[med-svn] [clustalx] 03/06: fix more spelling errors
Andreas Tille
tille at debian.org
Thu Jul 21 15:22:40 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository clustalx.
commit 18783b610e19e8276de5ee457ac1060692a75f70
Author: Andreas Tille <tille at debian.org>
Date: Thu Jul 21 14:55:03 2016 +0200
fix more spelling errors
---
debian/changelog | 1 +
debian/patches/spelling.patch | 468 ++++++++++++++++++++++++++++++++++++++++++
2 files changed, 469 insertions(+)
diff --git a/debian/changelog b/debian/changelog
index cd18285..ea48346 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -3,6 +3,7 @@ clustalx (2.1+lgpl-5) UNRELEASED; urgency=medium
* cme fix dpkg-control
* debian/rules: fix sed expression
Closes: #832013
+ * fix more spelling errors
-- Andreas Tille <tille at debian.org> Thu, 21 Jul 2016 14:25:14 +0200
diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch
index 533f95e..ee4fc13 100644
--- a/debian/patches/spelling.patch
+++ b/debian/patches/spelling.patch
@@ -13,3 +13,471 @@ Description: Fix spelling
"\n"
"PHYLIP format output can be used for input to the PHYLIP package of Joe \n"
"Felsenstein. This is an extremely widely used package for doing every \n"
+--- a/clustalW/alignment/Alignment.cpp
++++ b/clustalW/alignment/Alignment.cpp
+@@ -431,7 +431,7 @@ void Alignment::addSequencesToVector(vec
+ && ((int)titles.size() == numSeqs + 1) && ((int)sequenceIds.size() == numSeqs + 1)))
+ {
+ cerr << "There has been an error adding the sequences to Alignment.\n"
+- << "Must terminate the program. EaddSequencesrror occured in addSequences.\n";
++ << "Must terminate the program. EaddSequencesrror occurred in addSequences.\n";
+ exit(1);
+ }
+ }
+--- a/clustalW/alignment/AlignmentOutput.cpp
++++ b/clustalW/alignment/AlignmentOutput.cpp
+@@ -62,7 +62,7 @@ AlignmentOutput::AlignmentOutput()
+ }
+ catch(const exception& e)
+ {
+- cerr << "An exception has occured in the contructor of AlignmentOutput.\n"
++ cerr << "An exception has occurred in the contructor of AlignmentOutput.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+@@ -236,7 +236,7 @@ void AlignmentOutput::createAlignmentOut
+ }
+ catch(const exception& e)
+ {
+- cerr << "An exception has occured in the createAlignmentOutput function.\n"
++ cerr << "An exception has occurred in the createAlignmentOutput function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+@@ -666,21 +666,21 @@ void AlignmentOutput::fastaOut(Alignment
+ catch(const bad_alloc& e)
+ {
+ fastaOutFile->close();
+- cerr << "A bad_alloc exception has occured in the fastaOut function.\n"
++ cerr << "A bad_alloc exception has occurred in the fastaOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(VectorOutOfRange e)
+ {
+ fastaOutFile->close();
+- cerr << "An exception has occured in the fastaOut function.\n"
++ cerr << "An exception has occurred in the fastaOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(...)
+ {
+ fastaOutFile->close();
+- cerr << "An exception has occured in the fastaOut function.\n";
++ cerr << "An exception has occurred in the fastaOut function.\n";
+ exit(1);
+ }
+
+@@ -861,21 +861,21 @@ void AlignmentOutput::gcgOut(Alignment*
+ catch(const bad_alloc& e)
+ {
+ gcgOutFile->close();
+- cerr << "A bad_alloc exception has occured in the gcgOut function.\n"
++ cerr << "A bad_alloc exception has occurred in the gcgOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(VectorOutOfRange e)
+ {
+ gcgOutFile->close();
+- cerr << "An exception has occured in the gcgOut function.\n"
++ cerr << "An exception has occurred in the gcgOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(...)
+ {
+ gcgOutFile->close();
+- cerr << "An exception has occured in the gcgOut function.\n";
++ cerr << "An exception has occurred in the gcgOut function.\n";
+ exit(1);
+ }
+ }
+@@ -1020,21 +1020,21 @@ void AlignmentOutput::phylipOut(Alignmen
+ catch(const bad_alloc& e)
+ {
+ phylipOutFile->close();
+- cerr << "A bad_alloc exception has occured in the phylipOut function.\n"
++ cerr << "A bad_alloc exception has occurred in the phylipOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(VectorOutOfRange e)
+ {
+ phylipOutFile->close();
+- cerr << "An exception has occured in the phylipOut function.\n"
++ cerr << "An exception has occurred in the phylipOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(...)
+ {
+ phylipOutFile->close();
+- cerr << "An exception has occured in the phylipOut function.\n";
++ cerr << "An exception has occurred in the phylipOut function.\n";
+ exit(1);
+ }
+ }
+@@ -1149,21 +1149,21 @@ void AlignmentOutput::nexusOut(Alignment
+ catch(const bad_alloc& e)
+ {
+ nexusOutFile->close();
+- cerr << "A bad_alloc exception has occured in the nexusOut function.\n"
++ cerr << "A bad_alloc exception has occurred in the nexusOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(VectorOutOfRange e)
+ {
+ nexusOutFile->close();
+- cerr << "An exception has occured in the nexusOut function.\n"
++ cerr << "An exception has occurred in the nexusOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(...)
+ {
+ nexusOutFile->close();
+- cerr << "An exception has occured in the nexusOut function.\n";
++ cerr << "An exception has occurred in the nexusOut function.\n";
+ exit(1);
+ }
+ }
+@@ -1438,21 +1438,21 @@ void AlignmentOutput::gdeOut(Alignment*
+ catch(const bad_alloc& e)
+ {
+ gdeOutFile->close();
+- cerr << "A bad_alloc exception has occured in the gdeOut function.\n"
++ cerr << "A bad_alloc exception has occurred in the gdeOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(VectorOutOfRange e)
+ {
+ gdeOutFile->close();
+- cerr << "An exception has occured in the gdeOut function.\n"
++ cerr << "An exception has occurred in the gdeOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(...)
+ {
+ gdeOutFile->close();
+- cerr << "An exception has occured in the gdeOut function.\n";
++ cerr << "An exception has occurred in the gdeOut function.\n";
+ exit(1);
+ }
+ }
+@@ -1553,21 +1553,21 @@ void AlignmentOutput::nbrfOut(Alignment*
+ catch(const bad_alloc& e)
+ {
+ nbrfOutFile->close();
+- cerr << "A bad_alloc exception has occured in the nbrfOut function.\n"
++ cerr << "A bad_alloc exception has occurred in the nbrfOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(VectorOutOfRange e)
+ {
+ nbrfOutFile->close();
+- cerr << "An exception has occured in the nbrfOut function.\n"
++ cerr << "An exception has occurred in the nbrfOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(...)
+ {
+ nbrfOutFile->close();
+- cerr << "An exception has occured in the nbrfOut function.\n";
++ cerr << "An exception has occurred in the nbrfOut function.\n";
+ exit(1);
+ }
+ }
+@@ -2088,28 +2088,28 @@ void AlignmentOutput::clustalOut(Alignme
+ catch(const bad_alloc& e)
+ {
+ clustalOutFile->close();
+- cerr << "A bad_alloc exception has occured in the clustalOut function.\n"
++ cerr << "A bad_alloc exception has occurred in the clustalOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(VectorOutOfRange e)
+ {
+ clustalOutFile->close();
+- cerr << "An exception has occured in the clustalOut function.\n"
++ cerr << "An exception has occurred in the clustalOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(exception e)
+ {
+ clustalOutFile->close();
+- cerr << "An exception has occured in the clustalOut function.\n"
++ cerr << "An exception has occurred in the clustalOut function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(...)
+ {
+ clustalOutFile->close();
+- cerr << "An exception has occured in the clustalOut function.\n";
++ cerr << "An exception has occurred in the clustalOut function.\n";
+ exit(1);
+ }
+ }
+@@ -2350,13 +2350,13 @@ void AlignmentOutput::findRangeValues(Al
+ }
+ catch(VectorOutOfRange e)
+ {
+- cerr << "An exception has occured in the findRangeValues function.\n"
++ cerr << "An exception has occurred in the findRangeValues function.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+ catch(...)
+ {
+- cerr << "An exception has occured in findRangeValues function\n";
++ cerr << "An exception has occurred in findRangeValues function\n";
+ exit(1);
+ }
+ }
+@@ -2383,7 +2383,7 @@ string AlignmentOutput::nameonly(string
+ }
+ catch(const exception& e)
+ {
+- cerr << "An exception has occured in the function nameonly\n"
++ cerr << "An exception has occurred in the function nameonly\n"
+ << e.what();
+ exit(1);
+ }
+--- a/clustalW/fileInput/EMBLFileParser.cpp
++++ b/clustalW/fileInput/EMBLFileParser.cpp
+@@ -229,7 +229,7 @@ int EMBLFileParser::countSeqs()
+ catch(...)
+ {
+ _fileIn->close();
+- cerr << "An exception has occured in the function EMBLFileParser::countSeqs()\n"
++ cerr << "An exception has occurred in the function EMBLFileParser::countSeqs()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+@@ -394,7 +394,7 @@ void EMBLFileParser::getSecStructure(vec
+ catch(...)
+ {
+ _fileIn->close();
+- cerr << "An exception has occured in the function EMBLFileParser::getSecStructure()\n"
++ cerr << "An exception has occurred in the function EMBLFileParser::getSecStructure()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+@@ -445,7 +445,7 @@ void EMBLFileParser::getSwissFeature(cha
+ }
+ catch(...)
+ {
+- cerr << "An exception has occured in the function EMBLFileParser::getSwissFeature()\n"
++ cerr << "An exception has occurred in the function EMBLFileParser::getSwissFeature()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+@@ -481,7 +481,7 @@ void EMBLFileParser::getSwissMask(char*
+ }
+ catch(...)
+ {
+- cerr << "An exception has occured in the function EMBLFileParser::getSwissMask()\n"
++ cerr << "An exception has occurred in the function EMBLFileParser::getSwissMask()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+--- a/clustalW/fileInput/GDEFileParser.cpp
++++ b/clustalW/fileInput/GDEFileParser.cpp
+@@ -206,7 +206,7 @@ int GDEFileParser::countSeqs()
+ catch(...)
+ {
+ _fileIn->close();
+- cerr << "An exception has occured in the function GDEFileParser::countSeqs()\n"
++ cerr << "An exception has occurred in the function GDEFileParser::countSeqs()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+@@ -429,7 +429,7 @@ void GDEFileParser::getSecStructure(vect
+ catch(...)
+ {
+ _fileIn->close();
+- cerr << "An exception has occured in the function GDEFileParser::getSecStructure()\n"
++ cerr << "An exception has occurred in the function GDEFileParser::getSecStructure()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+--- a/clustalW/pairwise/FastPairwiseAlign.cpp
++++ b/clustalW/pairwise/FastPairwiseAlign.cpp
+@@ -133,7 +133,7 @@ void FastPairwiseAlign::pairwiseAlign(Al
+ }
+ catch(const exception& e)
+ {
+- cerr << "An exception has occured in the FastPairwiseAlign class.\n"
++ cerr << "An exception has occurred in the FastPairwiseAlign class.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+--- a/clustalW/fileInput/ClustalFileParser.cpp
++++ b/clustalW/fileInput/ClustalFileParser.cpp
+@@ -165,7 +165,7 @@ Sequence ClustalFileParser::getSeq(int s
+ catch(...)
+ {
+ freeFileResources(_fileIn);
+- cerr << "An exception has occured in the function ClustalFileParser::getSeq()\n"
++ cerr << "An exception has occurred in the function ClustalFileParser::getSeq()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+@@ -225,7 +225,7 @@ int ClustalFileParser::countSeqs()
+ catch(...)
+ {
+ freeFileResources(_fileIn);
+- cerr << "An exception has occured in the function ClustalFileParser::countSeqs()\n"
++ cerr << "An exception has occurred in the function ClustalFileParser::countSeqs()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+@@ -582,7 +582,7 @@ void ClustalFileParser::getSecStructure(
+ catch(...)
+ {
+ freeFileResources(_fileIn);
+- cerr << "An exception has occured in the function ClustalFileParser::getSecStructure()\n"
++ cerr << "An exception has occurred in the function ClustalFileParser::getSecStructure()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+--- a/clustalW/fileInput/PearsonFileParser.cpp
++++ b/clustalW/fileInput/PearsonFileParser.cpp
+@@ -426,7 +426,7 @@ int PearsonFileParser::countSeqs()
+ catch(...)
+ {
+ freeFileResources(_fileIn);
+- cerr << "An exception has occured in the function PearsonFileParser::countSeqs()\n"
++ cerr << "An exception has occurred in the function PearsonFileParser::countSeqs()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+--- a/clustalW/fileInput/RSFFileParser.cpp
++++ b/clustalW/fileInput/RSFFileParser.cpp
+@@ -223,7 +223,7 @@ int RSFFileParser::countSeqs()
+ catch(...)
+ {
+ _fileIn->close();
+- cerr << "An exception has occured in the function RSFFileParser::countSeqs()\n"
++ cerr << "An exception has occurred in the function RSFFileParser::countSeqs()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+@@ -364,7 +364,7 @@ void RSFFileParser::getSecStructure(vect
+ catch(...)
+ {
+ _fileIn->close();
+- cerr << "An exception has occured in the function RSFFileParser::getSecStructure()\n"
++ cerr << "An exception has occurred in the function RSFFileParser::getSecStructure()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+@@ -418,7 +418,7 @@ void RSFFileParser::getRSFFeature(char*
+ }
+ catch(...)
+ {
+- cerr << "An exception has occured in the function RSFFileParser::getRSFFeature()\n"
++ cerr << "An exception has occurred in the function RSFFileParser::getRSFFeature()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+--- a/clustalW/pairwise/FullPairwiseAlign.cpp
++++ b/clustalW/pairwise/FullPairwiseAlign.cpp
+@@ -198,7 +198,7 @@ void FullPairwiseAlign::pairwiseAlign(Al
+ }
+ catch(const exception& e)
+ {
+- cerr << "An exception has occured in the FullPairwiseAlign class.\n"
++ cerr << "An exception has occurred in the FullPairwiseAlign class.\n"
+ << e.what() << "\n";
+ exit(1);
+ }
+--- a/clustalW/tree/UPGMA/RootedClusterTree.cpp
++++ b/clustalW/tree/UPGMA/RootedClusterTree.cpp
+@@ -90,14 +90,14 @@ auto_ptr<AlignmentSteps> RootedClusterTr
+ }
+ catch(const exception &ex)
+ {
+- cerr << "ERROR: Error has occured in treeFromDistMatrix. "
++ cerr << "ERROR: Error has occurred in treeFromDistMatrix. "
+ << "Need to terminate program.\n"
+ << ex.what();
+ exit(1);
+ }
+ catch(...)
+ {
+- cerr << "ERROR: Error has occured in treeFromDistMatrix. "
++ cerr << "ERROR: Error has occurred in treeFromDistMatrix. "
+ << "Need to terminate program.\n";
+ exit(1);
+ }
+--- a/clustalW/tree/UnRootedClusterTree.cpp
++++ b/clustalW/tree/UnRootedClusterTree.cpp
+@@ -257,14 +257,14 @@ void UnRootedClusterTree::treeFromDistMa
+ }
+ catch(const exception &ex)
+ {
+- cerr << "ERROR: Error has occured in treeFromDistMatrix. "
++ cerr << "ERROR: Error has occurred in treeFromDistMatrix. "
+ << "Need to terminate program.\n"
+ << ex.what();
+ exit(1);
+ }
+ catch(...)
+ {
+- cerr << "ERROR: Error has occured in treeFromDistMatrix. "
++ cerr << "ERROR: Error has occurred in treeFromDistMatrix. "
+ << "Need to terminate program.\n";
+ exit(1);
+ }
+--- a/clustalW/fileInput/MSFFileParser.cpp
++++ b/clustalW/fileInput/MSFFileParser.cpp
+@@ -171,7 +171,7 @@ Sequence MSFFileParser::getSeq(int seqNu
+ catch(...)
+ {
+ _fileIn->close();
+- cerr << "An exception has occured in the function MSFFileParser::getSeq()\n"
++ cerr << "An exception has occurred in the function MSFFileParser::getSeq()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+@@ -229,7 +229,7 @@ int MSFFileParser::countSeqs()
+ catch(...)
+ {
+ _fileIn->close();
+- cerr << "An exception has occured in the function MSFFileParser::countSeqs()\n"
++ cerr << "An exception has occurred in the function MSFFileParser::countSeqs()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+--- a/clustalW/fileInput/PIRFileParser.cpp
++++ b/clustalW/fileInput/PIRFileParser.cpp
+@@ -275,7 +275,7 @@ int PIRFileParser::countSeqs()
+ catch(...)
+ {
+ _fileIn->close();
+- cerr << "An exception has occured in the function PIRFileParser::countSeqs()\n"
++ cerr << "An exception has occurred in the function PIRFileParser::countSeqs()\n"
+ << "Program needs to terminate.\nPlease contact the Clustal developers\n";
+ exit(1);
+ }
+--- a/mainwindow.cpp
++++ b/mainwindow.cpp
+@@ -3108,7 +3108,7 @@ void MainWindow::errorHandler(int errorC
+ else
+ {
+ QMessageBox::information(this, "",
+- "An unknown error occured reading in the file!",
++ "An unknown error occurred reading in the file!",
+ QMessageBox::Ok);
+ }
+ }
--
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