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()
89         code = readSeqs(alignPtr, 1, offendingSeq);  //  1 is the first seq to be read   in seqInput()
142     int FileReader::readSeqs(Alignment *alignPtr, int firstSeq, string *offendingSeq)  in readSeqs()  argument
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()
367         code = readSeqs(alignPtr, profile1NumOfSeqs + 1, &offendingSeq);   in profileInput()