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Searched refs:offendingSeq (Results 1 – 22 of 22) sorted by relevance

/dports/biology/clustalw/clustalw-2.1/src/fileInput/
H A DFileReader.cpp50 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 …]
H A DPearsonFileParser.cpp52 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
H A DFileReader.h34 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);
H A DPIRFileParser.cpp35 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()
H A DClustalFileParser.cpp37 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()
H A DMSFFileParser.cpp34 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()
H A DGDEFileParser.cpp40 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()
H A DMSFFileParser.h20 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
21 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
H A DPIRFileParser.h20 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
21 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
H A DRSFFileParser.cpp31 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()
H A DGDEFileParser.h21 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
22 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
H A DClustalFileParser.h21 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
22 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
H A DPearsonFileParser.h25 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
26 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
H A DRSFFileParser.h20 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
21 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
H A DFileParser.h36 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq) = 0;
37 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL) = 0;
H A DEMBLFileParser.h21 virtual Sequence getSeq(int seqNum, string *offendingSeq=NULL);
22 virtual vector<Sequence> getSeqRange(int firstSeq, int num, string *offendingSeq=NULL);
H A DEMBLFileParser.cpp42 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()
/dports/biology/clustalw/clustalw-2.1/src/alignment/
H A DAlignment.h100 bool checkAllNamesDifferent(string *offendingSeq);
101 bool testUniqueNames(vector<Sequence>* seqVector, string *offendingSeq);
H A DAlignment.cpp393 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()
/dports/biology/clustalw/clustalw-2.1/src/
H A DClustal.cpp973 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()
H A DClustal.h40 int sequenceInput(bool append, string *offendingSeq);
/dports/biology/clustalw/clustalw-2.1/src/interface/
H A DInteractiveMenu.cpp110 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()