/dports/biology/clustalw/clustalw-2.1/src/fileInput/ |
H A D | FileReader.cpp | 50 bool FileReader::noEmptySequence(vector<Sequence> seqVector, string *offendingSeq) in noEmptySequence() argument 55 offendingSeq->assign(si->getName()); in noEmptySequence() 70 int FileReader::seqInput(Alignment *alignPtr, bool append, string *offendingSeq) in seqInput() argument 85 code = readSeqs(alignPtr, numSeqsAlready + 1, offendingSeq); in seqInput() 217 seqRangeVector = fileParser->getSeqRange(1, noSeqs, offendingSeq); in readSeqs() 222 if (noEmptySequence(seqRangeVector, offendingSeq) == false) { in readSeqs() 256 if(alignPtr->checkAllNamesDifferent(offendingSeq) == false) { //nige moved in readSeqs() 269 if (! alignPtr->testUniqueNames(&seqVector, offendingSeq)) { //nige added in readSeqs() 320 string offendingSeq; in profileInput() local 330 code = readSeqs(alignPtr, 1, &offendingSeq); in profileInput() [all …]
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H A D | PearsonFileParser.cpp | 52 PearsonFileParser::getSeqRange(int firstSeq, int nSeqsToRead, string *offendingSeq) in getSeqRange() argument 155 if (offendingSeq!=NULL) in getSeqRange() 156 offendingSeq->assign(name); in getSeqRange() 164 if (offendingSeq!=NULL) in getSeqRange() 165 offendingSeq->assign(name); in getSeqRange() 199 Sequence PearsonFileParser::getSeq(int seqNum, string *offendingSeq) in getSeq() argument
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H A D | FileReader.h | 34 int seqInput(Alignment* alignPtr, bool append, string *offendingSeq); 35 int readSeqs(Alignment* alignPtr, int firstSeq, string *offendingSeq); 45 bool noEmptySequence(vector<Sequence> seqRangeVector, string *offendingSeq);
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H A D | PIRFileParser.cpp | 35 vector<Sequence> PIRFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) in getSeqRange() argument 42 Sequence tempSeq = getSeq(firstSeq + i, offendingSeq); in getSeqRange() 59 Sequence PIRFileParser::getSeq(int seqNum, string *offendingSeq) in getSeq() argument 151 if (offendingSeq!=NULL) in getSeq() 152 offendingSeq->assign(name); in getSeq()
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H A D | ClustalFileParser.cpp | 37 vector<Sequence> ClustalFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) in getSeqRange() argument 44 Sequence tempSeq = getSeq(firstSeq + i, offendingSeq); in getSeqRange() 55 Sequence ClustalFileParser::getSeq(int seqNum, string *offendingSeq) in getSeq() argument 135 if (offendingSeq!=NULL) in getSeq() 136 offendingSeq->assign(name); in getSeq() 157 if (offendingSeq!=NULL) in getSeq() 158 offendingSeq->assign(name); in getSeq()
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H A D | MSFFileParser.cpp | 34 vector<Sequence> MSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) in getSeqRange() argument 58 Sequence MSFFileParser::getSeq(int seqNum, string *offendingSeq) in getSeq() argument 164 if (offendingSeq!=NULL) in getSeq() 165 offendingSeq->assign(name); in getSeq()
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H A D | GDEFileParser.cpp | 40 vector<Sequence> GDEFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) in getSeqRange() argument 47 Sequence tempSeq = getSeq(firstSeq + i, offendingSeq); in getSeqRange() 61 Sequence GDEFileParser::getSeq(int seqNum, string *offendingSeq) in getSeq() argument 156 if (offendingSeq!=NULL) in getSeq() 157 offendingSeq->assign(name); in getSeq()
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H A D | MSFFileParser.h | 20 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL); 21 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
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H A D | PIRFileParser.h | 20 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL); 21 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
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H A D | RSFFileParser.cpp | 31 vector<Sequence> RSFFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) in getSeqRange() argument 38 Sequence tempSeq = getSeq(firstSeq + i, offendingSeq); in getSeqRange() 54 Sequence RSFFileParser::getSeq(int seqNum, string *offendingSeq) in getSeq() argument 165 if (offendingSeq!=NULL) in getSeq() 166 offendingSeq->assign(name); in getSeq()
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H A D | GDEFileParser.h | 21 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL); 22 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
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H A D | ClustalFileParser.h | 21 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL); 22 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
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H A D | PearsonFileParser.h | 25 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL); 26 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
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H A D | RSFFileParser.h | 20 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL); 21 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
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H A D | FileParser.h | 36 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq) = 0; 37 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL) = 0;
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H A D | EMBLFileParser.h | 21 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL); 22 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
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H A D | EMBLFileParser.cpp | 42 vector<Sequence> EMBLFileParser::getSeqRange(int firstSeq, int no, string *offendingSeq) in getSeqRange() argument 49 Sequence tempSeq = getSeq(firstSeq + i, offendingSeq); in getSeqRange() 63 Sequence EMBLFileParser::getSeq(int seqNum, string *offendingSeq) in getSeq() argument 179 if (offendingSeq!=NULL) in getSeq() 180 offendingSeq->assign(name); in getSeq()
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/dports/biology/clustalw/clustalw-2.1/src/alignment/ |
H A D | Alignment.h | 100 bool checkAllNamesDifferent(string *offendingSeq); 101 bool testUniqueNames(vector<Sequence>* seqVector, string *offendingSeq);
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H A D | Alignment.cpp | 393 bool Alignment::testUniqueNames(vector<Sequence>* seqVector, string *offendingSeq) in testUniqueNames() argument 404 offendingSeq->assign(*oldName); in testUniqueNames() 811 bool Alignment::checkAllNamesDifferent(string *offendingSeq) in checkAllNamesDifferent() argument 834 offendingSeq->assign((*namesIter1)); in checkAllNamesDifferent()
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/dports/biology/clustalw/clustalw-2.1/src/ |
H A D | Clustal.cpp | 973 int Clustal::sequenceInput(bool append, string *offendingSeq) in sequenceInput() argument 983 code = readSeqFile.seqInput(&alignmentObj, append, offendingSeq); in sequenceInput() 1084 string offendingSeq; in commandLineReadSeq() local 1086 code = readInputFile.readSeqs(&alignmentObj, firstSeq, &offendingSeq); in commandLineReadSeq() 1100 …>error("Multiple sequences found with same name (found %s at least twice)!", offendingSeq.c_str()); in commandLineReadSeq() 1104 utilityObject->error("Empty sequences found: %s\n", offendingSeq.c_str()); in commandLineReadSeq() 1108 utilityObject->error("Sequence(s) too big: %s\n", offendingSeq.c_str()); in commandLineReadSeq()
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H A D | Clustal.h | 40 int sequenceInput(bool append, string *offendingSeq);
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/dports/biology/clustalw/clustalw-2.1/src/interface/ |
H A D | InteractiveMenu.cpp | 110 string offendingSeq; // unused here in mainMenu() local 114 clustalObj->sequenceInput(false, &offendingSeq); in mainMenu() 585 string offendingSeq; // unused here in phylogeneticTreeMenu() local 589 clustalObj->sequenceInput(false, &offendingSeq); in phylogeneticTreeMenu()
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