- if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
- }
- }
-
- return 0;
- }
-
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveOtusCommand::readListGroup(){
- try {
- InputData* input = new InputData(listfile, "list");
- ListVector* list = input->getListVector();
- string lastLabel = list->getLabel();
-
- //using first label seen if none is provided
- if (label == "") { label = lastLabel; }
-
- string thisOutputDir = outputDir;
- if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
- map<string, string> variables;
- variables["[filename]"] = thisOutputDir + m->getRootName(m->getSimpleName(listfile));
- variables["[tag]"] = label;
- variables["[extension]"] = m->getExtension(listfile);
- string outputFileName = getOutputFileName("list", variables);
-
- ofstream out;
- m->openOutputFile(outputFileName, out);
-
- string GroupOutputDir = outputDir;
- if (outputDir == "") { GroupOutputDir += m->hasPath(groupfile); }
- variables["[filename]"] = GroupOutputDir + m->getRootName(m->getSimpleName(groupfile));
- variables["[extension]"] = m->getExtension(groupfile);
- string outputGroupFileName = getOutputFileName("group", variables);
-
- ofstream outGroup;
- m->openOutputFile(outputGroupFileName, outGroup);
-
- //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
- set<string> labels; labels.insert(label);
- set<string> processedLabels;
- set<string> userLabels = labels;
-
- bool wroteSomething = false;
-
- //as long as you are not at the end of the file or done wih the lines you want
- while((list != NULL) && (userLabels.size() != 0)) {
-
- if (m->control_pressed) { delete list; delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName);return 0; }
-
- if(labels.count(list->getLabel()) == 1){
- processList(list, groupMap, out, outGroup, wroteSomething);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
- }
-
- if ((m->anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
- string saveLabel = list->getLabel();
-
- delete list;
-
- list = input->getListVector(lastLabel);
-
- processList(list, groupMap, out, outGroup, wroteSomething);
-
- processedLabels.insert(list->getLabel());
- userLabels.erase(list->getLabel());
-
- //restore real lastlabel to save below
- list->setLabel(saveLabel);
- }
-
- lastLabel = list->getLabel();
-
- delete list; list = NULL;
-
- //get next line to process
- list = input->getListVector();
- }
-
-
- if (m->control_pressed) { if (list != NULL) { delete list; } delete input; out.close(); outGroup.close(); m->mothurRemove(outputFileName); m->mothurRemove(outputGroupFileName); return 0; }
-
- //output error messages about any remaining user labels
- set<string>::iterator it;
- bool needToRun = false;
- for (it = userLabels.begin(); it != userLabels.end(); it++) {
- m->mothurOut("Your file does not include the label " + *it);
- if (processedLabels.count(lastLabel) != 1) {
- m->mothurOut(". I will use " + lastLabel + "."); m->mothurOutEndLine();
- needToRun = true;
- }else {
- m->mothurOut(". Please refer to " + lastLabel + "."); m->mothurOutEndLine();
- }
- }
-
- //run last label if you need to
- if (needToRun == true) {
- if (list != NULL) { delete list; }
-
- list = input->getListVector(lastLabel);
-
- processList(list, groupMap, out, outGroup, wroteSomething);
-
- delete list; list = NULL;
- }
-
- out.close();
- outGroup.close();
-
- if (wroteSomething == false) { m->mothurOut("At distance " + label + " your file ONLY contains otus containing sequences from the groups you wish to remove."); m->mothurOutEndLine(); }
- outputTypes["list"].push_back(outputFileName); outputNames.push_back(outputFileName);
- outputTypes["group"].push_back(outputGroupFileName); outputNames.push_back(outputGroupFileName);
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "readList");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-int RemoveOtusCommand::processList(ListVector*& list, GroupMap*& groupMap, ofstream& out, ofstream& outGroup, bool& wroteSomething){
- try {
-
- //make a new list vector
- ListVector newList;
- newList.setLabel(list->getLabel());
-
- int numOtus = 0;
- //for each bin
- vector<string> binLabels = list->getLabels();
- vector<string> newBinLabels;
- for (int i = 0; i < list->getNumBins(); i++) {
- if (m->control_pressed) { return 0; }
-
- //parse out names that are in accnos file
- string binnames = list->get(i);
-
- bool removeBin = false;
- string groupFileOutput = "";
-
- //parse names
- string individual = "";
- int length = binnames.length();
- for(int j=0;j<length;j++){
- if(binnames[j] == ','){
- string group = groupMap->getGroup(individual);
- if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (m->inUsersGroups(group, Groups)) { removeBin = true; break; }
- groupFileOutput += individual + "\t" + group + "\n";
- individual = "";
-
- }
- else{ individual += binnames[j]; }
- }
-
- if (!removeBin) {
- //get last name
- string group = groupMap->getGroup(individual);
- if (group == "not found") { m->mothurOut("[ERROR]: " + individual + " is not in your groupfile. please correct."); m->mothurOutEndLine(); group = "NOTFOUND"; }
-
- if (m->inUsersGroups(group, Groups)) { removeBin = true; }
- groupFileOutput += individual + "\t" + group + "\n";
-
- if (!removeBin) {
- //if there are no sequences from the groups we want to remove in this bin add to new list, output to groupfile
- newList.push_back(binnames);
- newBinLabels.push_back(binLabels[i]);
- outGroup << groupFileOutput;
- }else {
- numOtus++;
- }
- }else {
- numOtus++;
- }
-
- }
-
- //print new listvector
- if (newList.getNumBins() != 0) {
- wroteSomething = true;
- newList.setLabels(newBinLabels);
- newList.printHeaders(out);
- newList.print(out);
- }
-
- m->mothurOut(newList.getLabel() + " - removed " + toString(numOtus) + " of the " + toString(list->getNumBins()) + " OTUs."); m->mothurOutEndLine();
-
- return 0;
-
- }
- catch(exception& e) {
- m->errorOut(e, "RemoveOtusCommand", "processList");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
-
diff --git a/source/commands/removeotuscommand.h b/source/commands/removeotuscommand.h
deleted file mode 100644
index a7fcf0e..0000000
--- a/source/commands/removeotuscommand.h
+++ /dev/null
@@ -1,52 +0,0 @@
-#ifndef REMOVEOTUSCOMMAND_H
-#define REMOVEOTUSCOMMAND_H
-
-/*
- * removeotuscommand.h
- * Mothur
- *
- * Created by westcott on 11/12/10.
- * Copyright 2010 Schloss Lab. All rights reserved.
- *
- */
-
-#include "command.hpp"
-#include "groupmap.h"
-#include "listvector.hpp"
-
-class RemoveOtusCommand : public Command {
-
-public:
-
- RemoveOtusCommand(string);
- RemoveOtusCommand();
- ~RemoveOtusCommand(){}
-
- vector<string> setParameters();
- string getCommandName() { return "remove.otus"; }
- string getCommandCategory() { return "OTU-Based Approaches"; }
-
- string getHelpString();
- string getOutputPattern(string);
- string getCitation() { return "http://www.mothur.org/wiki/Remove.otus"; }
- string getDescription() { return "outputs a new list file containing the otus NOT containing sequences from the groups specified"; }
-
- int execute();
- void help() { m->mothurOut(getHelpString()); }
-
-private:
- string accnosfile, groupfile, listfile, outputDir, groups, label;
- bool abort;
- vector<string> outputNames, Groups;
- GroupMap* groupMap;
-
- int readListGroup();
- int processList(ListVector*&, GroupMap*&, ofstream&, ofstream&, bool&);
-
-};
-
-#endif
-
-
-
-
diff --git a/source/commands/removeseqscommand.cpp b/source/commands/removeseqscommand.cpp
index 514add7..ec9d71f 100644
--- a/source/commands/removeseqscommand.cpp
+++ b/source/commands/removeseqscommand.cpp
@@ -959,9 +959,9 @@ int RemoveSeqsCommand::readTax(){
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; m->gobble(in); //read from first column
- in >> tax; //read from second column
-
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
+
if (!dups) {//adjust name if needed
map<string, string>::iterator it = uniqueMap.find(name);
if (it != uniqueMap.end()) { name = it->second; }
@@ -978,8 +978,6 @@ int RemoveSeqsCommand::readTax(){
m->mothurOut("[WARNING]: " + name + " is in your taxonomy file more than once. Mothur requires sequence names to be unique. I will only add it once.\n");
}
}else { removedCount++; }
-
- m->gobble(in);
}
in.close();
out.close();
diff --git a/source/commands/renamefilecommand.cpp b/source/commands/renamefilecommand.cpp
index 2190908..18387fc 100644
--- a/source/commands/renamefilecommand.cpp
+++ b/source/commands/renamefilecommand.cpp
@@ -463,13 +463,14 @@ RenameFileCommand::RenameFileCommand(string option) {
temp = validParameter.validFile(parameters, "deleteold", false); if (temp == "not found") { temp = "T"; }
deleteOld = m->isTrue(temp);
- prefix = validParameter.validFile(parameters, "prefix", false); if (prefix == "not found") { temp = ""; }
+ prefix = validParameter.validFile(parameters, "prefix", false); if (prefix == "not found") { prefix = ""; }
outputfile = validParameter.validFile(parameters, "new", false);
if (outputfile == "not found") {
if (!mothurGenerated) { m->mothurOut("[ERROR]: you must enter an output file name"); m->mothurOutEndLine(); abort=true; }
outputfile = "";
- }else if (outputDir != "") { outputfile = outputDir + m->getSimpleName(outputfile); }
+ }else { mothurGenerated=false; }
+ if (outputDir != "") { outputfile = outputDir + m->getSimpleName(outputfile); }
if ((!mothurGenerated) && (numFiles > 1)) {
m->mothurOut("[ERROR]: You cannot use more than one file parameter unless mothur is generating the output filenames for you.\n"); abort= true;
@@ -584,7 +585,7 @@ int RenameFileCommand::execute(){
if (constaxonomyfile != "") {
newName = getNewName(constaxonomyfile, "constaxonomy");
renameOrCopy(constaxonomyfile, newName);
- m->setTaxonomyFile(newName);
+ m->setConsTaxonomyFile(newName);
}
if (flowfile != "") {
newName = getNewName(flowfile, "flow");
@@ -632,6 +633,7 @@ int RenameFileCommand::execute(){
string RenameFileCommand::getNewName(string name, string type){
try {
string newName = outputfile;
+ name = m->getFullPathName(name);
if (mothurGenerated) {
string extension = m->getExtension(name);
@@ -644,12 +646,15 @@ string RenameFileCommand::getNewName(string name, string type){
}else { basicName = prefix; }
if ((type == "shared") || (type == "list") || (type == "relabund") || (type == "rabund") || (type == "sabund")) {
- vector<string> tags; tags.push_back(".an."); tags.push_back(".tx."); tags.push_back(".agc."); tags.push_back(".dgc."); tags.push_back(".nn."); tags.push_back(".fn."); tags.push_back(".wn.");
- vector<string> newTags; newTags.push_back("an"); newTags.push_back("tx"); newTags.push_back("agc"); newTags.push_back("dgc"); newTags.push_back("nn"); newTags.push_back("fn"); newTags.push_back("wn");
+ vector<string> tags; tags.push_back(".an."); tags.push_back(".tx."); tags.push_back(".agc."); tags.push_back(".dgc."); tags.push_back(".nn."); tags.push_back(".fn."); tags.push_back(".wn."); tags.push_back(".opti_");
for (int i = 0; i < tags.size(); i++) {
- int pos2 = name.find_first_of(tags[i]);
- if (pos2 != string::npos) { tag = newTags[i]; break; }
+ int pos2 = name.find(tags[i]);
+ if (pos2 != string::npos) {
+ int pos3 = name.substr(pos2+1).find_first_of('.');
+ tag = name.substr(pos2+1, pos3);
+ break;
+ }
}
}else if (type == "constaxonomy") {
extension = ".cons.taxonomy";
diff --git a/source/commands/screenseqscommand.cpp b/source/commands/screenseqscommand.cpp
index 2dea059..ce86e74 100644
--- a/source/commands/screenseqscommand.cpp
+++ b/source/commands/screenseqscommand.cpp
@@ -259,6 +259,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) {
}
}
+ fileType = "name file";
//check for required parameters
fastafile = validParameter.validFile(parameters, "fasta", true);
if (fastafile == "not found") {
@@ -287,7 +288,7 @@ ScreenSeqsCommand::ScreenSeqsCommand(string option) {
countfile = validParameter.validFile(parameters, "count", true);
if (countfile == "not open") { countfile = ""; abort = true; }
else if (countfile == "not found") { countfile = ""; }
- else { m->setCountTableFile(countfile); }
+ else { m->setCountTableFile(countfile); fileType = "count file"; }
contigsreport = validParameter.validFile(parameters, "contigsreport", true);
if (contigsreport == "not open") { contigsreport = ""; abort = true; }
@@ -545,21 +546,22 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
try{
int numFastaSeqs = 0;
bool summarizedFasta = false;
+ //use the namefile to optimize correctly
+ if (namefile != "") { nameMap = m->readNames(namefile); }
+ else if (countfile != "") {
+ CountTable ct;
+ ct.readTable(countfile, true, false);
+ nameMap = ct.getNameMap();
+ }
+
//did not provide a summary file, but set a parameter that requires summarizing the fasta file
//or did provide a summary file, but set maxn parameter so we must summarize the fasta file
vector<unsigned long long> positions;
if (((summaryfile == "") && ((m->inUsersGroups("maxambig", optimize)) ||(m->inUsersGroups("maxhomop", optimize)) ||(m->inUsersGroups("maxlength", optimize)) || (m->inUsersGroups("minlength", optimize)) || (m->inUsersGroups("start", optimize)) || (m->inUsersGroups("end", optimize)))) || ((summaryfile != "") && m->inUsersGroups("maxn", optimize))) {
- //use the namefile to optimize correctly
- if (namefile != "") { nameMap = m->readNames(namefile); }
- else if (countfile != "") {
- CountTable ct;
- ct.readTable(countfile, true, false);
- nameMap = ct.getNameMap();
- }
- getSummary(positions);
+ getSummary(positions);
summarizedFasta = true;
- } else {
+ }else {
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(fastafile, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
@@ -582,12 +584,6 @@ int ScreenSeqsCommand::screenReports(map<string, string>& badSeqNames){
}
if ((summaryfile != "") && ((m->inUsersGroups("maxambig", optimize)) ||(m->inUsersGroups("maxhomop", optimize)) ||(m->inUsersGroups("maxlength", optimize)) || (m->inUsersGroups("minlength", optimize)) || (m->inUsersGroups("start", optimize)) || (m->inUsersGroups("end", optimize))) && !summarizedFasta) { //summarize based on summaryfile
- if (namefile != "") { nameMap = m->readNames(namefile); }
- else if (countfile != "") {
- CountTable ct;
- ct.readTable(countfile, true, false);
- nameMap = ct.getNameMap();
- }
getSummaryReport();
}else if ((contigsreport != "") && ((m->inUsersGroups("minoverlap", optimize)) || (m->inUsersGroups("ostart", optimize)) || (m->inUsersGroups("oend", optimize)) || (m->inUsersGroups("mismatches", optimize)))) { //optimize settings based on contigs file
optimizeContigs();
@@ -1060,7 +1056,7 @@ int ScreenSeqsCommand::getSummaryReport(){
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(name);
- if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your " + fileType + " please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
else { num = it->second; }
}
@@ -1194,7 +1190,7 @@ int ScreenSeqsCommand::driverContigsSummary(vector<int>& oLength, vector<int>& o
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(name);
- if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your " + fileType + " please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
else { num = it->second; }
}
@@ -1462,12 +1458,12 @@ int ScreenSeqsCommand::optimizeAlign(){
sort(inserts.begin(), inserts.end());
//numSeqs is the number of unique seqs, startPosition.size() is the total number of seqs, we want to optimize using all seqs
- int criteriaPercentile = int(sims.size() * (criteria / (float) 100));
+ //int criteriaPercentile = int(sims.size() * (criteria / (float) 100));
for (int i = 0; i < optimize.size(); i++) {
if (optimize[i] == "minsim") { int mincriteriaPercentile = int(sims.size() * ((100 - criteria) / (float) 100)); minSim = sims[mincriteriaPercentile]; m->mothurOut("Optimizing minsim to " + toString(minSim) + "."); m->mothurOutEndLine();}
else if (optimize[i] == "minscore") { int mincriteriaPercentile = int(scores.size() * ((100 - criteria) / (float) 100)); minScore = scores[mincriteriaPercentile]; m->mothurOut("Optimizing minscore to " + toString(minScore) + "."); m->mothurOutEndLine(); }
- else if (optimize[i] == "maxinsert") { maxInsert = inserts[criteriaPercentile]; m->mothurOut("Optimizing maxinsert to " + toString(maxInsert) + "."); m->mothurOutEndLine(); }
+ else if (optimize[i] == "maxinsert") { int criteriaPercentile = int(inserts.size() * ((100 - criteria) / (float) 100)); maxInsert = inserts[criteriaPercentile]; m->mothurOut("Optimizing maxinsert to " + toString(maxInsert) + "."); m->mothurOutEndLine(); }
}
return 0;
@@ -1509,7 +1505,7 @@ int ScreenSeqsCommand::driverAlignSummary(vector<float>& sims, vector<float>& sc
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(name);
- if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + name + " is not in your " + fileType + " please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
else { num = it->second; }
}
@@ -1823,7 +1819,7 @@ int ScreenSeqsCommand::driverCreateSummary(vector<int>& startPosition, vector<in
//make sure this sequence is in the namefile, else error
map<string, int>::iterator it = nameMap.find(current.getName());
- if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your namefile, please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
+ if (it == nameMap.end()) { m->mothurOut("[ERROR]: " + current.getName() + " is not in your " + fileType + " please correct."); m->mothurOutEndLine(); m->control_pressed = true; }
else { num = it->second; }
}
@@ -2192,14 +2188,15 @@ int ScreenSeqsCommand::screenTaxonomy(map<string, string> badSeqNames){
while(!input.eof()){
if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
- input >> seqName; m->gobble(input); input >> tax;
+ input >> seqName; m->gobble(input);
+ tax = m->getline(input); m->gobble(input);
+
it = badSeqNames.find(seqName);
if(it != badSeqNames.end()){ badSeqNames.erase(it); }
else{
goodTaxOut << seqName << '\t' << tax << endl;
}
- m->gobble(input);
}
if (m->control_pressed) { goodTaxOut.close(); input.close(); m->mothurRemove(goodTaxFile); return 0; }
diff --git a/source/commands/screenseqscommand.h b/source/commands/screenseqscommand.h
index c394f55..20a8844 100644
--- a/source/commands/screenseqscommand.h
+++ b/source/commands/screenseqscommand.h
@@ -62,7 +62,7 @@ private:
int createProcessesAlignSummary(vector<float>&, vector<float>&, vector<int>&, vector<linePair>);
bool abort;
- string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy, countfile, contigsreport, summaryfile;
+ string fastafile, namefile, groupfile, alignreport, outputDir, qualfile, taxonomy, countfile, contigsreport, summaryfile, fileType;
int startPos, endPos, maxAmbig, maxHomoP, minLength, maxLength, processors, minOverlap, oStart, oEnd, mismatches, maxN, maxInsert;
float minSim, minScore, criteria;
vector<string> outputNames;
diff --git a/source/commands/sensspeccommand.cpp b/source/commands/sensspeccommand.cpp
index d00f076..3eb2374 100644
--- a/source/commands/sensspeccommand.cpp
+++ b/source/commands/sensspeccommand.cpp
@@ -20,7 +20,6 @@ vector<string> SensSpecCommand::setParameters(){
CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
CommandParameter pcutoff("cutoff", "Number", "", "-1.00", "", "", "","",false,false); parameters.push_back(pcutoff);
CommandParameter pprecision("precision", "Number", "", "100", "", "", "","",false,false); parameters.push_back(pprecision);
- CommandParameter phard("hard", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(phard);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
@@ -223,13 +222,6 @@ SensSpecCommand::SensSpecCommand(string option) {
outputDir += m->hasPath(listFile); //if user entered a file with a path then preserve it
}
- //check for optional parameter and set defaults
- // ...at some point should added some additional type checking...
- temp = validParameter.validFile(parameters, "hard", false);
- if (temp == "not found"){ hard = 1; }
- else if(!m->isTrue(temp)) { hard = 0; }
- else if(m->isTrue(temp)) { hard = 1; }
-
temp = validParameter.validFile(parameters, "cutoff", false); if (temp == "not found") { temp = "-1.00"; }
m->mothurConvert(temp, cutoff);
@@ -303,14 +295,15 @@ int SensSpecCommand::process(map<string, int>& seqMap, ListVector*& list, bool&
try {
string label = list->getLabel();
- int numSeqs = list->getNumSeqs();
+ long long numSeqs = list->getNumSeqs();
int numOTUs = list->getNumBins();
if(getCutoff == 1){
if(label != "unique"){
origCutoff = label;
convert(label, cutoff);
- if(!hard){ cutoff += (0.49 / double(precision)); }
+ cutoff = m->ceilDist(cutoff, precision);
+ origCutoff = toString(m->ceilDist(cutoff, precision));
}
else{
origCutoff = "unique";
@@ -439,6 +432,7 @@ int SensSpecCommand::process(map<string, int>& seqMap, ListVector*& list, bool&
}
}
}
+
falseNegatives = distanceMap.size();
trueNegatives = numSeqs * (numSeqs-1)/2 - (falsePositives + falseNegatives + truePositives);
@@ -459,9 +453,9 @@ int SensSpecCommand::processListFile(){
string origCutoff = "";
bool getCutoff = 0;
- if(cutoff == -1.00) { getCutoff = 1; }
- else if( !hard ) { origCutoff = toString(cutoff); cutoff += (0.49 / double(precision)); }
- else { origCutoff = toString(cutoff); }
+
+ if(cutoff == -1.00) { getCutoff = 1; }
+ else { origCutoff = toString(m->ceilDist(cutoff, precision)); }
map<string, int> seqMap;
@@ -563,25 +557,25 @@ void SensSpecCommand::setUpOutput(){
void SensSpecCommand::outputStatistics(string label, string cutoff){
try{
- double tp = (double) truePositives;
- double fp = (double) falsePositives;
- double tn = (double) trueNegatives;
- double fn = (double) falseNegatives;
-
- double p = tp + fn;
- double n = fp + tn;
- double pPrime = tp + fp;
- double nPrime = tn + fn;
-
- double sensitivity = tp / p;
- double specificity = tn / n;
- double positivePredictiveValue = tp / pPrime;
- double negativePredictiveValue = tn / nPrime;
- double falseDiscoveryRate = fp / pPrime;
-
- double accuracy = (tp + tn) / (p + n);
- double matthewsCorrCoef = (tp * tn - fp * fn) / sqrt(p * n * pPrime * nPrime); if(p == 0 || n == 0){ matthewsCorrCoef = 0; }
- double f1Score = 2.0 * tp / (p + pPrime);
+ long long tp = truePositives;
+ long long fp = falsePositives;
+ long long tn = trueNegatives;
+ long long fn = falseNegatives;
+
+ long long p = tp + fn;
+ long long n = fp + tn;
+ long long pPrime = tp + fp;
+ long long nPrime = tn + fn;
+
+ double sensitivity = tp / (double) p;
+ double specificity = tn / (double)n;
+ double positivePredictiveValue = tp / (double)pPrime;
+ double negativePredictiveValue = tn / (double)nPrime;
+ double falseDiscoveryRate = fp / (double)pPrime;
+
+ double accuracy = (tp + tn) / (double)(p + n);
+ double matthewsCorrCoef = (tp * tn - fp * fn) / (double)sqrt(p * n * pPrime * nPrime); if(p == 0 || n == 0){ matthewsCorrCoef = 0; }
+ double f1Score = 2.0 * tp / (double)(p + pPrime);
if(p == 0) { sensitivity = 0; matthewsCorrCoef = 0; }
diff --git a/source/commands/sensspeccommand.h b/source/commands/sensspeccommand.h
index b6460a7..f79290c 100644
--- a/source/commands/sensspeccommand.h
+++ b/source/commands/sensspeccommand.h
@@ -47,9 +47,8 @@ private:
vector<string> outputNames;
set<string> labels; //holds labels to be used
- long int truePositives, falsePositives, trueNegatives, falseNegatives;
+ long long truePositives, falsePositives, trueNegatives, falseNegatives;
bool abort, allLines, square;
- bool hard;
double cutoff;
int precision;
diff --git a/source/commands/setcurrentcommand.cpp b/source/commands/setcurrentcommand.cpp
index 115f7c1..06f7c1c 100644
--- a/source/commands/setcurrentcommand.cpp
+++ b/source/commands/setcurrentcommand.cpp
@@ -25,6 +25,7 @@ vector<string> SetCurrentCommand::setParameters(){
CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pgroup);
CommandParameter plist("list", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(plist);
CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(ptaxonomy);
+ CommandParameter pconstaxonomy("constaxonomy", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pconstaxonomy);
CommandParameter pqfile("qfile", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(pqfile);
CommandParameter paccnos("accnos", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(paccnos);
CommandParameter prabund("rabund", "InputTypes", "", "", "none", "none", "none","",false,false); parameters.push_back(prabund);
@@ -58,7 +59,7 @@ string SetCurrentCommand::getHelpString(){
try {
string helpString = "";
helpString += "The set.current command allows you to set the current files saved by mothur.\n";
- helpString += "The set.current command parameters are: current, clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count, summary, file and taxonomy.\n";
+ helpString += "The set.current command parameters are: current, clear, phylip, column, list, rabund, sabund, name, group, design, order, tree, shared, ordergroup, relabund, fasta, qfile, sff, oligos, accnos, biom, count, summary, file, constaxonomy and taxonomy.\n";
helpString += "The current parameter is used to input the output file from get.current. This function is intended to allow you to input filenames from previous instances on mothur. NOTE: If you have a current file set in the file *.current_files.summary file, and also set a value for that file type, the value set takes precedence. For example, if you run set.current(current=current_files.summary, fasta=abrecovery.fasta) and your have fasta=final.fasta in the *.current_files.su [...]
helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
helpString += "The set.current command should be in the following format: \n";
@@ -298,6 +299,14 @@ SetCurrentCommand::SetCurrentCommand(string option) {
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
}
+
+ it = parameters.find("constaxonomy");
+ //user has given a template file
+ if(it != parameters.end()){
+ path = m->hasPath(it->second);
+ //if the user has not given a path then, add inputdir. else leave path alone.
+ if (path == "") { parameters["constaxonomy"] = inputDir + it->second; }
+ }
it = parameters.find("flow");
//user has given a template file
@@ -448,6 +457,11 @@ SetCurrentCommand::SetCurrentCommand(string option) {
if (taxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["taxonomy"]); m->mothurOutEndLine(); taxonomyfile = ""; }
else if (taxonomyfile == "not found") { taxonomyfile = ""; }
if (taxonomyfile != "") { m->setTaxonomyFile(taxonomyfile); }
+
+ constaxonomyfile = validParameter.validFile(parameters, "constaxonomy", true);
+ if (constaxonomyfile == "not open") { m->mothurOut("Ignoring: " + parameters["constaxonomy"]); m->mothurOutEndLine(); constaxonomyfile = ""; }
+ else if (constaxonomyfile == "not found") { constaxonomyfile = ""; }
+ if (constaxonomyfile != "") { m->setConsTaxonomyFile(constaxonomyfile); }
flowfile = validParameter.validFile(parameters, "flow", true);
if (flowfile == "not open") { m->mothurOut("Ignoring: " + parameters["flow"]); m->mothurOutEndLine(); flowfile = ""; }
@@ -536,6 +550,8 @@ int SetCurrentCommand::execute(){
m->setAccnosFile("");
}else if (types[i] == "taxonomy") {
m->setTaxonomyFile("");
+ }else if (types[i] == "constaxonomy") {
+ m->setConsTaxonomyFile("");
}else if (types[i] == "flow") {
m->setFlowFile("");
}else if (types[i] == "biom") {
diff --git a/source/commands/setcurrentcommand.h b/source/commands/setcurrentcommand.h
index 0370e58..6465dca 100644
--- a/source/commands/setcurrentcommand.h
+++ b/source/commands/setcurrentcommand.h
@@ -41,7 +41,7 @@ private:
vector<string> types;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, countfile, summaryfile, currentFile, outputDir;
- string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, filefile;
+ string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, filefile, constaxonomyfile;
int readCurrentFiles();
diff --git a/source/commands/setdircommand.cpp b/source/commands/setdircommand.cpp
index 79851f7..6e79a08 100644
--- a/source/commands/setdircommand.cpp
+++ b/source/commands/setdircommand.cpp
@@ -13,6 +13,7 @@
vector<string> SetDirectoryCommand::setParameters(){
try {
CommandParameter ptempdefault("tempdefault", "String", "", "", "", "", "","",false,false); parameters.push_back(ptempdefault);
+ CommandParameter pblast("blastdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pblast);
CommandParameter pdebug("debug", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pdebug);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pmodnames("modifynames", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmodnames);
@@ -37,6 +38,7 @@ string SetDirectoryCommand::getHelpString(){
helpString += "The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n";
helpString += "The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n";
helpString += "The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n";
+ helpString += "The set.dir command can also be used to set the location of the blast directory if other than mothur's executable location, the directory must exist.\n";
helpString += "The set.dir command can also be used to run mothur in debug mode.\n";
helpString += "The set.dir command can also be used to seed random.\n";
helpString += "The set.dir command can also be used to set the modifynames parameter. Default=t, meaning if your sequence names contain ':' change them to '_' to avoid issues while making trees. modifynames=F will leave sequence names as they are.\n";
@@ -45,6 +47,7 @@ string SetDirectoryCommand::getHelpString(){
helpString += "To seed random set seed=yourRandomValue. By default mothur seeds random with the start time.\n";
helpString += "To return the output to the same directory as the input files you may enter: output=clear.\n";
helpString += "To return the input to the current working directory you may enter: input=clear.\n";
+ helpString += "To set the blast location to the directory where the blast executables are located you may enter: blastdir=yourBlastLocation.\n";
helpString += "To set the output to the directory where mothur.exe is located you may enter: output=default.\n";
helpString += "To set the input to the directory where mothur.exe is located you may enter: input=default.\n";
helpString += "To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n";
@@ -90,6 +93,9 @@ SetDirectoryCommand::SetDirectoryCommand(string option) {
tempdefault = validParameter.validFile(parameters, "tempdefault", false);
if (tempdefault == "not found") { tempdefault = ""; }
+ blastLocation = validParameter.validFile(parameters, "blastdir", false);
+ if (blastLocation == "not found") { blastLocation = ""; }
+
bool debug = false;
bool nodebug = false;
debugorSeedOnly = false;
@@ -118,9 +124,9 @@ SetDirectoryCommand::SetDirectoryCommand(string option) {
m->mothurOut("Setting random seed to " + toString(random) + ".\n\n");
}
- if ((input == "") && (output == "") && (tempdefault == "") && nodebug && nomod && !seed) {
- m->mothurOut("[ERROR]: You must provide either an input, output, tempdefault, debug or modifynames for the set.dir command."); m->mothurOutEndLine(); abort = true;
- }else if((input == "") && (output == "") && (tempdefault == "")) { debugorSeedOnly = true; }
+ if ((input == "") && (output == "") && (tempdefault == "") && (blastLocation == "") && nodebug && nomod && !seed) {
+ m->mothurOut("[ERROR]: You must provide either an input, output, tempdefault, blastdir, debug or modifynames for the set.dir command."); m->mothurOutEndLine(); abort = true;
+ }else if((input == "") && (output == "") && (tempdefault == "") && (blastLocation == "")) { debugorSeedOnly = true; }
}
}
catch(exception& e) {
@@ -143,8 +149,8 @@ int SetDirectoryCommand::execute(){
//redirect output
if ((output == "clear") || (output == "")) { output = ""; commandFactory->setOutputDirectory(output); }
else if (output == "default") {
- string exepath = m->argv;
- output = exepath.substr(0, (exepath.find_last_of('m')));
+ string output = m->mothurProgramPath;
+ //output = exepath.substr(0, (exepath.find_last_of('m')));
m->mothurOut("outputDir=" + output); m->mothurOutEndLine();
commandFactory->setOutputDirectory(output);
@@ -158,8 +164,8 @@ int SetDirectoryCommand::execute(){
//redirect input
if ((input == "clear") || (input == "")) { input = ""; commandFactory->setInputDirectory(input); }
else if (input == "default") {
- string exepath = m->argv;
- input = exepath.substr(0, (exepath.find_last_of('m')));
+ string input = m->mothurProgramPath;
+ //input = exepath.substr(0, (exepath.find_last_of('m')));
m->mothurOut("inputDir=" + input); m->mothurOutEndLine();
commandFactory->setInputDirectory(input);
@@ -183,8 +189,8 @@ int SetDirectoryCommand::execute(){
#endif
}else if (tempdefault == "") { //do nothing
}else if (tempdefault == "default") {
- string exepath = m->argv;
- tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
+ string tempdefault = m->mothurProgramPath;
+ //tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
m->mothurOut("tempDefault=" + tempdefault); m->mothurOutEndLine();
m->setDefaultPath(tempdefault);
@@ -194,6 +200,21 @@ int SetDirectoryCommand::execute(){
m->setDefaultPath(tempdefault);
}
}
+
+ //set default
+ if (blastLocation == "") { //do nothing }
+ }else if ((blastLocation == "default") || (blastLocation == "clear")){
+ string blastLocation = m->mothurProgramPath;
+
+ m->mothurOut("Blast Location=" + blastLocation); m->mothurOutEndLine();
+ m->setBlastPath(blastLocation);
+ }else {
+ if (m->dirCheck(blastLocation)) {
+ m->mothurOut("Blast Location=" + blastLocation); m->mothurOutEndLine();
+ m->setBlastPath(blastLocation);
+ }
+ }
+
}
return 0;
}
diff --git a/source/commands/setdircommand.h b/source/commands/setdircommand.h
index 8789bd7..920bc64 100644
--- a/source/commands/setdircommand.h
+++ b/source/commands/setdircommand.h
@@ -36,7 +36,7 @@ public:
private:
CommandFactory* commandFactory;
- string output, input, tempdefault;
+ string output, input, tempdefault, blastLocation;
bool abort, debugorSeedOnly, modifyNames;
int random;
vector<string> outputNames;
diff --git a/source/commands/sffinfocommand.cpp b/source/commands/sffinfocommand.cpp
index d467f6b..a3f7e40 100644
--- a/source/commands/sffinfocommand.cpp
+++ b/source/commands/sffinfocommand.cpp
@@ -1383,6 +1383,8 @@ int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& pr
int currentSeqsDiffs = 0;
string seq = read.bases;
+
+ for (int i = 0; i < seq.length(); i++) { seq[i] = toupper(seq[i]); }
if (trim) {
if(header.clipQualRight < header.clipQualLeft){
@@ -1398,16 +1400,6 @@ int SffInfoCommand::findGroup(Header header, seqRead read, int& barcode, int& pr
else {
seq = seq.substr(header.clipQualLeft-1);
}
- }else{
- //if you wanted the sfftxt then you already converted the bases to the right case
- if (!sfftxt) {
- int endValue = header.clipQualRight;
- //make the bases you want to clip lowercase and the bases you want to keep upper case
- if(endValue == 0){ endValue = seq.length(); }
- for (int i = 0; i < (header.clipQualLeft-1); i++) { seq[i] = tolower(seq[i]); }
- for (int i = (header.clipQualLeft-1); i < (endValue-1); i++) { seq[i] = toupper(seq[i]); }
- for (int i = (endValue-1); i < seq.length(); i++) { seq[i] = tolower(seq[i]); }
- }
}
Sequence currSeq(header.name, seq);
diff --git a/source/commands/sffmultiplecommand.cpp b/source/commands/sffmultiplecommand.cpp
index abd012d..19c04b9 100644
--- a/source/commands/sffmultiplecommand.cpp
+++ b/source/commands/sffmultiplecommand.cpp
@@ -293,10 +293,10 @@ SffMultipleCommand::SffMultipleCommand(string option) {
temp = validParameter.validFile(parameters, "lookup", true);
if (temp == "not found") {
- string path = m->argv;
- string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
+ string path = m->mothurProgramPath;
+ //string tempPath = path;
+ //for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ //path = path.substr(0, (tempPath.find_last_of('m')));
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
path += "lookupFiles/";
@@ -311,10 +311,10 @@ SffMultipleCommand::SffMultipleCommand(string option) {
lookupFileName = validParameter.validFile(parameters, "lookup", false);
//if you can't open it its not inputDir, try mothur excutable location
- string exepath = m->argv;
- string tempPath = exepath;
- for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
- exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+ string exepath = m->mothurProgramPath;
+ //string tempPath = exepath;
+ //for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+ //exepath = exepath.substr(0, (tempPath.find_last_of('m')));
string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
diff --git a/source/commands/sharedcommand.cpp b/source/commands/sharedcommand.cpp
index eb7986a..f3e643c 100644
--- a/source/commands/sharedcommand.cpp
+++ b/source/commands/sharedcommand.cpp
@@ -476,6 +476,8 @@ int SharedCommand::createSharedFromBiom() {
//read data
vector<SharedRAbundVector*> lookup = readData(matrixFormat, thisLine, matrixElementType, groupNames, otuNames.size());
+
+ eliminateZeroOTUS(lookup);
m->mothurOutEndLine(); m->mothurOut(lookup[0]->getLabel()); m->mothurOutEndLine();
lookup[0]->printHeaders(out);
@@ -527,7 +529,7 @@ vector<SharedRAbundVector*> SharedCommand::readData(string matrixFormat, string
inBrackets = false;
int temp;
float temp2;
- if (matrixElementType == "float") { m->mothurConvert(num, temp2); temp = (int)temp2; }
+ if (matrixElementType == "float") { m->mothurConvert(num, temp2); temp = floor(temp2); }
else { m->mothurConvert(num, temp); }
nums.push_back(temp);
num = "";
@@ -556,7 +558,9 @@ vector<SharedRAbundVector*> SharedCommand::readData(string matrixFormat, string
if (inBrackets) {
if (line[i] == ',') {
int temp;
- m->mothurConvert(num, temp);
+ float temp2;
+ if (matrixElementType == "float") { m->mothurConvert(num, temp2); temp = floor(temp2); }
+ else { m->mothurConvert(num, temp); }
nums.push_back(temp);
num = "";
}else { if (!isspace(line[i])) { num += line[i]; } }
diff --git a/source/commands/shhhercommand.cpp b/source/commands/shhhercommand.cpp
index d36a323..d91e01f 100644
--- a/source/commands/shhhercommand.cpp
+++ b/source/commands/shhhercommand.cpp
@@ -231,10 +231,10 @@ ShhherCommand::ShhherCommand(string option) {
//if you can't open it its not in current working directory or inputDir, try mothur excutable location
if (ableToOpen == 1) {
- string exepath = m->argv;
- string tempPath = exepath;
- for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
- exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+ string exepath = m->mothurProgramPath;
+ //string tempPath = exepath;
+ //for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+ //exepath = exepath.substr(0, (tempPath.find_last_of('m')));
string tryPath = m->getFullPathName(exepath) + m->getSimpleName(fName);
m->mothurOut("Unable to open " + fName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
@@ -261,10 +261,10 @@ ShhherCommand::ShhherCommand(string option) {
string temp;
temp = validParameter.validFile(parameters, "lookup", true);
if (temp == "not found") {
- string path = m->argv;
- string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
+ string path = m->mothurProgramPath;
+ //string tempPath = path;
+ //for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ //path = path.substr(0, (tempPath.find_last_of('m')));
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
path += "lookupFiles/";
@@ -304,10 +304,10 @@ ShhherCommand::ShhherCommand(string option) {
//if you can't open it its not in current working directory or inputDir, try mothur excutable location
if (ableToOpen == 1) {
- string exepath = m->argv;
- string tempPath = exepath;
- for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
- exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+ string exepath = m->mothurProgramPath;
+ //string tempPath = exepath;
+ //for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+ //exepath = exepath.substr(0, (tempPath.find_last_of('m')));
string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
@@ -324,10 +324,10 @@ ShhherCommand::ShhherCommand(string option) {
lookupFileName = validParameter.validFile(parameters, "lookup", false);
//if you can't open it its not inputDir, try mothur excutable location
- string exepath = m->argv;
- string tempPath = exepath;
- for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
- exepath = exepath.substr(0, (tempPath.find_last_of('m')));
+ string exepath = m->mothurProgramPath;
+ //string tempPath = exepath;
+ //for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
+ //exepath = exepath.substr(0, (tempPath.find_last_of('m')));
string tryPath = m->getFullPathName(exepath) + m->getSimpleName(lookupFileName);
m->mothurOut("Unable to open " + lookupFileName + ". Trying mothur's executable location " + tryPath); m->mothurOutEndLine();
diff --git a/source/commands/shhhseqscommand.cpp b/source/commands/shhhseqscommand.cpp
index ea25a04..206cf24 100644
--- a/source/commands/shhhseqscommand.cpp
+++ b/source/commands/shhhseqscommand.cpp
@@ -213,7 +213,8 @@ int ShhhSeqsCommand::execute() {
if (groupfile != "") {
//Parse sequences by group
- SequenceParser parser(groupfile, fastafile, namefile);
+ vector<string> temp;
+ SequenceParser parser(groupfile, fastafile, namefile, temp);
vector<string> groups = parser.getNamesOfGroups();
if (m->control_pressed) { return 0; }
diff --git a/source/commands/shhhseqscommand.h b/source/commands/shhhseqscommand.h
index 77bf61b..4c11638 100644
--- a/source/commands/shhhseqscommand.h
+++ b/source/commands/shhhseqscommand.h
@@ -103,7 +103,8 @@ static DWORD WINAPI MyShhhSeqsThreadFunction(LPVOID lpParam){
try {
//parse fasta and name file by group
- SequenceParser parser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile);
+ vector<string> temp;
+ SequenceParser parser(pDataArray->groupfile, pDataArray->fastafile, pDataArray->namefile, temp);
//precluster each group
for (int k = pDataArray->start; k < pDataArray->end; k++) {
diff --git a/source/commands/sortseqscommand.cpp b/source/commands/sortseqscommand.cpp
index 2b8a916..b5753f8 100644
--- a/source/commands/sortseqscommand.cpp
+++ b/source/commands/sortseqscommand.cpp
@@ -1156,8 +1156,8 @@ int SortSeqsCommand::readTax(){
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; m->gobble(in);
- in >> tax; m->gobble(in);
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
if (name != "") {
map<string, int>::iterator it = names.find(name);
@@ -1186,8 +1186,8 @@ int SortSeqsCommand::readTax(){
while(!in.eof()){
if (m->control_pressed) { in.close(); out.close(); m->mothurRemove(outputFileName); return 0; }
- in >> name; m->gobble(in);
- in >> tax; m->gobble(in);
+ in >> name; m->gobble(in);
+ tax = m->getline(in); m->gobble(in);
if (name != "") {
//if this name is in the accnos file
diff --git a/source/commands/sparcccommand.cpp b/source/commands/sparcccommand.cpp
index 5cfc9b2..3175d6a 100644
--- a/source/commands/sparcccommand.cpp
+++ b/source/commands/sparcccommand.cpp
@@ -199,6 +199,9 @@ int SparccCommand::execute(){
vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
string lastLabel = lookup[0]->getLabel();
+ int numOTUs = lookup[0]->getNumBins();
+ if (numOTUs >= maxIterations) { m->mothurOut("[WARNING]: The number of iterations is set higher than the number of OTUs, reducing to " + toString(numOTUs-1) + "\n"); maxIterations = numOTUs-1; }
+
//if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
set<string> processedLabels;
set<string> userLabels = labels;
@@ -607,7 +610,6 @@ vector<vector<float> > SparccCommand::createProcesses(vector<vector<float> >& sh
exit(1);
}
}
-
//**********************************************************************************************************************
vector<vector<float> > SparccCommand::driver(vector<vector<float> >& sharedVector, vector<vector<float> >& origCorrMatrix, int numPerms){
try {
@@ -631,7 +633,9 @@ vector<vector<float> > SparccCommand::driver(vector<vector<float> >& sharedVecto
else if(observedValue < 0 && randValue < observedValue){ pValues[j][k]++; }//pvalues of small rho values
}
}
- if((i+1) % (int)(numPermutations * 0.05) == 0){ cout << i+1 << endl; }
+
+ float done = ceil(numPermutations * 0.05);
+ if((i+1) % (int)(done) == 0){ cout << i+1 << endl; }
}
return pValues;
diff --git a/source/commands/splitgroupscommand.cpp b/source/commands/splitgroupscommand.cpp
index 50b80a4..d6fd2eb 100644
--- a/source/commands/splitgroupscommand.cpp
+++ b/source/commands/splitgroupscommand.cpp
@@ -270,8 +270,8 @@ int SplitGroupCommand::execute(){
int SplitGroupCommand::runNameGroup(){
try {
SequenceParser* parser;
- if (namefile == "") { parser = new SequenceParser(groupfile, fastafile); }
- else { parser = new SequenceParser(groupfile, fastafile, namefile); }
+ if (namefile == "") { parser = new SequenceParser(groupfile, fastafile, Groups); }
+ else { parser = new SequenceParser(groupfile, fastafile, namefile, Groups); }
if (m->control_pressed) { delete parser; return 0; }
@@ -294,7 +294,8 @@ int SplitGroupCommand::runNameGroup(){
variables["[filename]"] = namefileRoot;
string newName = getOutputFileName("name",variables);
- parser->getSeqs(Groups[i], newFasta, "/ab=", "/", false);
+ long long numSeqs = 0;
+ parser->getSeqs(Groups[i], newFasta, "/ab=", "/", numSeqs, false);
outputNames.push_back(newFasta); outputTypes["fasta"].push_back(newFasta);
if (m->control_pressed) { delete parser; for (int i = 0; i < outputNames.size(); i++) { m->mothurRemove(outputNames[i]); } return 0; }
diff --git a/source/commands/sracommand.cpp b/source/commands/sracommand.cpp
index 17fac11..65b5a2a 100644
--- a/source/commands/sracommand.cpp
+++ b/source/commands/sracommand.cpp
@@ -34,7 +34,7 @@ vector<string> SRACommand::setParameters(){
CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
-
+ CommandParameter ptrim("trim", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(ptrim);
//every command must have inputdir and outputdir. This allows mothur users to redirect input and output files.
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
@@ -67,6 +67,7 @@ string SRACommand::getHelpString(){
helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
helpString += "The checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. The default is false.\n";
+ helpString += "The trim parameter allows you to indicate if you would like a sequences and quality scores trimmed to the clipQualLeft and clipQualRight values. sff files only Default=True. \n";
helpString += "The includescrap parameter is used to indicate whether or not to include the scrapped sequences in your submission. The default is true.\n";
helpString += "The platform parameter is used to specify platform you are using choices are: _LS454,ILLUMINA,ION_TORRENT,PACBIO_SMRT. Default=_LS454. This is a controlled vocabulary section in the XML file that will be generated.\n";
helpString += "The orientation parameter is used to specify sequence orientation. Choices are: forward and reverse. Default=forward. This is a controlled vocabulary section in the XML file that will be generated.\n";
@@ -289,6 +290,8 @@ SRACommand::SRACommand(string option) {
checkorient = validParameter.validFile(parameters, "checkorient", false); if (temp == "not found") { temp = "F"; }
+ trim = validParameter.validFile(parameters, "trim", false); if (trim == "not found"){ temp = "T"; }
+
temp = validParameter.validFile(parameters, "includescrap", false); if (temp == "not found") { temp = "T"; }
includeScrap = m->isTrue(temp);
@@ -1245,6 +1248,7 @@ int SRACommand::parseSffFile(map<string, vector<string> >& files){
if (sdiffs != 0) { commandString += ", sdiffs=" + toString(sdiffs); }
if (tdiffs != 0) { commandString += ", tdiffs=" + toString(tdiffs); }
if (m->isTrue(checkorient)) { commandString += ", checkorient=" + checkorient; }
+ if (m->isTrue(trim)) { commandString += ", trim=" + trim; }
m->mothurOutEndLine();
m->mothurOut("/******************************************/"); m->mothurOutEndLine();
diff --git a/source/commands/sracommand.h b/source/commands/sracommand.h
index 56394bf..a590b64 100644
--- a/source/commands/sracommand.h
+++ b/source/commands/sracommand.h
@@ -44,7 +44,7 @@ private:
bool abort, isSFF, pairedOligos, setOligosParameter, includeScrap;
int tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, fileOption;
- string sfffile, fastqfile, outputDir, file, oligosfile, contactfile, inputfile, mimarksfile;
+ string sfffile, fastqfile, outputDir, file, oligosfile, contactfile, inputfile, mimarksfile, trim;
string libStrategy, libSource, libSelection, libLayout, platform, instrumentModel, fileType, dataType, checkorient;
string submissionName, lastName, firstName, email, centerName, centerType, ownership, description, website, orientation, packageType;
string projectName, projectTitle, inputDir;
diff --git a/source/commands/subsamplecommand.cpp b/source/commands/subsamplecommand.cpp
index 19e7555..1bab26e 100644
--- a/source/commands/subsamplecommand.cpp
+++ b/source/commands/subsamplecommand.cpp
@@ -1731,8 +1731,8 @@ int SubSampleCommand::getTax(set<string>& subset) {
if (m->control_pressed) { inTax.close(); outTax.close(); return 0; }
- inTax >> tname; m->gobble(inTax); //read from first column
- inTax >> tax; m->gobble(inTax); //read from second column
+ inTax >> tname; m->gobble(inTax);
+ tax = m->getline(inTax); m->gobble(inTax);
//does the subset contain a sequence that this sequence represents
itNameMap = nameMap.find(tname);
diff --git a/source/commands/summarytaxcommand.cpp b/source/commands/summarytaxcommand.cpp
index 5c4b00a..18efb98 100644
--- a/source/commands/summarytaxcommand.cpp
+++ b/source/commands/summarytaxcommand.cpp
@@ -220,7 +220,9 @@ SummaryTaxCommand::SummaryTaxCommand(string option) {
int SummaryTaxCommand::execute(){
try{
-
+
+ int maxLevel = findMaxLevel(taxfile);
+
if (abort == true) { if (calledHelp) { return 0; } return 2; }
int start = time(NULL);
@@ -241,63 +243,45 @@ int SummaryTaxCommand::execute(){
if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
int numSeqs = 0;
- if ((threshold == 0) && ((namefile == "") || (countfile != ""))) { numSeqs = taxaSum->summarize(taxfile); }
- else if (threshold != 0) {
- ifstream in;
- m->openInputFile(taxfile, in);
+ map<string, vector<string> > nameMap;
+ map<string, vector<string> >::iterator itNames;
+ if (namefile != "") { m->readNames(namefile, nameMap); }
+
+ ifstream in;
+ m->openInputFile(taxfile, in);
+
+ string name, taxon;
+ while(!in.eof()){
- string name, taxon;
- while(!in.eof()){
-
- if (m->control_pressed) { break; }
-
- in >> name >> taxon; m->gobble(in);
-
- if (threshold != 0) { taxon = processTaxMap(taxon); }
-
- //cout << taxon << endl;
+ if (m->control_pressed) { break; }
+
+ in >> name; m->gobble(in);
+ taxon = m->getline(in); m->gobble(in);
+
+ string newTax = m->addUnclassifieds(taxon, maxLevel, true);
+
+ if (threshold != 0) { newTax = processTaxMap(newTax); }
+
+ //add sequence to summary, countfile info included from Phylosummary constructor
+ if (namefile != "") {
+ itNames = nameMap.find(name);
- //add sequence to summary, countfile info included from Phylosummary constructor
- taxaSum->addSeqToTree(name, taxon);
+ if (itNames == nameMap.end()) {
+ m->mothurOut(name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
+ }else{
+ for (int i = 0; i < itNames->second.size(); i++) {
+ taxaSum->addSeqToTree(itNames->second[i], newTax); //add it as many times as there are identical seqs
+ }
+ itNames->second.clear();
+ nameMap.erase(itNames->first);
+ }
+ }else {
+ taxaSum->addSeqToTree(name, newTax);
}
- in.close();
+
}
- else if (namefile != "") {
- map<string, vector<string> > nameMap;
- map<string, vector<string> >::iterator itNames;
- m->readNames(namefile, nameMap);
-
- if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
-
- ifstream in;
- m->openInputFile(taxfile, in);
-
- //read in users taxonomy file and add sequences to tree
- string name, taxon;
-
- while(!in.eof()){
-
- if (m->control_pressed) { break; }
-
- in >> name >> taxon; m->gobble(in);
-
- if (threshold != 0) { taxon = processTaxMap(taxon); }
-
- itNames = nameMap.find(name);
-
- if (itNames == nameMap.end()) {
- m->mothurOut("[ERROR]: " + name + " is not in your name file please correct."); m->mothurOutEndLine(); exit(1);
- }else{
- for (int i = 0; i < itNames->second.size(); i++) {
- numSeqs++;
- taxaSum->addSeqToTree(itNames->second[i], taxon); //add it as many times as there are identical seqs
- }
- itNames->second.clear();
- nameMap.erase(itNames->first);
- }
- }
- in.close();
- }else if (threshold == 0) { numSeqs = taxaSum->summarize(taxfile); }
+ in.close();
+
if (m->control_pressed) { if (groupMap != NULL) { delete groupMap; } if (ct != NULL) { delete ct; } delete taxaSum; return 0; }
@@ -382,10 +366,10 @@ string SummaryTaxCommand::processTaxMap(string tax) {
if (spot != 0) {
newTax = "";
for (int i = 0; i < taxons.size(); i++) { newTax += taxons[i] + ";"; }
- for (int i = spot; i < taxLength; i++) {
- if(tax[i] == ';'){ newTax += "unclassified;"; }
+ //for (int i = spot; i < taxLength; i++) {
+ //if(tax[i] == ';'){ newTax += "unclassified;"; }
m->removeConfidences(newTax);
- }
+ //}
}else { m->removeConfidences(tax); newTax = tax; } //leave tax alone
return newTax;
@@ -395,6 +379,21 @@ string SummaryTaxCommand::processTaxMap(string tax) {
exit(1);
}
}
+/**************************************************************************************************/
+int SummaryTaxCommand::findMaxLevel(string file) {
+ try{
+ GroupMap* groupMap = NULL;
+ PhyloSummary taxaSum(groupMap, false, -1);
+
+ taxaSum.summarize(file);
+
+ return taxaSum.getMaxLevel();
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SummaryTaxCommand", "findMaxLevel");
+ exit(1);
+ }
+}
/**************************************************************************************/
diff --git a/source/commands/summarytaxcommand.h b/source/commands/summarytaxcommand.h
index 28b4f73..d58375d 100644
--- a/source/commands/summarytaxcommand.h
+++ b/source/commands/summarytaxcommand.h
@@ -41,6 +41,7 @@ class SummaryTaxCommand : public Command {
map<string, int> nameMap;
string processTaxMap(string);
+ int findMaxLevel(string);
};
/**************************************************************************************************/
diff --git a/source/datastructures/alignmentdb.cpp b/source/datastructures/alignmentdb.cpp
index ea65c8e..cdc5e67 100644
--- a/source/datastructures/alignmentdb.cpp
+++ b/source/datastructures/alignmentdb.cpp
@@ -13,7 +13,7 @@
#include "blastdb.hpp"
/**************************************************************************************************/
-AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid){ // This assumes that the template database is in fasta format, may
+AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gapOpen, float gapExtend, float match, float misMatch, int tid, bool writeShortcut){ // This assumes that the template database is in fasta format, may
try { // need to alter this in the future?
m = MothurOut::getInstance();
longest = 0;
@@ -104,8 +104,8 @@ AlignmentDB::AlignmentDB(string fastaFileName, string s, int kmerSize, float gap
if (m->control_pressed) { templateSequences.clear(); }
- search->generateDB();
-
+ if ((method != "kmer") || ((method == "kmer") && (writeShortcut))) { search->generateDB(); }
+
}else if ((method == "kmer") && (!needToGenerate)) {
ifstream kmerFileTest(kmerDBName.c_str());
search->readKmerDB(kmerFileTest);
diff --git a/source/datastructures/alignmentdb.h b/source/datastructures/alignmentdb.h
index 537af8d..0d66ddf 100644
--- a/source/datastructures/alignmentdb.h
+++ b/source/datastructures/alignmentdb.h
@@ -20,7 +20,7 @@ class AlignmentDB {
public:
- AlignmentDB(string, string, int, float, float, float, float, int); //reads fastafile passed in and stores sequences
+ AlignmentDB(string, string, int, float, float, float, float, int, bool); //reads fastafile passed in and stores sequences
AlignmentDB(string);
~AlignmentDB();
diff --git a/source/datastructures/blastalign.cpp b/source/datastructures/blastalign.cpp
index bb7192a..8109a3b 100644
--- a/source/datastructures/blastalign.cpp
+++ b/source/datastructures/blastalign.cpp
@@ -22,8 +22,7 @@ BlastAlignment::BlastAlignment(float go, float ge, float ma, float mm) :
match(ma), // This is the score to award for two nucleotides matching (match >= 0)
mismatch(mm) // This is the penalty to assess for a mismatch (mismatch <= 0)
{
- path = m->argv;
- path = path.substr(0, (path.find_last_of('m')));
+ path = m->getBlastPath();
gapOpen = abs(go); // This is the penalty to assess for opening a gap (gapOpen >= 0)
gapExtend = abs(ge); // This is the penalty to assess for extending a gap (gapExtend >= 0)
diff --git a/source/datastructures/blastdb.cpp b/source/datastructures/blastdb.cpp
index a77880e..9a7de16 100644
--- a/source/datastructures/blastdb.cpp
+++ b/source/datastructures/blastdb.cpp
@@ -33,10 +33,10 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
//make sure blast exists in the write place
if (path == "") {
- path = m->argv;
- string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
+ path = m->getBlastPath();
+ //string tempPath = path;
+ //for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ //path = path.substr(0, (tempPath.find_last_of('m')));
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
path += "blast/bin/";
@@ -87,7 +87,7 @@ gapOpen(gO), gapExtend(gE), match(mm), misMatch(mM) {
megablastCommand = m->getFullPathName(megablastCommand);
ableToOpen = m->openInputFile(megablastCommand, in3, "no error"); in3.close();
if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + megablastCommand + " file does not exist. mothur requires megablast.exe."); m->mothurOutEndLine(); m->control_pressed = true; }
-
+
}
catch(exception& e) {
m->errorOut(e, "BlastDB", "BlastDB");
@@ -105,10 +105,10 @@ BlastDB::BlastDB(string b, int tid) : Database() {
//make sure blast exists in the write place
if (path == "") {
- path = m->argv;
- string tempPath = path;
- for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
- path = path.substr(0, (tempPath.find_last_of('m')));
+ path = m->getBlastPath();
+ //string tempPath = path;
+ //for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); }
+ //path = path.substr(0, (tempPath.find_last_of('m')));
#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
path += "blast/bin/";
diff --git a/source/datastructures/counttable.h b/source/datastructures/counttable.h
index f9150d1..5883800 100644
--- a/source/datastructures/counttable.h
+++ b/source/datastructures/counttable.h
@@ -50,7 +50,7 @@ class CountTable {
//reads and creates smart enough to eliminate groups with zero counts
int createTable(set<string>&, map<string, string>&, set<string>&); //seqNames, seqName->group, groupNames
int createTable(string, string, bool); //namefile, groupfile, createGroup
- int readTable(string, bool, bool); //file, readGroups, mothurRunning
+ int readTable(string, bool, bool); //filename, readGroups, mothurRunning
int printTable(string);
int printHeaders(ofstream&);
diff --git a/source/datastructures/kmerdb.cpp b/source/datastructures/kmerdb.cpp
index 9a5d235..df7d3e4 100644
--- a/source/datastructures/kmerdb.cpp
+++ b/source/datastructures/kmerdb.cpp
@@ -123,7 +123,7 @@ vector<int> KmerDB::findClosestSequences(Sequence* candidateSeq, int num){
}
/**************************************************************************************************/
-
+//print shortcut file
void KmerDB::generateDB(){
try {
diff --git a/source/datastructures/optimatrix.cpp b/source/datastructures/optimatrix.cpp
new file mode 100644
index 0000000..8372b41
--- /dev/null
+++ b/source/datastructures/optimatrix.cpp
@@ -0,0 +1,445 @@
+//
+// optimatrix.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 4/20/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#include "optimatrix.h"
+#include "progress.hpp"
+#include "counttable.h"
+
+/***********************************************************************/
+
+OptiMatrix::OptiMatrix(string d, string df, double c, bool s) : distFile(d), distFormat(df), cutoff(c), sim(s) {
+ m = MothurOut::getInstance();
+ countfile = ""; namefile = "";
+
+ if (distFormat == "phylip") { readPhylip(); }
+ else { readColumn(); }
+}
+/***********************************************************************/
+OptiMatrix::OptiMatrix(string d, string nc, string f, string df, double c, bool s) : distFile(d), distFormat(df), format(f), cutoff(c), sim(s) {
+ m = MothurOut::getInstance();
+
+ if (format == "name") { namefile = nc; countfile = ""; }
+ else if (format == "count") { countfile = nc; namefile = ""; }
+ else { countfile = ""; namefile = ""; }
+
+ if (distFormat == "phylip") { readPhylip(); }
+ else { readColumn(); }
+}
+/***********************************************************************/
+int OptiMatrix::readFile(string d, string nc, string f, string df, double c, bool s) {
+ distFile = d; format = f; cutoff = c; sim = s; distFormat = df;
+
+ if (format == "name") { namefile = nc; countfile = ""; }
+ else if (format == "count") { countfile = nc; namefile = ""; }
+ else { countfile = ""; namefile = ""; }
+
+ if (distFormat == "phylip") { readPhylip(); }
+ else { readColumn(); }
+
+ return 0;
+}
+/***********************************************************************/
+ListVector* OptiMatrix::getListSingle() {
+ try {
+ ListVector* singlelist = NULL;
+
+ if (singletons.size() == 0) { }
+ else {
+ singlelist = new ListVector();
+
+ for (int i = 0; i < singletons.size(); i++) {
+ string otu = singletons[i];
+ singlelist->push_back(otu);
+ }
+ }
+
+ return singlelist;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiMatrix", "getListSingle");
+ exit(1);
+ }
+}
+/***********************************************************************/
+long int OptiMatrix::print(ostream& out) {
+ try {
+ long int count = 0;
+ for (int i = 0; i < closeness.size(); i++) {
+ for(set<int>::iterator it = closeness[i].begin(); it != closeness[i].end(); it++){
+ out << *it << '\t';
+ count++;
+ }
+ out << endl;
+ }
+ out << endl;
+ return count;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiMatrix", "getName");
+ exit(1);
+ }
+}
+/***********************************************************************/
+string OptiMatrix::getName(int index) {
+ try {
+ if (index > closeness.size()) { m->mothurOut("[ERROR]: index is not valid.\n"); m->control_pressed = true; return ""; }
+ string name = nameMap[index];
+ return name;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiMatrix", "getName");
+ exit(1);
+ }
+}
+/***********************************************************************/
+bool OptiMatrix::isClose(int i, int toFind){
+ try {
+ bool found = false;
+ if (closeness[i].count(toFind) != 0) { found = true; }
+ return found;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiMatrix", "isClose");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+string OptiMatrix::findDistFormat(string distFile){
+ try {
+ string fileFormat = "column";
+
+ ifstream fileHandle;
+ string numTest;
+
+ m->openInputFile(distFile, fileHandle);
+ fileHandle >> numTest;
+ fileHandle.close();
+
+ if (m->isContainingOnlyDigits(numTest)) { fileFormat = "phylip"; }
+
+ return fileFormat;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiMatrix", "findDistFormat");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+int OptiMatrix::readPhylip(){
+ try {
+ float distance;
+ int square, nseqs;
+ string name;
+
+ ifstream fileHandle;
+ string numTest;
+
+ m->openInputFile(distFile, fileHandle);
+ fileHandle >> numTest >> name;
+ nameMap.push_back(name);
+
+ if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
+ else { convert(numTest, nseqs); }
+
+ //square test
+ char d;
+ while((d=fileHandle.get()) != EOF){
+ if(isalnum(d)){ square = 1; fileHandle.putback(d); for(int i=0;i<nseqs;i++){ fileHandle >> distance; } break; }
+ if(d == '\n'){ square = 0; break; }
+ }
+
+ map<int, int> singletonIndexSwap;
+ vector<bool> singleton; singleton.resize(nseqs, true);
+ ///////////////////// Read to eliminate singletons ///////////////////////
+ if(square == 0){
+
+ for(int i=1;i<nseqs;i++){
+ if (m->control_pressed) { fileHandle.close(); return 0; }
+
+ fileHandle >> name; nameMap.push_back(name);
+
+ for(int j=0;j<i;j++){
+
+ fileHandle >> distance;
+
+ if (distance == -1) { distance = 1000000; } else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ singleton[i] = false;
+ singleton[j] = false;
+ singletonIndexSwap[i] = i;
+ singletonIndexSwap[j] = j;
+
+ }
+ }
+ }
+ }else{
+ for(int i=1;i<nseqs;i++){
+ if (m->control_pressed) { fileHandle.close(); return 0; }
+
+ fileHandle >> name; nameMap.push_back(name);
+
+ for(int j=0;j<nseqs;j++){
+ fileHandle >> distance;
+
+ if (distance == -1) { distance = 1000000; } else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ singleton[i] = false;
+ singleton[j] = false;
+ singletonIndexSwap[i] = i;
+ singletonIndexSwap[j] = j;
+ }
+ }
+ }
+ }
+ fileHandle.close();
+ //////////////////////////////////////////////////////////////////////////
+
+ int nonSingletonCount = 0;
+ for (int i = 0; i < singleton.size(); i++) {
+ if (!singleton[i]) { //if you are not a singleton
+ singletonIndexSwap[i] = nonSingletonCount;
+ nonSingletonCount++;
+ }else { singletons.push_back(nameMap[i]); }
+ }
+ singleton.clear();
+
+ closeness.resize(nonSingletonCount);
+
+ map<string, string> names;
+ if (namefile != "") { m->readNames(namefile, names); }
+
+ Progress* reading;
+ ifstream in;
+
+ m->openInputFile(distFile, in);
+ in >> nseqs >> name;
+
+ int newA = singletonIndexSwap[0];
+ if (namefile != "") {
+ name = names[name]; //redundant names
+ }
+ nameMap[newA] = name;
+
+ int fivepercent = (int)(0.05 * nseqs);
+
+ string line = "";
+ if(square == 0){
+
+ reading = new Progress("Reading matrix: ", nseqs * (nseqs - 1) / 2);
+ int index = 0;
+
+ for(int i=1;i<nseqs;i++){
+
+ if (m->control_pressed) { in.close(); delete reading; return 0; }
+
+ in >> name;
+
+ for(int j=0;j<i;j++){
+
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; } else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ int newB = singletonIndexSwap[j];
+ int newA = singletonIndexSwap[i];
+ closeness[newA].insert(newB);
+ closeness[newB].insert(newA);
+
+ if (namefile != "") {
+ name = names[name]; //redundant names
+ }
+ nameMap[newA] = name;
+ }
+ index++; reading->update(index);
+ }
+
+ if (m->debug) {
+ if((i % fivepercent) == 0){
+ unsigned long long ramUsed = m->getRAMUsed(); unsigned long long total = m->getTotalRAM();
+ m->mothurOut("\nCurrent RAM usage: " + toString(ramUsed/(double)GIG) + " Gigabytes. Total Ram: " + toString(total/(double)GIG) + " Gigabytes.\n");
+ }
+ }
+ }
+ }else{
+ reading = new Progress("Reading matrix: ", nseqs * nseqs);
+ int index = nseqs;
+
+ for(int i=0;i<nseqs;i++){ in >> distance; } m->gobble(in);
+
+ for(int i=1;i<nseqs;i++){
+ if (m->control_pressed) { in.close(); delete reading; return 0; }
+
+ in >> name;
+
+ for(int j=0;j<nseqs;j++){
+ in >> distance;
+
+ if (distance == -1) { distance = 1000000; } else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff && j < i){
+ int newB = singletonIndexSwap[j];
+ int newA = singletonIndexSwap[i];
+ closeness[newA].insert(newB);
+ closeness[newB].insert(newA);
+
+ if (namefile != "") {
+ name = names[name]; //redundant names
+ }
+ nameMap[newA] = name;
+ }
+ index++; reading->update(index);
+ }
+
+ if (m->debug) {
+ if((i % fivepercent) == 0){
+ unsigned long long ramUsed = m->getRAMUsed(); unsigned long long total = m->getTotalRAM();
+ m->mothurOut("\nCurrent RAM usage: " + toString(ramUsed/(double)GIG) + " Gigabytes. Total Ram: " + toString(total/(double)GIG) + " Gigabytes.\n");
+ }
+ }
+ }
+ }
+ in.close();
+ reading->finish();
+ delete reading;
+
+ if (m->debug) { unsigned long long ramUsed = m->getRAMUsed(); unsigned long long total = m->getTotalRAM();
+ m->mothurOut("\nCurrent RAM usage: " + toString(ramUsed/(double)GIG) + " Gigabytes. Total Ram: " + toString(total/(double)GIG) + " Gigabytes.\n"); }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiMatrix", "readPhylip");
+ exit(1);
+ }
+}
+/***********************************************************************/
+
+int OptiMatrix::readColumn(){
+ try {
+ map<string, int> nameAssignment;
+ if (namefile != "") { nameAssignment = m->readNames(namefile); }
+ else { CountTable ct; ct.readTable(countfile, false, true); nameAssignment = ct.getNameMap(); }
+ int count = 0;
+ for (map<string, int>::iterator it = nameAssignment.begin(); it!= nameAssignment.end(); it++) {
+ it->second = count; count++;
+ nameMap.push_back(it->first);
+ }
+
+ string firstName, secondName;
+ float distance;
+
+ ///////////////////// Read to eliminate singletons ///////////////////////
+ ifstream fileHandle;
+ m->openInputFile(distFile, fileHandle);
+
+ map<int, int> singletonIndexSwap;
+ vector<bool> singleton; singleton.resize(nameAssignment.size(), true);
+ while(fileHandle){ //let's assume it's a triangular matrix...
+
+ fileHandle >> firstName; m->gobble(fileHandle);
+ fileHandle >> secondName; m->gobble(fileHandle);
+ fileHandle >> distance; m->gobble(fileHandle); // get the row and column names and distance
+
+ if (m->debug) { cout << firstName << '\t' << secondName << '\t' << distance << endl; }
+
+ if (m->control_pressed) { fileHandle.close(); return 0; }
+
+ map<string,int>::iterator itA = nameAssignment.find(firstName);
+ map<string,int>::iterator itB = nameAssignment.find(secondName);
+
+ if(itA == nameAssignment.end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the name or count file, please correct\n"); exit(1); }
+ if(itB == nameAssignment.end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the name or count file, please correct\n"); exit(1); }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ int indexA = (itA->second);
+ int indexB = (itB->second);
+ singleton[indexA] = false;
+ singleton[indexB] = false;
+ singletonIndexSwap[indexA] = indexA;
+ singletonIndexSwap[indexB] = indexB;
+ }
+ }
+ fileHandle.close();
+ //////////////////////////////////////////////////////////////////////////
+
+ int nonSingletonCount = 0;
+ for (int i = 0; i < singleton.size(); i++) {
+ if (!singleton[i]) { //if you are a singleton
+ singletonIndexSwap[i] = nonSingletonCount;
+ nonSingletonCount++;
+ }else { singletons.push_back(nameMap[i]); }
+ }
+ singleton.clear();
+
+ ifstream in;
+ m->openInputFile(distFile, in);
+
+ closeness.resize(nonSingletonCount);
+
+ map<string, string> names;
+ if (namefile != "") { m->readNames(namefile, names); }
+
+ while(in){ //let's assume it's a triangular matrix...
+
+ in >> firstName; m->gobble(in);
+ in >> secondName; m->gobble(in);
+ in >> distance; m->gobble(in); // get the row and column names and distance
+
+ if (m->debug) { cout << firstName << '\t' << secondName << '\t' << distance << endl; }
+
+ if (m->control_pressed) { in.close(); return 0; }
+
+ map<string,int>::iterator itA = nameAssignment.find(firstName);
+ map<string,int>::iterator itB = nameAssignment.find(secondName);
+
+ if(itA == nameAssignment.end()){ m->mothurOut("AAError: Sequence '" + firstName + "' was not found in the name or count file, please correct\n"); exit(1); }
+ if(itB == nameAssignment.end()){ m->mothurOut("ABError: Sequence '" + secondName + "' was not found in the name or count file, please correct\n"); exit(1); }
+
+ if (distance == -1) { distance = 1000000; }
+ else if (sim) { distance = 1.0 - distance; } //user has entered a sim matrix that we need to convert.
+
+ if(distance < cutoff){
+ int indexA = (itA->second);
+ int indexB = (itB->second);
+
+ int newB = singletonIndexSwap[indexB];
+ int newA = singletonIndexSwap[indexA];
+ closeness[newA].insert(newB);
+ closeness[newB].insert(newA);
+
+ if (namefile != "") {
+ firstName = names[firstName]; //redundant names
+ secondName = names[secondName]; //redundant names
+ }
+
+ nameMap[newA] = firstName;
+ nameMap[newB] = secondName;
+ }
+ }
+ in.close();
+ nameAssignment.clear();
+
+ return 1;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiMatrix", "readColumn");
+ exit(1);
+ }
+}
+/***********************************************************************/
diff --git a/source/datastructures/optimatrix.h b/source/datastructures/optimatrix.h
new file mode 100644
index 0000000..d16f98b
--- /dev/null
+++ b/source/datastructures/optimatrix.h
@@ -0,0 +1,60 @@
+//
+// optimatrix.h
+// Mothur
+//
+// Created by Sarah Westcott on 4/20/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__optimatrix__
+#define __Mothur__optimatrix__
+
+#include "mothurout.h"
+#include "listvector.hpp"
+
+class OptiMatrix {
+
+#ifdef UNIT_TEST
+ friend class TestOptiMatrix;
+#endif
+
+
+public:
+ OptiMatrix() { m = MothurOut::getInstance(); }
+ OptiMatrix(string, string, double, bool); //distfile, distformat, cutoff, sim
+ OptiMatrix(string, string, string, string, double, bool); //distfile, name or count, format, distformat, cutoff, sim
+ ~OptiMatrix(){ }
+
+ set<int> getCloseSeqs(int i) { return closeness[i]; }
+ //int get(int i, int j) { return closeness[i][j]; }
+ bool isClose(int, int);
+ int getNumClose(int index) { return closeness[index].size(); }
+ int getNumSeqs() { return closeness.size(); }
+ int getNumSingletons() { return singletons.size(); }
+ //map<int, string> getNameMap() { return nameMap; }
+ string getName(int); //name from nameMap index
+ ListVector* getListSingle();
+ long int print(ostream&);
+ int readFile(string, string, string, string, double, bool); //distfile, name or count, format, distformat, cutoff, sim
+
+private:
+
+ vector< set<int> > closeness; //closeness[0] contains indexes of seqs "close" to seq 0.
+ vector<string> singletons;
+ vector<string> nameMap;
+
+ string distFile, namefile, countfile, format, distFormat;
+ double cutoff;
+ bool sim;
+
+ MothurOut* m;
+
+ string findDistFormat(string distFile);
+ int readPhylip();
+ int readColumn();
+ map<string, int> readNames(string namefile, vector<string>&);
+
+};
+
+
+#endif /* defined(__Mothur__optimatrix__) */
diff --git a/source/datastructures/sequencecountparser.cpp b/source/datastructures/sequencecountparser.cpp
index e49ba98..32646a7 100644
--- a/source/datastructures/sequencecountparser.cpp
+++ b/source/datastructures/sequencecountparser.cpp
@@ -7,9 +7,10 @@
//
#include "sequencecountparser.h"
+#include "sharedutilities.h"
/************************************************************/
-SequenceCountParser::SequenceCountParser(string countfile, string fastafile) {
+SequenceCountParser::SequenceCountParser(string countfile, string fastafile, vector<string> groupsSelected) {
try {
m = MothurOut::getInstance();
@@ -17,58 +18,72 @@ SequenceCountParser::SequenceCountParser(string countfile, string fastafile) {
//read count file
CountTable countTable;
countTable.readTable(countfile, true, false);
+ vector<string> allNames = countTable.getNamesOfGroups();
//initialize maps
- namesOfGroups = countTable.getNamesOfGroups();
+ if (groupsSelected.size() == 0) { //select all
+ namesOfGroups = countTable.getNamesOfGroups();
+ for (int i = 0; i < allNames.size(); i++) { indexes.push_back(i); }
+ }else{
+ SharedUtil util; util.setGroups(groupsSelected, allNames);
+ namesOfGroups = groupsSelected;
+ map<string, int> temp;
+ for (int i = 0; i < allNames.size(); i++) {
+ for (int j = 0; j < groupsSelected.size(); j++) {
+ if (allNames[i] == groupsSelected[j]) {
+ temp[groupsSelected[j]] = i;
+ }
+ }
+ }
+ for (map<string, int>::iterator it = temp.begin(); it != temp.end(); it++) {
+ indexes.push_back(it->second);
+ }
+ }
+
for (int i = 0; i < namesOfGroups.size(); i++) {
vector<Sequence> temp;
map<string, int> tempMap;
seqs[namesOfGroups[i]] = temp;
countTablePerGroup[namesOfGroups[i]] = tempMap;
}
-
- //read fasta file making sure each sequence is in the group file
- ifstream in;
- m->openInputFile(fastafile, in);
-
- int fastaCount = 0;
- while (!in.eof()) {
-
- if (m->control_pressed) { break; }
-
- Sequence seq(in); m->gobble(in);
- fastaCount++;
- if (m->debug) { if((fastaCount) % 1000 == 0){ m->mothurOut("[DEBUG]: reading seq " + toString(fastaCount) + "\n."); } }
-
- if (seq.getName() != "") {
-
- allSeqsMap[seq.getName()] = seq.getName();
- vector<int> groupCounts = countTable.getGroupCounts(seq.getName());
-
- for (int i = 0; i < namesOfGroups.size(); i++) {
- if (groupCounts[i] != 0) {
- seqs[namesOfGroups[i]].push_back(seq);
- countTablePerGroup[namesOfGroups[i]][seq.getName()] = groupCounts[i];
- }
- }
- }
- }
- in.close();
- }
+
+ readFasta(fastafile, countTable);
+ }
catch(exception& e) {
m->errorOut(e, "SequenceCountParser", "SequenceCountParser");
exit(1);
}
}
/************************************************************/
-SequenceCountParser::SequenceCountParser(string fastafile, CountTable& countTable) {
+SequenceCountParser::SequenceCountParser(string fastafile, CountTable& countTable, vector<string> groupsSelected) {
try {
m = MothurOut::getInstance();
//initialize maps
if (countTable.hasGroupInfo()) {
- namesOfGroups = countTable.getNamesOfGroups();
+ vector<string> allNames = countTable.getNamesOfGroups();
+
+ //initialize maps
+ if (groupsSelected.size() == 0) { //select all
+ namesOfGroups = countTable.getNamesOfGroups();
+ for (int i = 0; i < allNames.size(); i++) { indexes.push_back(i); }
+ }else{
+ SharedUtil util; util.setGroups(groupsSelected, allNames);
+ namesOfGroups = groupsSelected;
+ map<string, int> temp;
+ for (int i = 0; i < allNames.size(); i++) {
+ for (int j = 0; j < groupsSelected.size(); j++) {
+ if (allNames[i] == groupsSelected[j]) {
+ temp[groupsSelected[j]] = i;
+ }
+ }
+ }
+ for (map<string, int>::iterator it = temp.begin(); it != temp.end(); it++) {
+ indexes.push_back(it->second);
+ }
+ }
+
for (int i = 0; i < namesOfGroups.size(); i++) {
vector<Sequence> temp;
map<string, int> tempMap;
@@ -76,33 +91,8 @@ SequenceCountParser::SequenceCountParser(string fastafile, CountTable& countTabl
countTablePerGroup[namesOfGroups[i]] = tempMap;
}
- //read fasta file making sure each sequence is in the group file
- ifstream in;
- m->openInputFile(fastafile, in);
+ readFasta(fastafile, countTable);
- int fastaCount = 0;
- while (!in.eof()) {
-
- if (m->control_pressed) { break; }
-
- Sequence seq(in); m->gobble(in);
- fastaCount++;
- if (m->debug) { if((fastaCount) % 1000 == 0){ m->mothurOut("[DEBUG]: reading seq " + toString(fastaCount) + "\n."); } }
-
- if (seq.getName() != "") {
-
- allSeqsMap[seq.getName()] = seq.getName();
- vector<int> groupCounts = countTable.getGroupCounts(seq.getName());
-
- for (int i = 0; i < namesOfGroups.size(); i++) {
- if (groupCounts[i] != 0) {
- seqs[namesOfGroups[i]].push_back(seq);
- countTablePerGroup[namesOfGroups[i]][seq.getName()] = groupCounts[i];
- }
- }
- }
- }
- in.close();
}else { m->control_pressed = true; m->mothurOut("[ERROR]: cannot parse fasta file by group with a count table that does not include group data, please correct.\n"); }
}
@@ -112,6 +102,43 @@ SequenceCountParser::SequenceCountParser(string fastafile, CountTable& countTabl
}
}
/************************************************************/
+int SequenceCountParser::readFasta(string fastafile, CountTable& countTable) {
+ try {
+
+
+ ifstream in;
+ m->openInputFile(fastafile, in);
+
+
+ while (!in.eof()) {
+
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
+
+ if (seq.getName() != "") {
+
+ //allSeqsMap[seq.getName()] = seq.getName();
+ vector<int> groupCounts = countTable.getGroupCounts(seq.getName());
+
+ for (int i = 0; i < namesOfGroups.size(); i++) {
+ if (groupCounts[indexes[i]] != 0) {
+ seqs[namesOfGroups[i]].push_back(seq);
+ countTablePerGroup[namesOfGroups[i]][seq.getName()] = groupCounts[indexes[i]];
+ }
+ }
+ }
+ }
+ in.close();
+
+ return 0;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SequenceCountParser", "readFasta");
+ exit(1);
+ }
+}
+/************************************************************/
SequenceCountParser::~SequenceCountParser(){ }
/************************************************************/
int SequenceCountParser::getNumGroups(){ return namesOfGroups.size(); }
@@ -138,6 +165,24 @@ int SequenceCountParser::getNumSeqs(string g){
}
}
/************************************************************/
+map<string, string> SequenceCountParser::getAllSeqsMap(){
+ try {
+ map<string, string > allSeqsMap;
+ map<string, vector<Sequence> >::iterator it;
+
+ for (it = seqs.begin(); it != seqs.end(); it++) {
+ vector<Sequence> temp = it->second;
+ for (int i = 0; i < temp.size(); i++) { allSeqsMap[temp[i].getName()] = temp[i].getName(); }
+ }
+
+ return allSeqsMap;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "SequenceCountParser", "getAllSeqsMap");
+ exit(1);
+ }
+}
+/************************************************************/
vector<Sequence> SequenceCountParser::getSeqs(string g){
try {
map<string, vector<Sequence> >::iterator it;
@@ -159,7 +204,7 @@ vector<Sequence> SequenceCountParser::getSeqs(string g){
}
}
/************************************************************/
-int SequenceCountParser::getSeqs(string g, string filename, string tag, string tag2, bool uchimeFormat=false){
+int SequenceCountParser::getSeqs(string g, string filename, string tag, string tag2, long long& numSeqs, bool uchimeFormat=false){
try {
map<string, vector<Sequence> >::iterator it;
vector<Sequence> seqForThisGroup;
@@ -169,11 +214,13 @@ int SequenceCountParser::getSeqs(string g, string filename, string tag, string t
if(it == seqs.end()) {
m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
}else {
-
+
ofstream out;
m->openOutputFile(filename, out);
seqForThisGroup = it->second;
+
+ numSeqs = seqForThisGroup.size();
if (uchimeFormat) {
// format should look like
diff --git a/source/datastructures/sequencecountparser.h b/source/datastructures/sequencecountparser.h
index cce8e32..2975902 100644
--- a/source/datastructures/sequencecountparser.h
+++ b/source/datastructures/sequencecountparser.h
@@ -26,8 +26,8 @@ class SequenceCountParser {
public:
- SequenceCountParser(string, string); //count, fasta - file mismatches will set m->control_pressed = true
- SequenceCountParser(string, CountTable&); //fasta, counttable - file mismatches will set m->control_pressed = true
+ SequenceCountParser(string, string, vector<string>); //count, fasta - file mismatches will set m->control_pressed = true
+ SequenceCountParser(string, CountTable&, vector<string>); //fasta, counttable - file mismatches will set m->control_pressed = true
~SequenceCountParser();
//general operations
@@ -38,20 +38,22 @@ public:
vector<Sequence> getSeqs(string); //returns unique sequences in a specific group
map<string, int> getCountTable(string); //returns seqName -> numberOfRedundantSeqs for a specific group - the count file format, but each line is parsed by group.
- int getSeqs(string, string, string, string, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false, tag (/ab= or ;size=), tag2(/ or ;)
+ int getSeqs(string, string, string, string, long long&, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false, tag (/ab= or ;size=), tag2(/ or ;)
int getCountTable(string, string); //print seqName -> numberRedundantSeqs for a specific group - group, filename
- map<string, string> getAllSeqsMap(){ return allSeqsMap; } //returns map where the key=sequenceName and the value=representativeSequence - helps us remove duplicates after group by group processing
+ map<string, string> getAllSeqsMap(); //returns map where the key=sequenceName and the value=representativeSequence - helps us remove duplicates after group by group processing
private:
CountTable countTable;
MothurOut* m;
int numSeqs;
- map<string, string> allSeqsMap;
+ vector<int> indexes;
+ //map<string, string> allSeqsMap;
map<string, vector<Sequence> > seqs; //a vector for each group
map<string, map<string, int> > countTablePerGroup; //countTable for each group
vector<string> namesOfGroups;
+ int readFasta(string fastafile, CountTable&);
};
diff --git a/source/datastructures/sequencedb.cpp b/source/datastructures/sequencedb.cpp
index e798ee1..55d4ef1 100644
--- a/source/datastructures/sequencedb.cpp
+++ b/source/datastructures/sequencedb.cpp
@@ -56,60 +56,6 @@ SequenceDB::SequenceDB(ifstream& filehandle) {
exit(1);
}
}
-/*******************************************************************************/
-string SequenceDB::readName(ifstream& in) {
- try{
- string name = "";
- int c;
- string temp;
-
- while ((c = in.get()) != EOF) {
- //if c is not a line return
- if (c != 10) {
- name += c;
- }else { break; }
- }
-
- return name;
- }
- catch(exception& e) {
- m->errorOut(e, "SequenceDB", "readName");
- exit(1);
- }
-}
-
-/*******************************************************************************/
-string SequenceDB::readSequence(ifstream& in) {
- try{
- string sequence = "";
- string line;
- int pos, c;
-
- while (!in.eof()) {
- //save position in file in case next line is a new name.
- pos = in.tellg();
- line = "";
- in >> line;
- //if you are at a new name
- if (line[0] == '>') {
- //put file pointer back since you are now at a new name
- in.seekg(pos, ios::beg);
- c = in.get(); //because you put it back to a newline char
- break;
- }else { sequence += line; }
- }
-
- if (length == 0) { length = sequence.length(); }
- if (length != sequence.length()) { samelength = false; }
-
- return sequence;
- }
- catch(exception& e) {
- m->errorOut(e, "SequenceDB", "readSequence");
- exit(1);
- }
-}
-
/***********************************************************************/
int SequenceDB::getNumSeqs() {
diff --git a/source/datastructures/sequencedb.h b/source/datastructures/sequencedb.h
index 8f7640e..940eb07 100644
--- a/source/datastructures/sequencedb.h
+++ b/source/datastructures/sequencedb.h
@@ -41,8 +41,6 @@ public:
private:
vector<Sequence> data;
- string readName(ifstream&);
- string readSequence(ifstream&);
MothurOut* m;
bool samelength;
int length;
diff --git a/source/datastructures/sequenceparser.cpp b/source/datastructures/sequenceparser.cpp
index 0c8ce7d..4ec13a1 100644
--- a/source/datastructures/sequenceparser.cpp
+++ b/source/datastructures/sequenceparser.cpp
@@ -8,10 +8,10 @@
*/
#include "sequenceparser.h"
-
+#include "sharedutilities.h"
/************************************************************/
-SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFile) {
+SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFile, vector<string> groupsSelected) {
try {
m = MothurOut::getInstance();
@@ -24,220 +24,86 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
if (error == 1) { m->control_pressed = true; }
//initialize maps
- vector<string> namesOfGroups = groupMap->getNamesOfGroups();
- for (int i = 0; i < namesOfGroups.size(); i++) {
- vector<Sequence> temp;
- map<string, string> tempMap;
- seqs[namesOfGroups[i]] = temp;
- nameMapPerGroup[namesOfGroups[i]] = tempMap;
- }
-
+ vector<string> namesOfGroups = groupMap->getNamesOfGroups();
+ set<string> selectedGroups;
+ if (groupsSelected.size() != 0) {
+ SharedUtil util; util.setGroups(groupsSelected, namesOfGroups);
+ namesOfGroups = groupsSelected;
+ }
+
+ for (int i = 0; i < namesOfGroups.size(); i++) {
+ vector<Sequence> temp;
+ map<string, string> tempMap;
+ seqs[namesOfGroups[i]] = temp;
+ nameMapPerGroup[namesOfGroups[i]] = tempMap;
+ selectedGroups.insert(namesOfGroups[i]);
+ }
+
+ map<string, string>::iterator it;
+ map<string, string> nameMap;
+ m->readNames(nameFile, nameMap);
+
//read fasta file making sure each sequence is in the group file
ifstream in;
m->openInputFile(fastaFile, in);
-
- map<string, string> seqName; //stores name -> sequence string so we can make new "unique" sequences when we parse the name file
- int fastaCount = 0;
- while (!in.eof()) {
-
- if (m->control_pressed) { break; }
-
- Sequence seq(in); m->gobble(in);
- fastaCount++;
- if (m->debug) { if((fastaCount) % 1000 == 0){ m->mothurOut("[DEBUG]: reading seq " + toString(fastaCount) + "\n."); } }
-
- if (seq.getName() != "") {
-
- string group = groupMap->getGroup(seq.getName());
- if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine(); }
- else {
- seqs[group].push_back(seq);
- seqName[seq.getName()] = seq.getAligned();
- }
- }
- }
- in.close();
-
- if (error == 1) { m->control_pressed = true; }
-
- //read name file
- ifstream inName;
- m->openInputFile(nameFile, inName);
-
- //string first, second;
- int countName = 0;
- set<string> thisnames1;
-
- string rest = "";
- char buffer[4096];
- bool pairDone = false;
- bool columnOne = true;
- string firstCol, secondCol;
- while (!inName.eof()) {
- if (m->control_pressed) { break; }
-
- inName.read(buffer, 4096);
- vector<string> pieces = m->splitWhiteSpace(rest, buffer, inName.gcount());
+ while (!in.eof()) {
- for (int i = 0; i < pieces.size(); i++) {
- if (columnOne) { firstCol = pieces[i]; columnOne=false; }
- else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
-
- if (pairDone) { //save one line
- if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
- vector<string> names;
- m->splitAtChar(secondCol, names, ',');
-
- //get aligned string for these seqs from the fasta file
- string alignedString = "";
- map<string, string>::iterator itAligned = seqName.find(names[0]);
- if (itAligned == seqName.end()) {
- error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
- }else {
- alignedString = itAligned->second;
- }
-
- //separate by group - parse one line in name file
- map<string, string> splitMap; //group -> name1,name2,...
- map<string, string>::iterator it;
- for (int i = 0; i < names.size(); i++) {
-
- string group = groupMap->getGroup(names[i]);
- if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your name file and not in your groupfile, please correct."); m->mothurOutEndLine(); }
- else {
-
- it = splitMap.find(group);
- if (it != splitMap.end()) { //adding seqs to this group
- (it->second) += "," + names[i];
- thisnames1.insert(names[i]);
- countName++;
- }else { //first sighting of this group
- splitMap[group] = names[i];
- countName++;
- thisnames1.insert(names[i]);
-
- //is this seq in the fasta file?
- if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
- Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
- seqs[group].push_back(tempSeq);
- }
- }
- }
-
- allSeqsMap[names[i]] = names[0];
- }
-
-
- //fill nameMapPerGroup - holds all lines in namefile separated by group
- for (it = splitMap.begin(); it != splitMap.end(); it++) {
- //grab first name
- string firstName = "";
- for(int i = 0; i < (it->second).length(); i++) {
- if (((it->second)[i]) != ',') {
- firstName += ((it->second)[i]);
- }else { break; }
- }
-
- //group1 -> seq1 -> seq1,seq2,seq3
- nameMapPerGroup[it->first][firstName] = it->second;
- }
-
- pairDone = false;
- }
- }
- }
- inName.close();
-
- //in case file does not end in white space
- if (rest != "") {
- vector<string> pieces = m->splitWhiteSpace(rest);
+ if (m->control_pressed) { break; }
+
+ Sequence seq(in); m->gobble(in);
- for (int i = 0; i < pieces.size(); i++) {
- if (columnOne) { firstCol = pieces[i]; columnOne=false; }
- else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
+ if (seq.getName() != "") {
- if (pairDone) { //save one line
- if (m->debug) { m->mothurOut("[DEBUG]: reading names: " + firstCol + '\t' + secondCol + ".\n"); }
+ it = nameMap.find(seq.getName());
+
+ if (it != nameMap.end()) { //in namefile
+
vector<string> names;
+ string secondCol = it->second;
m->splitAtChar(secondCol, names, ',');
- //get aligned string for these seqs from the fasta file
- string alignedString = "";
- map<string, string>::iterator itAligned = seqName.find(names[0]);
- if (itAligned == seqName.end()) {
- error = 1; m->mothurOut("[ERROR]: " + names[0] + " is in your name file and not in your fasta file, please correct."); m->mothurOutEndLine();
- }else {
- alignedString = itAligned->second;
- }
-
- //separate by group - parse one line in name file
map<string, string> splitMap; //group -> name1,name2,...
- map<string, string>::iterator it;
+ map<string, string>::iterator itSplit;
for (int i = 0; i < names.size(); i++) {
-
string group = groupMap->getGroup(names[i]);
- if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your name file and not in your groupfile, please correct."); m->mothurOutEndLine(); }
- else {
-
- it = splitMap.find(group);
- if (it != splitMap.end()) { //adding seqs to this group
- (it->second) += "," + names[i];
- thisnames1.insert(names[i]);
- countName++;
- }else { //first sighting of this group
- splitMap[group] = names[i];
- countName++;
- thisnames1.insert(names[i]);
+
+ if (selectedGroups.count(group) != 0) { //this is a group we want
+ if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + names[i] + " is in your names file and not in your group file, please correct.\n"); }
+ else {
+ allSeqsMap[names[i]] = names[0];
- //is this seq in the fasta file?
- if (i != 0) { //if not then we need to add a duplicate sequence to the seqs for this group so the new "fasta" and "name" files will match
- Sequence tempSeq(names[i], alignedString); //get the first guys sequence string since he's in the fasta file.
- seqs[group].push_back(tempSeq);
+ itSplit = splitMap.find(group);
+ if (itSplit != splitMap.end()) { //adding seqs to this group
+ (itSplit->second) += "," + names[i];
+ }else { //first sighting of this group
+ splitMap[group] = names[i];
}
}
}
-
- allSeqsMap[names[i]] = names[0];
}
-
//fill nameMapPerGroup - holds all lines in namefile separated by group
- for (it = splitMap.begin(); it != splitMap.end(); it++) {
+ for (itSplit = splitMap.begin(); itSplit != splitMap.end(); itSplit++) {
//grab first name
string firstName = "";
- for(int i = 0; i < (it->second).length(); i++) {
- if (((it->second)[i]) != ',') {
- firstName += ((it->second)[i]);
+ for(int i = 0; i < (itSplit->second).length(); i++) {
+ if (((itSplit->second)[i]) != ',') {
+ firstName += ((itSplit->second)[i]);
}else { break; }
}
//group1 -> seq1 -> seq1,seq2,seq3
- nameMapPerGroup[it->first][firstName] = it->second;
+ nameMapPerGroup[itSplit->first][firstName] = itSplit->second;
+ seqs[itSplit->first].push_back(Sequence(firstName, seq.getAligned()));
}
-
- pairDone = false;
- }
+
+ }else { error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your name file, please correct.\n"); }
}
}
-
+ in.close();
+
if (error == 1) { m->control_pressed = true; }
-
- if (countName != (groupMap->getNumSeqs())) {
- vector<string> groupseqsnames = groupMap->getNamesSeqs();
-
- for (int i = 0; i < groupseqsnames.size(); i++) {
- set<string>::iterator itnamesfile = thisnames1.find(groupseqsnames[i]);
- if (itnamesfile == thisnames1.end()){
- cout << "missing name " + groupseqsnames[i] << '\t' << allSeqsMap[groupseqsnames[i]] << endl;
- }
- }
-
- m->mothurOutEndLine();
- m->mothurOut("[ERROR]: Your name file contains " + toString(countName) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
- m->mothurOutEndLine();
- m->control_pressed = true;
- }
}
catch(exception& e) {
@@ -246,7 +112,7 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile, string nameFi
}
}
/************************************************************/
-SequenceParser::SequenceParser(string groupFile, string fastaFile) {
+SequenceParser::SequenceParser(string groupFile, string fastaFile, vector<string> groupsSelected) {
try {
m = MothurOut::getInstance();
@@ -259,16 +125,22 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile) {
if (error == 1) { m->control_pressed = true; }
//initialize maps
- vector<string> namesOfGroups = groupMap->getNamesOfGroups();
+ vector<string> namesOfGroups = groupMap->getNamesOfGroups();
+ set<string> selectedGroups;
+ if (groupsSelected.size() != 0) {
+ SharedUtil util; util.setGroups(groupsSelected, namesOfGroups);
+ namesOfGroups = groupsSelected;
+ }
+
for (int i = 0; i < namesOfGroups.size(); i++) {
vector<Sequence> temp;
seqs[namesOfGroups[i]] = temp;
+ selectedGroups.insert(namesOfGroups[i]);
}
//read fasta file making sure each sequence is in the group file
ifstream in;
m->openInputFile(fastaFile, in);
- int count = 0;
while (!in.eof()) {
@@ -277,24 +149,20 @@ SequenceParser::SequenceParser(string groupFile, string fastaFile) {
Sequence seq(in); m->gobble(in);
if (seq.getName() != "") {
-
+
string group = groupMap->getGroup(seq.getName());
- if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine(); }
- else { seqs[group].push_back(seq); count++; }
+ if (selectedGroups.count(group) != 0) { //this is a group we want
+ if (group == "not found") { error = 1; m->mothurOut("[ERROR]: " + seq.getName() + " is in your fasta file and not in your groupfile, please correct."); m->mothurOutEndLine(); }
+ else {
+ seqs[group].push_back(seq);
+ }
+ }
}
}
in.close();
if (error == 1) { m->control_pressed = true; }
- if (count != (groupMap->getNumSeqs())) {
- m->mothurOutEndLine();
- m->mothurOut("[ERROR]: Your fasta file contains " + toString(count) + " valid sequences, and your groupfile contains " + toString(groupMap->getNumSeqs()) + ", please correct.");
- if (count < (groupMap->getNumSeqs())) { m->mothurOut(" Did you forget to include the name file?"); }
- m->mothurOutEndLine();
- m->control_pressed = true;
- }
-
}
catch(exception& e) {
m->errorOut(e, "SequenceParser", "SequenceParser");
@@ -351,7 +219,7 @@ vector<Sequence> SequenceParser::getSeqs(string g){
}
}
/************************************************************/
-int SequenceParser::getSeqs(string g, string filename, string tag, string tag2, bool uchimeFormat=false){
+int SequenceParser::getSeqs(string g, string filename, string tag, string tag2, long long& numSeqs, bool uchimeFormat=false){
try {
map<string, vector<Sequence> >::iterator it;
vector<Sequence> seqForThisGroup;
@@ -361,11 +229,14 @@ int SequenceParser::getSeqs(string g, string filename, string tag, string tag2,
if(it == seqs.end()) {
m->mothurOut("[ERROR]: No sequences available for group " + g + ", please correct."); m->mothurOutEndLine();
}else {
-
+
ofstream out;
m->openOutputFile(filename, out);
seqForThisGroup = it->second;
+
+ numSeqs = seqForThisGroup.size();
+
if (uchimeFormat) {
// format should look like
diff --git a/source/datastructures/sequenceparser.h b/source/datastructures/sequenceparser.h
index 5e79b8f..d13d1b2 100644
--- a/source/datastructures/sequenceparser.h
+++ b/source/datastructures/sequenceparser.h
@@ -28,8 +28,8 @@ class SequenceParser {
public:
- SequenceParser(string, string); //group, fasta - file mismatches will set m->control_pressed = true
- SequenceParser(string, string, string); //group, fasta, name - file mismatches will set m->control_pressed = true
+ SequenceParser(string, string, vector<string>); //group, fasta, groups (if blanks then all) - file mismatches will set m->control_pressed = true
+ SequenceParser(string, string, string, vector<string>); //group, fasta, name, groups (if blanks then all) - file mismatches will set m->control_pressed = true
~SequenceParser();
//general operations
@@ -41,7 +41,7 @@ class SequenceParser {
vector<Sequence> getSeqs(string); //returns unique sequences in a specific group
map<string, string> getNameMap(string); //returns seqName -> namesOfRedundantSeqs separated by commas for a specific group - the name file format, but each line is parsed by group.
- int getSeqs(string, string, string, string, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false, tag(/ab= or ;size=), tag2(/ or ;)
+ int getSeqs(string, string, string, string, long long&, bool); //prints unique sequences in a specific group to a file - group, filename, uchimeFormat=false, tag(/ab= or ;size=), tag2(/ or ;)
int getNameMap(string, string); //print seqName -> namesOfRedundantSeqs separated by commas for a specific group - group, filename
map<string, string> getAllSeqsMap(){ return allSeqsMap; } //returns map where the key=sequenceName and the value=representativeSequence - helps us remove duplicates after group by group processing
diff --git a/source/engine.cpp b/source/engine.cpp
index 780fd13..2cd43a5 100644
--- a/source/engine.cpp
+++ b/source/engine.cpp
@@ -36,8 +36,10 @@ InteractEngine::InteractEngine(string path){
//this will happen if you set the path variable to contain mothur's exe location
if (temppath == "") { path = mout->findProgramPath("mothur"); }
+ else { path = temppath; }
- mout->argv = path;
+ mout->mothurProgramPath = mout->getFullPathName(path);
+ mout->setBlastPath(mout->mothurProgramPath);
//if you haven't set your own location
#ifdef MOTHUR_FILES
@@ -173,8 +175,10 @@ BatchEngine::BatchEngine(string path, string batchFileName){
//this will happen if you set the path variable to contain mothur's exe location
if (temppath == "") { path = mout->findProgramPath("mothur"); }
+ else { path = temppath; }
- mout->argv = path;
+ mout->mothurProgramPath = mout->getFullPathName(path);
+ mout->setBlastPath(mout->mothurProgramPath);
//if you haven't set your own location
#ifdef MOTHUR_FILES
@@ -257,7 +261,8 @@ bool BatchEngine::getInput(){
//if we aborted command
if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + ".\n"); }
-
+
+ if (mout->control_pressed) { break; }
mout->control_pressed = 0;
mout->executing = false;
@@ -307,8 +312,10 @@ ScriptEngine::ScriptEngine(string path, string commandString){
//this will happen if you set the path variable to contain mothur's exe location
if (temppath == "") { path = mout->findProgramPath("mothur"); }
+ else { path = temppath; }
- mout->argv = path;
+ mout->mothurProgramPath = mout->getFullPathName(path);
+ mout->setBlastPath(mout->mothurProgramPath);
//if you haven't set your own location
#ifdef MOTHUR_FILES
@@ -391,7 +398,8 @@ bool ScriptEngine::getInput(){
//if we aborted command
if (quitCommandCalled == 2) { mout->mothurOut("[ERROR]: did not complete " + commandName + ".\n"); }
-
+
+ if (mout->control_pressed) { break; }
mout->control_pressed = 0;
mout->executing = false;
diff --git a/source/linearalgebra.cpp b/source/linearalgebra.cpp
index 5fe8928..0219493 100644
--- a/source/linearalgebra.cpp
+++ b/source/linearalgebra.cpp
@@ -460,7 +460,7 @@ int LinearAlgebra::qtli(vector<double>& d, vector<double>& e, vector<vector<doub
if(fabs(e[myM])+dd == dd) break;
}
if(myM != l){
- if(iter++ == 3000) cerr << "Too many iterations in tqli\n";
+ if(iter++ == 3000) cerr << "Too many iterations in qtli\n";
g = (d[l+1]-d[l]) / (2.0 * e[l]);
r = pythag(g, 1.0);
g = d[myM] - d[l] + e[l] / (g + SIGN(r,g));
diff --git a/source/makefile b/source/makefile
deleted file mode 100644
index fe1d1d4..0000000
--- a/source/makefile
+++ /dev/null
@@ -1,171 +0,0 @@
-###################################################
-#
-# Makefile for mothur
-#
-###################################################
-
-#
-# Macros
-#
-
-USEMPI ?= no
-64BIT_VERSION ?= yes
-USEREADLINE ?= yes
-USECOMPRESSION ?= no
-MOTHUR_FILES="\"Enter_your_default_path_here\""
-BOOST_INCLUDE_DIR="/usr/local/include/"
-BOOST_LIBRARY_DIR="/usr/local/lib/"
-RELEASE_DATE = "\"4/22/2015\""
-VERSION = "\"1.35.1\""
-FORTAN_COMPILER = gfortran
-FORTRAN_FLAGS =
-
-# Optimize to level 3:
-CXXFLAGS += -O3
-
-ifeq ($(strip $(64BIT_VERSION)),yes)
- #if you are using centos uncomment the following lines
- #CXX = g++44
-
- #if you are a mac user use the following line
- TARGET_ARCH += -arch x86_64
-
- #if you using cygwin to build Windows the following line
- #CXX = x86_64-w64-mingw32-g++
- #CC = x86_64-w64-mingw32-g++
- #FORTAN_COMPILER = x86_64-w64-mingw32-gfortran
- #TARGET_ARCH += -m64 -static
-
- #if you are a linux user use the following line
- #CXXFLAGS += -mtune=native -march=native
-
- CXXFLAGS += -DBIT_VERSION
- FORTRAN_FLAGS = -m64
-endif
-
-
-CXXFLAGS += -DRELEASE_DATE=${RELEASE_DATE} -DVERSION=${VERSION}
-
-ifeq ($(strip $(MOTHUR_FILES)),"\"Enter_your_default_path_here\"")
-else
- CXXFLAGS += -DMOTHUR_FILES=${MOTHUR_FILES}
-endif
-
-
-# if you do not want to use the readline library, set this to no.
-# make sure you have the library installed
-
-
-ifeq ($(strip $(USEREADLINE)),yes)
- CXXFLAGS += -DUSE_READLINE
- LIBS = \
- -lreadline\
- -lncurses
-endif
-
-#statically link boost libraries
-LDFLAGS += -L ${BOOST_LIBRARY_DIR}
-CXXFLAGS += -I ${BOOST_INCLUDE_DIR}
-
-LIBS += \
- ${BOOST_LIBRARY_DIR}libboost_atomic.a\
- ${BOOST_LIBRARY_DIR}libboost_iostreams.a\
- ${BOOST_LIBRARY_DIR}libboost_test_exec_monitor.a\
- ${BOOST_LIBRARY_DIR}libboost_chrono.a\
- ${BOOST_LIBRARY_DIR}libboost_locale.a\
- ${BOOST_LIBRARY_DIR}libboost_prg_exec_monitor.a\
- ${BOOST_LIBRARY_DIR}libboost_thread.a\
- ${BOOST_LIBRARY_DIR}libboost_container.a\
- ${BOOST_LIBRARY_DIR}libboost_log.a\
- ${BOOST_LIBRARY_DIR}libboost_program_options.a\
- ${BOOST_LIBRARY_DIR}libboost_timer.a\
- ${BOOST_LIBRARY_DIR}libboost_context.a\
- ${BOOST_LIBRARY_DIR}libboost_log_setup.a\
- ${BOOST_LIBRARY_DIR}libboost_python.a\
- ${BOOST_LIBRARY_DIR}libboost_unit_test_framework.a\
- ${BOOST_LIBRARY_DIR}libboost_coroutine.a\
- ${BOOST_LIBRARY_DIR}libboost_math_c99.a\
- ${BOOST_LIBRARY_DIR}libboost_random.a\
- ${BOOST_LIBRARY_DIR}libboost_wave.a\
- ${BOOST_LIBRARY_DIR}libboost_date_time.a\
- ${BOOST_LIBRARY_DIR}libboost_math_c99f.a\
- ${BOOST_LIBRARY_DIR}libboost_math_tr1l.a\
- ${BOOST_LIBRARY_DIR}libboost_math_c99l.a\
- ${BOOST_LIBRARY_DIR}libboost_math_tr1.a\
- ${BOOST_LIBRARY_DIR}libboost_math_tr1f.a\
- ${BOOST_LIBRARY_DIR}libboost_regex.a\
- ${BOOST_LIBRARY_DIR}libboost_wserialization.a\
- ${BOOST_LIBRARY_DIR}libboost_exception.a\
- ${BOOST_LIBRARY_DIR}libboost_serialization.a\
- ${BOOST_LIBRARY_DIR}libboost_filesystem.a\
- ${BOOST_LIBRARY_DIR}libboost_signals.a\
- ${BOOST_LIBRARY_DIR}libboost_graph.a\
- ${BOOST_LIBRARY_DIR}libboost_system.a\
- ${BOOST_LIBRARY_DIR}zlib.a
-
-ifeq ($(strip $(USEMPI)),yes)
- CXX = mpic++
- CXXFLAGS += -DUSE_MPI
-endif
-
-# if you want to enable reading and writing of compressed files, set to yes.
-# The default is no. this may only work on unix-like systems, not for windows.
-
-
-ifeq ($(strip $(USECOMPRESSION)),yes)
- CXXFLAGS += -DUSE_COMPRESSION
-endif
-
-#
-# INCLUDE directories for mothur
-#
-#
- VPATH=calculators:chimera:classifier:clearcut:commands:communitytype:datastructures:metastats:randomforest:read:svm
- skipUchime := uchime_src/
- subdirs := $(filter-out $(skipUchime), $(wildcard */))
- subDirIncludes = $(patsubst %, -I %, $(subdirs))
- subDirLinking = $(patsubst %, -L%, $(subdirs))
- CXXFLAGS += -I. $(subDirIncludes)
- LDFLAGS += $(subDirLinking)
-
-
-#
-# Get the list of all .cpp files, rename to .o files
-#
-
-
- OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs))))
- OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs))))
- OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
- OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
- OBJECTS+=$(patsubst %.f,%.o,$(wildcard *.f))
-
-mothur : fortranSource $(OBJECTS) uchime
- $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
- strip mothur
- mv mothur ..
-
-uchime:
- cd uchime_src && ./mk && mv uchime .. && cd ..
-
-fortranSource:
- ${FORTAN_COMPILER} -c $(FORTRAN_FLAGS) *.f
-
-install : mothur uchime
- mv mothur ..
- mv uchime ..
-
-
-%.o : %.c %.h
- $(COMPILE.c) $(OUTPUT_OPTION) $<
-%.o : %.cpp %.h
- $(COMPILE.cpp) $(OUTPUT_OPTION) $<
-%.o : %.cpp %.hpp
- $(COMPILE.cpp) $(OUTPUT_OPTION) $<
-
-
-
-clean :
- @rm -f $(OBJECTS)
- @rm -f uchime
-
diff --git a/source/mothur.cpp b/source/mothur.cpp
index e6e3a0e..5bcaf66 100644
--- a/source/mothur.cpp
+++ b/source/mothur.cpp
@@ -145,8 +145,6 @@ int main(int argc, char *argv[]){
m->mothurOut("Department of Microbiology & Immunology");
m->mothurOutEndLine();
m->mothurOut("University of Michigan");
- m->mothurOutEndLine();
- m->mothurOut("pschloss at umich.edu");
m->mothurOutEndLine();
m->mothurOut("http://www.mothur.org");
m->mothurOutEndLine();
@@ -161,7 +159,10 @@ int main(int argc, char *argv[]){
m->mothurOutEndLine();
m->mothurOut("Type 'help()' for information on the commands that are available");
m->mothurOutEndLine();
- m->mothurOutEndLine();
+ m->mothurOutEndLine();
+ m->mothurOut("For questions and analysis support, please visit our forum at https://www.mothur.org/forum");
+ m->mothurOutEndLine();
+ m->mothurOutEndLine();
m->mothurOut("Type 'quit()' to exit program");
m->mothurOutEndLine();
}
diff --git a/source/mothurout.cpp b/source/mothurout.cpp
index eadce7e..0c3adc0 100644
--- a/source/mothurout.cpp
+++ b/source/mothurout.cpp
@@ -44,6 +44,7 @@ set<string> MothurOut::getCurrentTypes() {
types.insert("sff");
types.insert("shared");
types.insert("taxonomy");
+ types.insert("constaxonomy");
types.insert("tree");
types.insert("flow");
types.insert("biom");
@@ -83,6 +84,7 @@ void MothurOut::printCurrentFiles(string filename) {
if (sfffile != "") { mothurOut("sff=" + sfffile, out); mothurOutEndLine(out); }
if (sharedfile != "") { mothurOut("shared=" + sharedfile, out); mothurOutEndLine(out); }
if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile, out); mothurOutEndLine(out); }
+ if (constaxonomyfile != "") { mothurOut("constaxonomy=" + constaxonomyfile, out); mothurOutEndLine(out);}
if (treefile != "") { mothurOut("tree=" + treefile, out); mothurOutEndLine(out); }
if (flowfile != "") { mothurOut("flow=" + flowfile, out); mothurOutEndLine(out); }
if (biomfile != "") { mothurOut("biom=" + biomfile, out); mothurOutEndLine(out); }
@@ -112,6 +114,7 @@ void MothurOut::printCurrentFiles(string filename) {
if (sfffile != "") { mothurOut("sff=" + sfffile); mothurOutEndLine(); }
if (sharedfile != "") { mothurOut("shared=" + sharedfile); mothurOutEndLine(); }
if (taxonomyfile != "") { mothurOut("taxonomy=" + taxonomyfile); mothurOutEndLine(); }
+ if (constaxonomyfile != "") { mothurOut("constaxonomy=" + constaxonomyfile); mothurOutEndLine();}
if (treefile != "") { mothurOut("tree=" + treefile); mothurOutEndLine(); }
if (flowfile != "") { mothurOut("flow=" + flowfile); mothurOutEndLine(); }
if (biomfile != "") { mothurOut("biom=" + biomfile); mothurOutEndLine(); }
@@ -150,6 +153,7 @@ bool MothurOut::hasCurrentFiles() {
if (sfffile != "") { return true; }
if (sharedfile != "") { return true; }
if (taxonomyfile != "") { return true; }
+ if (constaxonomyfile != "") { return true; }
if (treefile != "") { return true; }
if (flowfile != "") { return true; }
if (biomfile != "") { return true; }
@@ -313,7 +317,7 @@ void MothurOut::setDefaultPath(string pathname) {
if (lastChar != "\\") { pathname += "\\"; }
#endif
- defaultPath = pathname;
+ defaultPath = getFullPathName(pathname);
}
catch(exception& e) {
@@ -322,6 +326,27 @@ void MothurOut::setDefaultPath(string pathname) {
}
}
/*********************************************************************************************/
+void MothurOut::setBlastPath(string pathname) {
+ try {
+
+ //add / to name if needed
+ string lastChar = pathname.substr(pathname.length()-1);
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
+ if (lastChar != "/") { pathname += "/"; }
+#else
+ if (lastChar != "\\") { pathname += "\\"; }
+#endif
+
+ blastPath = getFullPathName(pathname);
+
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "setDefaultPath");
+ exit(1);
+ }
+}
+
+/*********************************************************************************************/
void MothurOut::setOutputDir(string pathname) {
try {
outputDir = pathname;
@@ -1879,7 +1904,10 @@ vector<consTax> MothurOut::readConsTax(string inputfile){
string otu = ""; string tax = "unknown";
int size = 0;
- in >> otu >> size >> tax; gobble(in);
+ in >> otu; gobble(in);
+ in >> size; gobble(in);
+ tax = getline(in); gobble(in);
+
consTax temp(otu, tax, size);
taxes.push_back(temp);
}
@@ -1908,7 +1936,10 @@ int MothurOut::readConsTax(string inputfile, map<int, consTax2>& taxes){
string otu = ""; string tax = "unknown";
int size = 0;
- in >> otu >> size >> tax; gobble(in);
+ in >> otu; gobble(in);
+ in >> size; gobble(in);
+ tax = getline(in); gobble(in);
+
consTax2 temp(otu, tax, size);
string simpleBin = getSimpleLabel(otu);
int bin;
@@ -2419,6 +2450,34 @@ vector<string> MothurOut::splitWhiteSpace(string input){
}
}
/***********************************************************************/
+int MothurOut::splitWhiteSpace(string input, vector<float>& pieces, int index){
+ try {
+ pieces.clear();
+ string rest = "";
+ int count = 0;
+
+ for (int i = 0; i < input.length(); i++) {
+ if (!isspace(input[i])) { rest += input[i]; }
+ else {
+ if (rest != "") { float tdist; mothurConvert(rest, tdist); pieces.push_back(tdist); count++; rest = ""; }
+ while (i < input.length()) { //gobble white space
+ if (isspace(input[i])) { i++; }
+ else { rest = input[i]; break; } //cout << "next piece buffer = " << nextPiece << endl;
+ }
+ if (count > index) { return 0; }
+ }
+ }
+
+ if (rest != "") { float tdist; mothurConvert(rest, tdist); count++; pieces.push_back(tdist); }
+
+ return 0;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "splitWhiteSpace");
+ exit(1);
+ }
+}
+/***********************************************************************/
vector<string> MothurOut::splitWhiteSpaceWithQuotes(string input){
try {
vector<string> pieces;
@@ -2459,78 +2518,39 @@ vector<string> MothurOut::splitWhiteSpaceWithQuotes(string input){
}
}
//**********************************************************************************************************************
-int MothurOut::readTax(string namefile, map<string, string>& taxMap, bool removeConfidence) {
+int MothurOut::readTax(string taxfile, map<string, string>& taxMap, bool removeConfidence) {
try {
//open input file
ifstream in;
- openInputFile(namefile, in);
+ openInputFile(taxfile, in);
- string rest = "";
- char buffer[4096];
- bool pairDone = false;
- bool columnOne = true;
- string firstCol, secondCol;
bool error = false;
+ string name, taxonomy;
while (!in.eof()) {
if (control_pressed) { break; }
- in.read(buffer, 4096);
- vector<string> pieces = splitWhiteSpace(rest, buffer, in.gcount());
+ in >> name; gobble(in);
+ taxonomy = getline(in); gobble(in);
- for (int i = 0; i < pieces.size(); i++) {
- if (columnOne) { firstCol = pieces[i]; columnOne=false; }
- else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
-
- if (pairDone) {
- checkName(firstCol);
- //are there confidence scores, if so remove them
- if (removeConfidence) { if (secondCol.find_first_of('(') != -1) { removeConfidences(secondCol); } }
- map<string, string>::iterator itTax = taxMap.find(firstCol);
-
- if(itTax == taxMap.end()) {
- bool ignore = false;
- if (secondCol != "") { if (secondCol[secondCol.length()-1] != ';') { mothurOut("[ERROR]: " + firstCol + " is missing the final ';', ignoring.\n"); ignore=true; }
- }
- if (!ignore) { taxMap[firstCol] = secondCol; }
- if (debug) { mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n"); }
- }else {
- mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique.\n"); error = true;
- }
- pairDone = false;
+ checkName(name);
+ //are there confidence scores, if so remove them
+ if (removeConfidence) { if (taxonomy.find_first_of('(') != -1) { removeConfidences(taxonomy); } }
+ map<string, string>::iterator itTax = taxMap.find(name);
+
+ if(itTax == taxMap.end()) {
+ bool ignore = false;
+ if (taxonomy != "") { if (taxonomy[taxonomy.length()-1] != ';') { mothurOut("[ERROR]: " + name + " is missing the final ';', ignoring.\n"); ignore=true; }
}
+ if (!ignore) { taxMap[name] = taxonomy; }
+ if (debug) { mothurOut("[DEBUG]: name = '" + name + "' tax = '" + taxonomy + "'\n"); }
+ }else {
+ mothurOut("[ERROR]: " + name + " is already in your taxonomy file, names must be unique./n"); error = true;
}
- }
- in.close();
-
- if (rest != "") {
- vector<string> pieces = splitWhiteSpace(rest);
-
- for (int i = 0; i < pieces.size(); i++) {
- if (columnOne) { firstCol = pieces[i]; columnOne=false; }
- else { secondCol = pieces[i]; pairDone = true; columnOne=true; }
-
- if (pairDone) {
- checkName(firstCol);
- //are there confidence scores, if so remove them
- if (removeConfidence) { if (secondCol.find_first_of('(') != -1) { removeConfidences(secondCol); } }
- map<string, string>::iterator itTax = taxMap.find(firstCol);
-
- if(itTax == taxMap.end()) {
- bool ignore = false;
- if (secondCol != "") { if (secondCol[secondCol.length()-1] != ';') { mothurOut("[ERROR]: " + firstCol + " is missing the final ';', ignoring.\n"); ignore=true; }
- }
- if (!ignore) { taxMap[firstCol] = secondCol; }
- if (debug) { mothurOut("[DEBUG]: name = '" + firstCol + "' tax = '" + secondCol + "'\n"); }
- }else {
- mothurOut("[ERROR]: " + firstCol + " is already in your taxonomy file, names must be unique./n"); error = true;
- }
- pairDone = false;
- }
- }
}
-
+ in.close();
+
if (error) { control_pressed = true; }
if (debug) { mothurOut("[DEBUG]: numSeqs saved = '" + toString(taxMap.size()) + "'\n"); }
return taxMap.size();
@@ -3446,13 +3466,16 @@ bool MothurOut::mothurConvert(string item, intDist& num){
string MothurOut::addUnclassifieds(string tax, int maxlevel, bool probs) {
try{
string newTax, taxon;
- int level = 1;
+ string savedTax = tax;
vector<string> taxons; splitAtChar(tax, taxons, ';'); taxons.pop_back();
vector<int> confidences;
+ if (taxons.size() == maxlevel) { return savedTax; }
+
int index = 0;
int confidence = 0;
+ int level = 1;
for (int i = 0; i < taxons.size(); i++) {
index = i;
string thisTax = taxons[i]+";";
@@ -3462,7 +3485,7 @@ string MothurOut::addUnclassifieds(string tax, int maxlevel, bool probs) {
if (thisTax == "unclassified;"){ index--; break; }
else{ newTax += taxons[i] + ";"; }
}
- level = index+2;
+ level = index+1;
string thisTax = taxons[index]+";";
@@ -3504,6 +3527,23 @@ bool MothurOut::isNumeric1(string stringToCheck){
}
/***********************************************************************/
+bool MothurOut::allSpaces(string stringToCheck){
+ try {
+
+ for (int i = 0; i < stringToCheck.length(); i++) {
+ char c = stringToCheck[i];
+ if (!isspace(c)) { return false; }
+ }
+
+ return true;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isNumeric1");
+ exit(1);
+ }
+
+}
+/***********************************************************************/
bool MothurOut::isInteger(string stringToCheck){
try {
bool isInt = false;
@@ -3534,6 +3574,22 @@ bool MothurOut::containsAlphas(string stringToCheck){
}
/***********************************************************************/
+bool MothurOut::isAllAlphas(string stringToCheck){
+ try {
+ bool allAlphas = true;
+
+ if(stringToCheck.find_first_not_of("AaBbCcDdEeFfGgHhIiJjKkLlMmNnOopPQqRrSsTtUuVvWwXxYyZz") != string::npos) { allAlphas = false; }
+
+ return allAlphas;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "isAllAlphas");
+ exit(1);
+ }
+
+}
+
+/***********************************************************************/
bool MothurOut::mothurConvert(string item, float& num){
try {
bool error = false;
@@ -3798,7 +3854,24 @@ int MothurOut::sum(vector<int> x) {
return value;
}
catch(exception& e) {
- errorOut(e, "MothurOut", "average - int");
+ errorOut(e, "MothurOut", "sum - int");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double MothurOut::sum(vector<double> x) {
+ try {
+ int value = 0;
+
+ for (int i = 0; i < x.size(); i++) {
+ if (control_pressed) { break; }
+ value += x[i];
+ }
+
+ return value;
+ }
+ catch(exception& e) {
+ errorOut(e, "MothurOut", "sum - double");
exit(1);
}
}
@@ -3884,7 +3957,7 @@ bool MothurOut::checkLocations(string& filename, string inputDir){
//if you can't open it its not in current working directory or inputDir, try mothur excutable location
if (ableToOpen == 1) {
- string exepath = argv;
+ string exepath = mothurProgramPath;
string tempPath = exepath;
for (int i = 0; i < exepath.length(); i++) { tempPath[i] = tolower(exepath[i]); }
exepath = exepath.substr(0, (tempPath.find_last_of('m')));
diff --git a/source/mothurout.h b/source/mothurout.h
index ca1ea12..667292c 100644
--- a/source/mothurout.h
+++ b/source/mothurout.h
@@ -46,6 +46,8 @@ class MothurOut {
void closeLog();
string getDefaultPath() { return defaultPath; }
void setDefaultPath(string);
+ string getBlastPath() { return blastPath; }
+ void setBlastPath(string);
string getOutputDir() { return outputDir; }
void setOutputDir(string);
@@ -69,7 +71,7 @@ class MothurOut {
vector<string> sharedBinLabelsInFile;
vector<string> currentSharedBinLabels;
vector<string> listBinLabelsInFile;
- string saveNextLabel, argv, sharedHeaderMode, groupMode, testDirectory;
+ string saveNextLabel, mothurProgramPath, sharedHeaderMode, groupMode, testDirectory;
bool printedSharedHeaders, printedListHeaders, commandInputsConvertError, changedSeqNames, modifyNames;
//functions from mothur.h
@@ -125,6 +127,7 @@ class MothurOut {
void zapGremlins(istringstream&);
vector<string> splitWhiteSpace(string& rest, char[], int);
vector<string> splitWhiteSpace(string);
+ int splitWhiteSpace(string, vector<float>&, int);
set<string> readAccnos(string);
int readAccnos(string, vector<string>&);
int readAccnos(string, vector<string>&, string);
@@ -163,9 +166,11 @@ class MothurOut {
bool isTrue(string);
bool isContainingOnlyDigits(string);
bool containsAlphas(string);
+ bool isAllAlphas(string);
bool isNumeric1(string);
bool isNumeric1(char);
bool isInteger(string);
+ bool allSpaces(string);
bool isLabelEquivalent(string, string);
string getSimpleLabel(string);
string findEdianness();
@@ -193,7 +198,7 @@ class MothurOut {
string makeList(vector<string>&);
bool isSubset(vector<string>, vector<string>); //bigSet, subset
int checkName(string&);
- bool checkGroupName(string name);
+ bool checkGroupName(string name);
map<string, vector<string> > parseClasses(string);
string addUnclassifieds(string tax, int maxlevel, bool probs);
@@ -212,6 +217,7 @@ class MothurOut {
int median(vector<int>);
int average(vector<int>);
int sum(vector<int>);
+ double sum(vector<double>);
int getRandomIndex(int); //highest
double getStandardDeviation(vector<int>&);
vector<double> getStandardDeviation(vector< vector<double> >&);
@@ -252,6 +258,7 @@ class MothurOut {
string getSummaryFile() { return summaryfile; }
string getFileFile() { return filefile; }
string getProcessors() { return processors; }
+ string getConsTaxonomyFile(){ return constaxonomyfile; }
int getNumErrors() { return numErrors; }
void setListFile(string f) { listfile = getFullPathName(f); }
@@ -277,6 +284,7 @@ class MothurOut {
void setBiomFile(string f) { biomfile = getFullPathName(f); }
void setSummaryFile(string f) { summaryfile = getFullPathName(f); }
void setFileFile(string f) { filefile = getFullPathName(f); }
+ void setConsTaxonomyFile(string f) { constaxonomyfile = getFullPathName(f); }
void setCountTableFile(string f) { counttablefile = getFullPathName(f); groupMode = "count"; }
void setProcessors(string p) { processors = p; mothurOut("\nUsing " + toString(p) + " processors.\n"); }
@@ -290,7 +298,7 @@ class MothurOut {
MothurOut( const MothurOut& ); // Disable copy constructor
void operator=( const MothurOut& ); // Disable assignment operator
MothurOut() {
- control_pressed = false; defaultPath="";
+ control_pressed = false; defaultPath=""; blastPath="";
filefile = "";
phylipfile = "";
columnfile = "";
@@ -311,6 +319,7 @@ class MothurOut {
oligosfile = "";
accnosfile = "";
taxonomyfile = "";
+ constaxonomyfile = "";
processors = "1";
flowfile = "";
biomfile = "";
@@ -333,11 +342,11 @@ class MothurOut {
~MothurOut();
string logFileName;
- string defaultPath, outputDir;
+ string defaultPath, outputDir, blastPath;
string releaseDate, version;
string accnosfile, phylipfile, columnfile, listfile, rabundfile, sabundfile, namefile, groupfile, designfile, taxonomyfile, biomfile, filefile;
- string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile;
+ string orderfile, treefile, sharedfile, ordergroupfile, relabundfile, fastafile, qualfile, sfffile, oligosfile, processors, flowfile, counttablefile, summaryfile, constaxonomyfile;
vector<string> Groups;
vector<string> namesOfGroups;
diff --git a/source/opticluster.cpp b/source/opticluster.cpp
new file mode 100644
index 0000000..4bbb797
--- /dev/null
+++ b/source/opticluster.cpp
@@ -0,0 +1,632 @@
+//
+// opticluster.cpp
+// Mothur
+//
+// Created by Sarah Westcott on 4/20/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#include "opticluster.h"
+
+/***********************************************************************/
+//randomly assign sequences to OTUs
+int OptiCluster::initialize(double& value, bool randomize, string initialize) {
+ try {
+ numSeqs = matrix->getNumSeqs();
+ truePositives = 0;
+ falsePositives = 0;
+ falseNegatives = 0;
+ trueNegatives = 0;
+
+ bins.resize(numSeqs); //place seqs in own bin
+
+ vector<int> temp;
+ bins.push_back(temp);
+ seqBin[numSeqs] = -1;
+ insertLocation = numSeqs;
+
+ if (initialize == "singleton") {
+
+ //put everyone in own bin
+ for (int i = 0; i < numSeqs; i++) { bins[i].push_back(i); }
+
+ //maps randomized sequences to bins
+ for (int i = 0; i < numSeqs; i++) {
+ seqBin[i] = bins[i][0];
+ randomizeSeqs.push_back(i);
+ }
+
+ if (randomize) { random_shuffle(randomizeSeqs.begin(), randomizeSeqs.end()); }
+
+ //for each sequence (singletons removed on read)
+ for (map<int, int>::iterator it = seqBin.begin(); it != seqBin.end(); it++) {
+ if (it->second == -1) { }
+ else {
+ long long numCloseSeqs = (matrix->getCloseSeqs(it->first)).size(); //does not include self
+ falseNegatives += numCloseSeqs;
+ }
+ }
+ falseNegatives /= 2; //square matrix
+ trueNegatives = numSeqs * (numSeqs-1)/2 - (falsePositives + falseNegatives + truePositives); //since everyone is a singleton no one clusters together. True negative = num far apart
+ totalPairs = trueNegatives + truePositives + falseNegatives + falsePositives;
+ }else {
+
+ //put everyone in first bin
+ for (int i = 0; i < numSeqs; i++) {
+ bins[0].push_back(i);
+ seqBin[i] = 0;
+ randomizeSeqs.push_back(i);
+ }
+
+ if (randomize) { random_shuffle(randomizeSeqs.begin(), randomizeSeqs.end()); }
+
+ //for each sequence (singletons removed on read)
+ for (map<int, int>::iterator it = seqBin.begin(); it != seqBin.end(); it++) {
+ if (it->second == -1) { }
+ else {
+ long long numCloseSeqs = (matrix->getCloseSeqs(it->first)).size(); //does not include self
+ truePositives += numCloseSeqs;
+ }
+ }
+ truePositives /= 2; //square matrix
+ falsePositives = numSeqs * (numSeqs-1)/2 - (trueNegatives + falseNegatives + truePositives);
+ }
+
+ value = 0;
+ if (metric == "mcc") { value = calcMCC(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "sens") { value = calcSens(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "spec") { value = calcSpec(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "tptn") { value = calcTPTN(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "tp") { value = calcTP(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "tn") { value = calcTN(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "fp") { value = calcFP(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "fn") { value = calcFN(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "fpfn") { value = calcFPFN(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "f1score") { value = calcF1Score(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "accuracy") { value = calcAccuracy(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "ppv") { value = calcPPV(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "npv") { value = calcNPV(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "fdr") { value = calcFDR(truePositives, trueNegatives, falsePositives, falseNegatives); }
+
+ return value;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "initialize");
+ exit(1);
+ }
+}
+/***********************************************************************/
+/* for each sequence with mutual information (close)
+* remove from current OTU and calculate MCC when sequence forms its own OTU or joins one of the other OTUs where there is a sequence within the `threshold` (no need to calculate MCC if the paired sequence is already in same OTU and no need to try every OTU - just those where there's a close sequence)
+ * keep or move the sequence to the OTU where the `metric` is the largest - flip a coin on ties */
+bool OptiCluster::update(double& listMetric) {
+ try {
+
+ //for each sequence (singletons removed on read)
+ for (int i = 0; i < randomizeSeqs.size(); i++) {
+
+ if (m->control_pressed) { break; }
+
+ map<int, int>::iterator it = seqBin.find(randomizeSeqs[i]);
+
+ int seqNumber = it->first;
+ int binNumber = it->second;
+
+
+ if (binNumber == -1) { }
+ else {
+
+ long long tn, tp, fp, fn;
+ double bestMetric = -1;
+ long long bestBin, bestTp, bestTn, bestFn, bestFp;
+ tn = trueNegatives; tp = truePositives; fp = falsePositives; fn = falseNegatives;
+
+ //this calculation is used to save time in the move and adjust function.
+ //we don't need to calculate the cost of moving out of our current bin each time we
+ //test moving into a new bin. Only calc this once per iteration.
+ long long cCount = 0; long long fCount = 0;
+ for (int i = 0; i < bins[binNumber].size(); i++) { //how many close sequences are in the old bin?
+ if (seqNumber == bins[binNumber][i]) {}
+ else if (!matrix->isClose(seqNumber, bins[binNumber][i])) { fCount++; }
+ else { cCount++; }
+ }
+
+ //metric in current bin
+ bestMetric = calcScoreCurrentBin(tp, tn, fp, fn); bestBin = binNumber; bestTp = tp; bestTn = tn; bestFp = fp; bestFn = fn;
+
+ //if not already singleton, then calc value if singleton was created
+ if (!((bins[binNumber].size()) == 1)) {
+ //make a singleton
+ //move out of old bin
+ fn+=cCount; tn+=fCount; fp-=fCount; tp-=cCount;
+ double singleMetric = moveAdjustTFValues(binNumber, seqNumber, -1, tp, tn, fp, fn);
+ if (singleMetric > bestMetric) {
+ bestBin = -1; bestTp = tp; bestTn = tn; bestFp = fp; bestFn = fn;
+ bestMetric = singleMetric;
+ }
+ }
+
+ set<int> binsToTry;
+ set<int> closeSeqs = matrix->getCloseSeqs(seqNumber);
+ for (set<int>::iterator itClose = closeSeqs.begin(); itClose != closeSeqs.end(); itClose++) { binsToTry.insert(seqBin[*itClose]); }
+
+ //merge into each "close" otu
+ for (set<int>::iterator it = binsToTry.begin(); it != binsToTry.end(); it++) {
+ tn = trueNegatives; tp = truePositives; fp = falsePositives; fn = falseNegatives;
+ fn+=cCount; tn+=fCount; fp-=fCount; tp-=cCount;
+ double newMetric = moveAdjustTFValues(binNumber, seqNumber, *it, tp, tn, fp, fn);
+
+ //new best
+ if (newMetric > bestMetric) { bestMetric = newMetric; bestBin = (*it); bestTp = tp; bestTn = tn; bestFp = fp; bestFn = fn; }
+ }
+
+ bool usedInsert = false;
+ if (bestBin == -1) { bestBin = insertLocation; usedInsert = true; }
+
+ if (bestBin != binNumber) {
+ truePositives = bestTp; trueNegatives = bestTn; falsePositives = bestFp; falseNegatives = bestFn;
+
+ //move seq from i to j
+ bins[bestBin].push_back(seqNumber); //add seq to bestbin
+ bins[binNumber].erase(remove(bins[binNumber].begin(), bins[binNumber].end(), seqNumber), bins[binNumber].end()); //remove from old bin i
+ }
+
+ if (usedInsert) { insertLocation = findInsert(); }
+
+ //update seqBins
+ seqBin[seqNumber] = bestBin; //set new OTU location
+ }
+ }
+
+ if (metric == "mcc") { listMetric = calcMCC(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "sens") { listMetric = calcSens(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "spec") { listMetric = calcSpec(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "tptn") { listMetric = calcTPTN(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "tp") { listMetric = calcTP(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "tn") { listMetric = calcTN(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "fp") { listMetric = calcFP(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "fn") { listMetric = calcFN(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "f1score") { listMetric = calcF1Score(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "accuracy") { listMetric = calcAccuracy(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "ppv") { listMetric = calcPPV(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "npv") { listMetric = calcNPV(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "fdr") { listMetric = calcFDR(truePositives, trueNegatives, falsePositives, falseNegatives); }
+ else if (metric == "fpfn") { listMetric = calcFPFN(truePositives, trueNegatives, falsePositives, falseNegatives); }
+
+ return 0;
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "update");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::moveAdjustTFValues(int bin, int seq, int newBin, long long& tp, long long& tn, long long& fp, long long& fn) {
+ try {
+
+ //making a singleton bin. Close but we are forcing apart.
+ if (newBin == -1) {
+ }else { //merging a bin
+ long long ncCount = 0; long long nfCount = 0;
+ for (int i = 0; i < bins[newBin].size(); i++) { //how many close sequences are in the old bin?
+ if (seq == bins[newBin][i]) {}
+ else if (!matrix->isClose(seq, bins[newBin][i])) { nfCount++; }
+ else { ncCount++; }
+ }
+
+ //move into new bin
+ fn-=ncCount; tn-=nfCount; tp+=ncCount; fp+=nfCount;
+ }
+
+ double result = 0.0;
+ if (metric == "mcc") {
+ result = calcMCC(tp, tn, fp, fn);
+ }else if (metric == "sens") {
+ result = calcSens(tp, tn, fp, fn);
+ }else if (metric == "spec") {
+ result = calcSpec(tp, tn, fp, fn);
+ }else if (metric == "tptn") {
+ result = calcTPTN(tp, tn, fp, fn);
+ }else if (metric == "tp") {
+ result = calcTP(tp, tn, fp, fn);
+ }else if (metric == "tn") {
+ result = calcTN(tp, tn, fp, fn);
+ }else if (metric == "fp") {
+ result = calcFP(tp, tn, fp, fn);
+ }else if (metric == "fn") {
+ result = calcFN(tp, tn, fp, fn);
+ }else if (metric == "f1score") {
+ result = calcF1Score(tp, tn, fp, fn);
+ }else if (metric == "accuracy") {
+ result = calcAccuracy(tp, tn, fp, fn);
+ }else if (metric == "ppv") {
+ result = calcPPV(tp, tn, fp, fn);
+ }else if (metric == "npv") {
+ result = calcNPV(tp, tn, fp, fn);
+ }else if (metric == "fdr") {
+ result = calcFDR(tp, tn, fp, fn);
+ }else if (metric == "fpfn") {
+ result = calcFPFN(tp, tn, fp, fn);
+ }
+
+ return result;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "moveAdjustTFValues");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcScoreCurrentBin( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ if (metric == "mcc") {
+ return calcMCC(tp, tn, fp, fn);
+ }else if (metric == "sens") {
+ return calcSens(tp, tn, fp, fn);
+ }else if (metric == "spec") {
+ return calcSpec(tp, tn, fp, fn);
+ }else if (metric == "tptn") {
+ return calcTPTN(tp, tn, fp, fn);
+ }else if (metric == "tp") {
+ return calcTP(tp, tn, fp, fn);
+ }else if (metric == "tn") {
+ return calcTN(tp, tn, fp, fn);
+ }else if (metric == "fp") {
+ return calcFP(tp, tn, fp, fn);
+ }else if (metric == "fn") {
+ return calcFN(tp, tn, fp, fn);
+ }else if (metric == "f1score") {
+ return calcF1Score(tp, tn, fp, fn);
+ }else if (metric == "accuracy") {
+ return calcAccuracy(tp, tn, fp, fn);
+ }else if (metric == "ppv") {
+ return calcPPV(tp, tn, fp, fn);
+ }else if (metric == "npv") {
+ return calcNPV(tp, tn, fp, fn);
+ }else if (metric == "fdr") {
+ return calcFDR(tp, tn, fp, fn);
+ }else if (metric == "fpfn") {
+ return calcFPFN(tp, tn, fp, fn);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcScoreCurrentBin");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+double OptiCluster::calcMCC( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ long long p = tp + fn;
+ long long n = fp + tn;
+ long long pPrime = tp + fp;
+ long long nPrime = tn + fn;
+
+ double matthewsCorrCoef = ((tp * tn) - (fp * fn)) / (double) sqrt(p * n * pPrime * nPrime);
+ if(p == 0 || n == 0 || pPrime == 0 || nPrime == 0){ matthewsCorrCoef = 0; }
+
+ return matthewsCorrCoef;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcMCC");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcSens( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ long long p = tp + fn;
+ double sensitivity = tp / (double) p;
+
+ if(p == 0) { sensitivity = 0; }
+
+ return sensitivity;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcSens");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcSpec( long long tp, long long tn, long long fp, long long fn) {
+ try {
+ long long n = fp + tn;
+ double specificity = tn / (double) n;
+
+ if(n == 0) { specificity = 0; }
+
+ return specificity;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcSpec");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcTPTN( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ long long p = tp + tn;
+
+ double tptn = p / (double)(tp + tn + fp + fn);
+
+ return tptn;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcTPTN");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcTP( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ double tpmax = tp / (double)(tp + tn + fp + fn);
+
+ return tpmax;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcTP");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcTN( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ double tnmax = tn / (double)(tp + tn + fp + fn);
+
+ return tnmax;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcTN");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcFP( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ double fpmin = fp / (double)(tp + tn + fp + fn);
+
+ return (1.0 - fpmin);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcFP");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcFN( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ double fnmin = fn / (double)(tp + tn + fp + fn);
+
+ return (1.0 - fnmin);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcFN");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+double OptiCluster::calcFPFN( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ long long p = fp + fn;
+
+ double fpfn = 1.0 - (p / (double)(tp + tn + fp + fn)); //minimize
+
+ return fpfn;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcFPFN");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcF1Score( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ long long p = tp + fn;
+ long long pPrime = tp + fp;
+ double f1Score = 2.0 * tp / (double) (p + pPrime);
+
+ if(p + pPrime == 0) { f1Score = 0; }
+
+ return f1Score;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcF1Score");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcAccuracy( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ long long p = tp + fn;
+ long long n = fp + tn;
+ double accuracy = (tp + tn) / (double) (p + n);
+ if(p + n == 0) { accuracy = 0; }
+ return accuracy;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcAccuracy");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcPPV( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ long long pPrime = tp + fp;
+ double positivePredictiveValue = tp / (double) pPrime;
+
+ if(pPrime == 0) { positivePredictiveValue = 0; }
+
+ return positivePredictiveValue;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcPPV");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcNPV( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ long long nPrime = tn + fn;
+ double negativePredictiveValue = tn / (double) nPrime;
+
+ if(nPrime == 0) { negativePredictiveValue = 0; }
+
+ return negativePredictiveValue;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcNPV");
+ exit(1);
+ }
+}
+/***********************************************************************/
+double OptiCluster::calcFDR( long long tp, long long tn, long long fp, long long fn) {
+ try {
+
+ long long pPrime = tp + fp;
+ double falseDiscoveryRate = fp / (double) pPrime;
+
+ if(pPrime == 0) { falseDiscoveryRate = 0; }
+
+ return (1.0-falseDiscoveryRate);
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "calcFDR");
+ exit(1);
+ }
+}
+/***********************************************************************/
+vector<double> OptiCluster::getStats( long long& tp, long long& tn, long long& fp, long long& fn) {
+ try {
+ long long singletn = matrix->getNumSingletons() + numSingletons;
+ long long tempnumSeqs = numSeqs + singletn;
+
+ tp = truePositives;
+ fp = falsePositives;
+ fn = falseNegatives;
+ tn = tempnumSeqs * (tempnumSeqs-1)/2 - (falsePositives + falseNegatives + truePositives); //adds singletons to tn
+
+ long long p = tp + fn;
+ long long n = fp + tn;
+ long long pPrime = tp + fp;
+ long long nPrime = tn + fn;
+
+ double sensitivity = tp /(double) p;
+ double specificity = tn / (double)n;
+ double positivePredictiveValue = tp / (double)pPrime;
+ double negativePredictiveValue = tn / (double)nPrime;
+ double falseDiscoveryRate = fp / (double)pPrime;
+
+ double accuracy = (tp + tn) / (double)(p + n);
+ double matthewsCorrCoef = (tp * tn - fp * fn) / (double) sqrt(p * n * pPrime * nPrime); if(p == 0 || n == 0){ matthewsCorrCoef = 0; }
+ double f1Score = 2.0 * tp / (double)(p + pPrime);
+
+
+ if(p == 0) { sensitivity = 0; matthewsCorrCoef = 0; }
+ if(n == 0) { specificity = 0; matthewsCorrCoef = 0; }
+ if(p + n == 0) { accuracy = 0; }
+ if(p + pPrime == 0) { f1Score = 0; }
+ if(pPrime == 0) { positivePredictiveValue = 0; falseDiscoveryRate = 0; matthewsCorrCoef = 0; }
+ if(nPrime == 0) { negativePredictiveValue = 0; matthewsCorrCoef = 0; }
+
+ vector<double> results;
+
+ //results.push_back(truePositives); results.push_back(tn); results.push_back(falsePositives); results.push_back(falseNegatives);
+ results.push_back(sensitivity); results.push_back(specificity); results.push_back(positivePredictiveValue); results.push_back(negativePredictiveValue);
+ results.push_back(falseDiscoveryRate); results.push_back(accuracy); results.push_back(matthewsCorrCoef); results.push_back(f1Score);
+
+ return results;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "getStats");
+ exit(1);
+ }
+}
+/***********************************************************************/
+ListVector* OptiCluster::getList() {
+ try {
+ ListVector* list = new ListVector();
+ ListVector* singleton = matrix->getListSingle();
+
+ if (singleton != NULL) { //add in any sequences above cutoff in read. Removing these saves clustering time.
+ for (int i = 0; i < singleton->getNumBins(); i++) {
+ if (singleton->get(i) != "") {
+ list->push_back(singleton->get(i));
+ }
+ }
+ delete singleton;
+ }
+
+ for (int i = 0; i < bins.size(); i++) {
+ if (bins[i].size() != 0) {
+ string otu = matrix->getName(bins[i][0]);
+
+ for (int j = 1; j < bins[i].size(); j++) {
+ otu += "," + matrix->getName(bins[i][j]);
+ }
+ list->push_back(otu);
+ }
+ }
+
+ return list;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "getList");
+ exit(1);
+ }
+}
+/***********************************************************************/
+long long OptiCluster::getNumBins() {
+ try {
+ long long singletn = matrix->getNumSingletons();
+
+ for (int i = 0; i < bins.size(); i++) {
+ if (bins[i].size() != 0) {
+ singletn++;
+ }
+ }
+
+ return singletn;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "getNumBins");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
+int OptiCluster::findInsert() {
+ try {
+
+ //for each sequence (singletons removed on read)
+ for (int i = 0; i < bins.size(); i++) {
+
+ if (m->control_pressed) { break; }
+
+ if (bins[i].size() == 0) { return i; }
+ }
+
+ return -1;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "OptiCluster", "getList");
+ exit(1);
+ }
+}
+
+/***********************************************************************/
diff --git a/source/opticluster.h b/source/opticluster.h
new file mode 100644
index 0000000..71d3077
--- /dev/null
+++ b/source/opticluster.h
@@ -0,0 +1,66 @@
+//
+// opticluster.h
+// Mothur
+//
+// Created by Sarah Westcott on 4/20/16.
+// Copyright (c) 2016 Schloss Lab. All rights reserved.
+//
+
+#ifndef __Mothur__opticluster__
+#define __Mothur__opticluster__
+
+#include "cluster.hpp"
+#include "optimatrix.h"
+
+/***********************************************************************/
+
+class OptiCluster : public Cluster {
+
+#ifdef UNIT_TEST
+ friend class TestOptiCluster;
+ OptiCluster() : Cluster() { m = MothurOut::getInstance(); truePositives = 0; trueNegatives = 0; falseNegatives = 0; falsePositives = 0; } //for testing class
+ void setVariables(OptiMatrix* mt, string met) { matrix = mt; metric = met; }
+#endif
+
+public:
+ OptiCluster(OptiMatrix* mt, string met, long long ns) : Cluster() {
+ m = MothurOut::getInstance(); matrix = mt; metric = met; truePositives = 0; trueNegatives = 0; falseNegatives = 0; falsePositives = 0; numSingletons = ns;
+ }
+ ~OptiCluster() {}
+ bool updateDistance(PDistCell& colCell, PDistCell& rowCell) { return false; } //inheritance compliant
+ string getTag() { string tag = "opti_" + metric; return tag; }
+ long long getNumBins();
+ int initialize(double&, bool, string); //randomize and place in "best" OTUs
+ bool update(double&); //returns whether list changed and MCC
+ vector<double> getStats( long long&, long long&, long long&, long long&);
+ ListVector* getList();
+
+private:
+ MothurOut* m;
+ map<int, int> seqBin; //sequence# -> bin#
+ OptiMatrix* matrix;
+ vector<int> randomizeSeqs;
+ vector< vector<int> > bins; //bin[0] -> seqs in bin[0]
+ string metric;
+ long long truePositives, trueNegatives, falsePositives, falseNegatives, numSeqs, insertLocation, totalPairs, numSingletons;
+
+ int findInsert();
+ double calcMCC(long long, long long, long long, long long);
+ double calcSens( long long, long long, long long, long long);
+ double calcSpec( long long, long long, long long, long long);
+ double calcTPTN( long long, long long, long long, long long);
+ double calcTP( long long, long long, long long, long long);
+ double calcTN( long long, long long, long long, long long);
+ double calcFP( long long, long long, long long, long long);
+ double calcFN( long long, long long, long long, long long);
+ double calcFPFN( long long, long long, long long, long long);
+ double calcF1Score( long long, long long, long long, long long);
+ double calcAccuracy( long long, long long, long long, long long);
+ double calcPPV( long long, long long, long long, long long);
+ double calcNPV( long long, long long, long long, long long);
+ double calcFDR( long long, long long, long long, long long);
+ double calcScoreCurrentBin( long long tp, long long tn, long long fp, long long fn);
+ double moveAdjustTFValues(int bin, int seq, int newBin, long long&, long long&, long long&, long long&);
+};
+
+#endif /* defined(__Mothur__opticluster__) */
diff --git a/source/optionparser.cpp b/source/optionparser.cpp
index 21ed661..38ffbdf 100644
--- a/source/optionparser.cpp
+++ b/source/optionparser.cpp
@@ -24,7 +24,11 @@ OptionParser::OptionParser(string option) {
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
key = m->splitWhiteSpace(key).front();
- value = m->splitWhiteSpace(value).front();
+ //if value is wrapped in '' preserve spaces
+ if ((value[0] == '\'') && (value[(value.length()-1)] == '\'')) { value = value.substr(1); value = value.substr(0, (value.length()-1)); }
+ else {
+ value = m->splitWhiteSpace(value).front();
+ }
parameters[key] = value;
}
@@ -33,7 +37,11 @@ OptionParser::OptionParser(string option) {
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
key = m->splitWhiteSpace(key).front();
- option = m->splitWhiteSpace(option).front();
+ //if value is wrapped in '' preserve spaces
+ if ((option[0] == '\'') && (option[(option.length()-1)] == '\'')) { option = option.substr(1); option = option.substr(0, (option.length()-1)); }
+ else {
+ option = m->splitWhiteSpace(option).front();
+ }
parameters[key] = option;
}
}
@@ -57,7 +65,11 @@ OptionParser::OptionParser(string option, map<string, string>& copy) {
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
key = m->splitWhiteSpace(key).front();
- value = m->splitWhiteSpace(value).front();
+ //if value is wrapped in '' preserve spaces
+ if ((value[0] == '\'') && (value[(value.length()-1)] == '\'')) { value = value.substr(1); value = value.substr(0, (value.length()-1)); }
+ else {
+ value = m->splitWhiteSpace(value).front();
+ }
parameters[key] = value;
}
@@ -66,7 +78,11 @@ OptionParser::OptionParser(string option, map<string, string>& copy) {
if ((key == "candidate") || (key == "query")) { key = "fasta"; }
if (key == "template") { key = "reference"; }
key = m->splitWhiteSpace(key).front();
- option = m->splitWhiteSpace(option).front();
+ //if value is wrapped in '' preserve spaces
+ if ((option[0] == '\'') && (option[(option.length()-1)] == '\'')) { option = option.substr(1); option = option.substr(0, (option.length()-1)); }
+ else {
+ option = m->splitWhiteSpace(option).front();
+ }
parameters[key] = option;
}
@@ -132,6 +148,8 @@ map<string, string> OptionParser::getParameters() {
it->second = m->getAccnosFile();
}else if (it->first == "taxonomy") {
it->second = m->getTaxonomyFile();
+ }else if (it->first == "constaxonomy") {
+ it->second = m->getConsTaxonomyFile();
}else if (it->first == "biom") {
it->second = m->getBiomFile();
}else if (it->first == "count") {
diff --git a/source/read/splitmatrix.cpp b/source/read/splitmatrix.cpp
index e938742..5301dc8 100644
--- a/source/read/splitmatrix.cpp
+++ b/source/read/splitmatrix.cpp
@@ -560,6 +560,7 @@ int SplitMatrix::splitNames(map<string, int>& seqGroup, int numGroups, vector<st
if (countfile != "") { headers = m->getline(bigNameFile); m->gobble(bigNameFile); }
string name, nameList;
+ numSingleton = 0;
while(!bigNameFile.eof()){
bigNameFile >> name >> nameList;
m->getline(bigNameFile); m->gobble(bigNameFile); //extra getline is for rest of countfile line if groups are given.
@@ -574,6 +575,7 @@ int SplitMatrix::splitNames(map<string, int>& seqGroup, int numGroups, vector<st
}else{
wroteExtra = true;
remainingNames << name << '\t' << nameList << endl;
+ numSingleton++;
}
}
bigNameFile.close();
@@ -585,6 +587,7 @@ int SplitMatrix::splitNames(map<string, int>& seqGroup, int numGroups, vector<st
//if there are valid distances
ifstream fileHandle;
fileHandle.open(tempDistFile.c_str());
+ bool removeDist = false;
if(fileHandle) {
m->gobble(fileHandle);
if (!fileHandle.eof()) { //check
@@ -610,12 +613,15 @@ int SplitMatrix::splitNames(map<string, int>& seqGroup, int numGroups, vector<st
in >> name >> nameList; m->gobble(in);
wroteExtra = true;
remainingNames << name << '\t' << nameList << endl;
+ numSingleton++;
}
in.close();
m->mothurRemove(tempNameFile);
+ removeDist = true;
}
}
fileHandle.close();
+ if (removeDist) { m->mothurRemove(tempDistFile); }
}
remainingNames.close();
@@ -623,6 +629,7 @@ int SplitMatrix::splitNames(map<string, int>& seqGroup, int numGroups, vector<st
if (!wroteExtra) {
m->mothurRemove(singleton);
singleton = "none";
+ numSingleton = 0;
}else if (countfile != "") {
//add header
ofstream out;
@@ -669,6 +676,7 @@ int SplitMatrix::splitNamesVsearch(map<string, int>& seqGroup, int numGroups, ve
vector<string> pieces = m->splitWhiteSpace(headers); if (pieces.size() != 2) { hasGroups = true; } }
string name, nameList;
+ numSingleton = 0;
while(!bigNameFile.eof()){
bigNameFile >> name >> nameList; m->gobble(bigNameFile);
if (hasGroups) { m->getline(bigNameFile); m->gobble(bigNameFile); }
@@ -680,9 +688,10 @@ int SplitMatrix::splitNamesVsearch(map<string, int>& seqGroup, int numGroups, ve
m->openOutputFileAppend((inputFile + "." + toString(it->second) + ".temp"), outFile);
outFile << name << '\t' << nameList << endl;
outFile.close();
- }else{//taxonomic groups of one
+ }else{
wroteExtra = true;
remainingNames << name << '\t' << nameList << endl;
+ numSingleton++;
}
}
bigNameFile.close();
@@ -720,6 +729,7 @@ int SplitMatrix::splitNamesVsearch(map<string, int>& seqGroup, int numGroups, ve
in >> name >> nameList; m->gobble(in);
wroteExtra = true;
remainingNames << name << '\t' << nameList << endl;
+ numSingleton++;
}
in.close();
m->mothurRemove(tempNameFile);
@@ -733,6 +743,7 @@ int SplitMatrix::splitNamesVsearch(map<string, int>& seqGroup, int numGroups, ve
if (!wroteExtra) {
m->mothurRemove(singleton);
singleton = "none";
+ numSingleton = 0;
}else if (countfile != "") {
//add header
ofstream out;
diff --git a/source/read/splitmatrix.h b/source/read/splitmatrix.h
index fa59984..71fcea7 100644
--- a/source/read/splitmatrix.h
+++ b/source/read/splitmatrix.h
@@ -26,6 +26,7 @@ class SplitMatrix {
int split();
vector< map<string, string> > getDistanceFiles(); //returns map of distance files -> namefile sorted by distance file size
string getSingletonNames() { return singleton; } //returns namesfile containing singletons
+ long long getNumSingleton() { return numSingleton; } //returns namesfile containing singletons
private:
MothurOut* m;
@@ -34,7 +35,8 @@ class SplitMatrix {
vector< map< string, string> > dists;
float cutoff, distCutoff;
bool large, classic;
- int processors;
+ int processors;
+ long long numSingleton;
int splitDistance();
int splitClassify();
diff --git a/source/singlelinkage.cpp b/source/singlelinkage.cpp
index ccea874..2c2cba5 100644
--- a/source/singlelinkage.cpp
+++ b/source/singlelinkage.cpp
@@ -1,5 +1,4 @@
-#include "mothur.h"
#include "cluster.hpp"
diff --git a/source/trimoligos.h b/source/trimoligos.h
index f49c3d6..78b6f1f 100644
--- a/source/trimoligos.h
+++ b/source/trimoligos.h
@@ -17,6 +17,12 @@
class TrimOligos {
+
+#ifdef UNIT_TEST
+ friend class TestTrimOligos;
+ TrimOligos() {};
+ //add set variables function when completeing unit tests for this class
+#endif
public:
TrimOligos(int,int,int, map<string, int>, map<string, int>, vector<string>); //pdiffs, bdiffs, primers, barcodes, revPrimers
diff --git a/source/validparameter.cpp b/source/validparameter.cpp
index 18638e5..74f9d0c 100644
--- a/source/validparameter.cpp
+++ b/source/validparameter.cpp
@@ -247,11 +247,11 @@ string ValidParameters::validFile(map<string, string>& container, string paramet
//if you can't open it, try mothur's location
if (ableToOpen == 1) {
- //look for uchime exe
- string mpath = m->argv;
- string tempPath = mpath;
- for (int i = 0; i < mpath.length(); i++) { tempPath[i] = tolower(mpath[i]); }
- mpath = mpath.substr(0, (tempPath.find_last_of('m')));
+ //look for mothurs exe
+ string mpath = m->mothurProgramPath;
+ //string tempPath = mpath;
+ //for (int i = 0; i < mpath.length(); i++) { tempPath[i] = tolower(mpath[i]); }
+ //mpath = mpath.substr(0, (tempPath.find_last_of('m')));
string tryPath = mpath + m->getSimpleName(it->second);
m->mothurOut("Unable to open " + it->second + ". Trying mothur's location " + tryPath); m->mothurOutEndLine();
diff --git a/source/vsearchfileparser.cpp b/source/vsearchfileparser.cpp
index 98492c2..44629ef 100644
--- a/source/vsearchfileparser.cpp
+++ b/source/vsearchfileparser.cpp
@@ -62,7 +62,7 @@ string VsearchFileParser::getVsearchFile() {
if (fastafile == "") { m->mothurOut("[ERROR]: no fasta file given, cannot continue.\n"); m->control_pressed = true; }
//Run unique.seqs on the data if a name or count file is not given
- if ((namefile == "") && (countfile == "")) { countfile = getNamesFile(fastafile); }
+ if ((namefile == "") && (countfile == "")) { getNamesFile(fastafile); }
else if (namefile != "") { counts = m->readNames(namefile); }
if (countfile != "") { CountTable countTable; countTable.readTable(countfile, false, false); counts = countTable.getNameMap(); }
@@ -124,7 +124,6 @@ string VsearchFileParser::createVsearchFasta(string inputFile){
string VsearchFileParser::getNamesFile(string& inputFile){
try {
- string nameFile = "";
m->mothurOutEndLine(); m->mothurOut("No namesfile given, running unique.seqs command to generate one."); m->mothurOutEndLine(); m->mothurOutEndLine();
@@ -146,7 +145,7 @@ string VsearchFileParser::getNamesFile(string& inputFile){
countfile = filenames["count"][0];
fastafile = filenames["fasta"][0];
- return nameFile;
+ return countfile;
}
catch(exception& e) {
m->errorOut(e, "VsearchFileParser", "getNamesFile");
--
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