Author: Andreas Tille <tille@debian.org>
Last-Update: Fri, 22 Jul 2016 04:04:40 +0300
Description: Fix spelling

--- a/clustalw_help
+++ b/clustalw_help
@@ -285,7 +285,7 @@ alignments (e.g. PRETTY, PROFILEMAKE, PL
 .msf format files (multiple sequence file); new in version 7 of GCG.
 
 Fasta output cis widely used because of it's simplicity. Each sequence name is
-preceeded by a '>'-sign. The sequence itself is printed out in the following lines
+preceded by a '>'-sign. The sequence itself is printed out in the following lines
 
 PHYLIP format output can be used for input to the PHYLIP package of Joe 
 Felsenstein.  This is an extremely widely used package for doing every 
--- a/src/Help.cpp
+++ b/src/Help.cpp
@@ -331,7 +331,7 @@ Help::Help()
 ".msf format files (multiple sequence file); new in version 7 of GCG.\n"
 "\n"
 "Fasta output cis widely used because of it's simplicity. Each sequence name is\n"
-"preceeded by a '>'-sign. The sequence itself is printed out in the following lines\n"
+"preceded by a '>'-sign. The sequence itself is printed out in the following lines\n"
 "\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/src/tree/ClusterTree.cpp
+++ b/src/tree/ClusterTree.cpp
@@ -956,7 +956,7 @@ void ClusterTree::printBootstrapHeaderTo
         (*clustalFile) << "\n Each column is 1 sequence; ";
         (*clustalFile) << "the stars in each line show 1 group; ";
         (*clustalFile) << "\n the dots show the other\n";
-        (*clustalFile) << "\n Numbers show occurences in bootstrap samples.";
+        (*clustalFile) << "\n Numbers show occurrences in bootstrap samples.";
     }
 }
 
--- a/src/alignment/Alignment.cpp
+++ b/src/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/src/alignment/AlignmentOutput.cpp
+++ b/src/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 constructor 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/src/fileInput/EMBLFileParser.cpp
+++ b/src/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/src/fileInput/GDEFileParser.cpp
+++ b/src/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/src/pairwise/FastPairwiseAlign.cpp
+++ b/src/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/src/fileInput/ClustalFileParser.cpp
+++ b/src/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/src/fileInput/PearsonFileParser.cpp
+++ b/src/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/src/fileInput/RSFFileParser.cpp
+++ b/src/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/src/pairwise/FullPairwiseAlign.cpp
+++ b/src/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/src/tree/UPGMA/RootedClusterTree.cpp
+++ b/src/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/src/tree/UnRootedClusterTree.cpp
+++ b/src/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/src/fileInput/MSFFileParser.cpp
+++ b/src/fileInput/MSFFileParser.cpp
@@ -19,7 +19,7 @@ namespace clustalw
 {
 
 /**
- * MSFFileParser contructor sets up the chartab array.
+ * MSFFileParser constructor sets up the chartab array.
  * @param filePath 
  * @return 
  */
@@ -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/src/fileInput/PIRFileParser.cpp
+++ b/src/fileInput/PIRFileParser.cpp
@@ -19,7 +19,7 @@ namespace clustalw
 {
 
 /**
- * PIRFileParser contructor sets up the chartab array.
+ * PIRFileParser constructor sets up the chartab array.
  * @param filePath 
  */
 PIRFileParser::PIRFileParser(string filePath)
@@ -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/src/alignment/Sequence.cpp
+++ b/src/alignment/Sequence.cpp
@@ -40,7 +40,7 @@ Sequence::Sequence(std::string& seq, std
 }
 
 /**
- * This is an overloaded contructor that is used to construct a seq object from an
+ * This is an overloaded constructor that is used to construct a seq object from an
  * encoded sequenced instead of a string.
  * @param encodedSequence 
  * @param name 
--- a/src/tree/RandomGenerator.cpp
+++ b/src/tree/RandomGenerator.cpp
@@ -12,7 +12,7 @@ namespace clustalw
 {
 
 /**
- * The contructor initialises the random algorithm.
+ * The constructor initialises the random algorithm.
  * @param s 
  * @return 
  */