[med-svn] [fastml] 04/04: Fix some spelling issues
Andreas Tille
tille at debian.org
Thu Nov 19 07:47:07 UTC 2015
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tille pushed a commit to branch master
in repository fastml.
commit 8619180a4326fe3d11bdade6aa7084a7a53f4569
Author: Andreas Tille <tille at debian.org>
Date: Thu Nov 19 08:33:19 2015 +0100
Fix some spelling issues
---
debian/fastml.1 | 4 +-
debian/patches/series | 1 +
debian/patches/spelling.patch | 86 +++++++++++++++++++++++++++++++++++++++++++
3 files changed, 89 insertions(+), 2 deletions(-)
diff --git a/debian/fastml.1 b/debian/fastml.1
index 7fb2f64..f29c8fa 100644
--- a/debian/fastml.1
+++ b/debian/fastml.1
@@ -30,7 +30,7 @@ sequences).
\fB\-t\fR tree input file (if tree is not given, a neighbor joining tree is computed).
.TP
\fB\-g\fR Assume among site rate variation model (Gamma) [By default the program
-will assume an homogenous model. very fast, but less accurate!]
+will assume an homogeneous model. very fast, but less accurate!]
.TP
\fB\-m\fR model name
.TP
@@ -79,7 +79,7 @@ Controling the output options:
.PP
Advanced options:
.TP
-\fB\-a\fR Treshold for computing again marginal probabilities [0.9]
+\fB\-a\fR Threshold for computing again marginal probabilities [0.9]
.TP
\fB\-b\fR Do not optimize branch lengths on starting tree
[by default branches and alpha are ML optimized from the data]
diff --git a/debian/patches/series b/debian/patches/series
index e174b80..0d7e8d4 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
gcc_5.patch
fix_makefile4test.patch
fix_intall_target.patch
+spelling.patch
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
new file mode 100644
index 0000000..17e6ed9
--- /dev/null
+++ b/debian/patches/spelling.patch
@@ -0,0 +1,86 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Mon, 22 Jun 2015 09:47:25 +0200
+Description: Fix some spelling issues
+
+--- a/libs/phylogeny/likeDist.cpp
++++ b/libs/phylogeny/likeDist.cpp
+@@ -145,10 +145,10 @@ MDOUBLE likeDist::giveDistanceThroughCTC
+ const sequence& s2,
+ const vector<MDOUBLE> * weights,
+ MDOUBLE* score) const {
+- // only in the case of homogenous model - work through pairwise EM like
++ // only in the case of homogeneous model - work through pairwise EM like
+ countTableComponentGam ctc;
+ if (_sp.categories() != 1) {
+- errorMsg::reportError("this function only work for homogenous model.");
++ errorMsg::reportError("this function only work for homogeneous model.");
+ }
+ ctc.countTableComponentAllocatePlace(s1.getAlphabet()->size(),1);
+ for (int i=0; i<s1.seqLen(); ++i) {
+--- a/programs/fastml/mainbb.cpp
++++ b/programs/fastml/mainbb.cpp
+@@ -98,7 +98,7 @@ void mainbb::getStartingEvolTreeTopology
+
+ void mainbb::getStartingNJtreeNjMLdis() {
+ // note that here ALWAYS, the ML distances are computed using
+- // an homogenous rate distribution.
++ // an homogeneous rate distribution.
+ uniDistribution lUni;
+ // const pijAccelerator* lpijAcc = _sp->getPijAccelerator();// note this is just a copy of the pointer.
+ const pijAccelerator* lpijAcc = _spVec[0].getPijAccelerator();// note this is just a copy of the pointer.
+@@ -248,9 +248,9 @@ void mainbb::getStartingStochasticProces
+ int numberOfCategories = _options->gammaCategies;
+ MDOUBLE alpha = _options->gammaPar;
+ if (_options->distributionName == bb_options::hom) {
+- numberOfCategories = 1; // forcing homogenous model.
++ numberOfCategories = 1; // forcing homogeneous model.
+ alpha = 1.0;
+- cout<<"Using homogenous model (no among site rate variation)"<<endl;
++ cout<<"Using homogeneous model (no among site rate variation)"<<endl;
+ } else {
+ cout<<"Using a Gamma model with: "<<numberOfCategories<<" discrete categories "<<endl;
+ }
+--- a/libs/phylogeny/numRec.cpp
++++ b/libs/phylogeny/numRec.cpp
+@@ -134,7 +134,7 @@ int MyJacobi(VVdouble &Insym, VVdouble &
+ } // end of for (ip = ...
+ } // end of for (i = 0; i< MaxNumberOfSweeps ; ++i) {
+ vector<string> err;
+- err.push_back("problems in function MyJacobi. more than MaxNumberOfSweeps were necesary.");
++ err.push_back("problems in function MyJacobi. more than MaxNumberOfSweeps were necessary.");
+ errorMsg::reportError(err);
+
+ return -1;
+--- a/programs/fastml/bb_options_list.h
++++ b/programs/fastml/bb_options_list.h
+@@ -36,7 +36,7 @@ static string usage() {
+ tmp +=" | -qm = MOLPHY, -qs = MASE, -qp = PHLIYP, -qn = Nexus |\n";
+ tmp +=" +----------------------------------------------------------------------------+\n";
+ tmp +=" |Advances options: |\n";
+- tmp +=" |-a Treshold for computing again marginal probabilities [0.9] |\n";
++ tmp +=" |-a Threshold for computing again marginal probabilities [0.9] |\n";
+ tmp +=" |-b Do not optimize branch lengths on starting tree |\n";
+ tmp +=" | [by default branches and alpha are ML optimized from the data] |\n";
+ tmp +=" |-c number of discrete Gamma categories for the gamma distribution [8] |\n";
+--- a/programs/gainLoss/computeCorrelations.cpp
++++ b/programs/gainLoss/computeCorrelations.cpp
+@@ -137,7 +137,7 @@ void computeCorrelations::runComputeCorr
+ numOfpositionsIn_B = _expChanges_PosNodeXY.size(); // if B is not given, it's copy
+
+ if(_isTwoSetsOfInputForCorrelation)
+- LOGnOUT(3, <<"NOTE: Two seperate dataset input.\n Compute correl for selectedSites="<<numOfSitesSelected<<" subset of A="<<numOfpositionsIn_A<<" against B="<<numOfpositionsIn_B<<endl);
++ LOGnOUT(3, <<"NOTE: Two separate dataset input.\n Compute correl for selectedSites="<<numOfSitesSelected<<" subset of A="<<numOfpositionsIn_A<<" against B="<<numOfpositionsIn_B<<endl);
+
+ //// Mapping vectors
+ LOGnOUT(4, <<"Fill events vectors..."<<endl);
+--- a/programs/gainLoss/gainLoss.cpp
++++ b/programs/gainLoss/gainLoss.cpp
+@@ -4525,7 +4525,7 @@ void gainLoss::startSimultePosteriorExpe
+ LOGnOUT(4,<<(gainLossOptions::_userAlphaLoss/gainLossOptions::_userBetaLoss) / (gainLossOptions::_userAlphaGain/gainLossOptions::_userBetaGain)<<endl);
+ if(!gainLossOptions::_isRootFreqEQstationaryInSimulations){
+ if(gainLossOptions::_initRootFreqAtRandPointsInSimPostExpEachPos)
+- LOGnOUT(4,<<"Root(1) freq is sampled seperatly for each pos"<<endl)
++ LOGnOUT(4,<<"Root(1) freq is sampled separately for each pos"<<endl)
+ else
+ LOGnOUT(4,<<"Root(1) freq is sampled once for the entire replication (sim all positions)"<<endl)
+ if(isComputeEmpiricalCorrection
--
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