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86 lines
2.5 KiB
C++
86 lines
2.5 KiB
C++
// $Id: molphyFormat.cpp 962 2006-11-07 15:13:34Z privmane $
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#include "molphyFormat.h"
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#include "someUtil.h"
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#include "errorMsg.h"
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sequenceContainer molphyFormat::read(istream &infile, const alphabet* alph) {
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sequenceContainer mySeqData = readUnAligned(infile, alph);
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mySeqData.makeSureAllSeqAreSameLengthAndGetLen();
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return mySeqData;
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}
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sequenceContainer molphyFormat::readUnAligned(istream &infile, const alphabet* alph) {
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vector<string> seqFileData;
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putFileIntoVectorStringArray(infile,seqFileData);
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if (seqFileData.empty()){
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errorMsg::reportError("unable to open file, or file is empty in molphy format");
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}
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vector<string>::iterator currentLinePosition = seqFileData.begin();
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string::const_iterator itStr = seqFileData.begin()->begin();
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string::const_iterator itStrEnd = seqFileData.begin()->end();
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int f_numSeq;
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bool readSeqNum= fromStringIterToInt(itStr,itStrEnd,f_numSeq);
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if (readSeqNum == false) errorMsg::reportError("Error reading number of sequences while reading MOLPHY sequence format");
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int f_seqLength;
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bool readSeqLen= fromStringIterToInt(itStr,itStrEnd,f_seqLength);
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if (readSeqLen == false) errorMsg::reportError("Error reading the sequences length while reading MOLPHY sequence format");
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currentLinePosition++; // we read the first line.
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//---------------------------------------------------------------------
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sequenceContainer mySeqData;
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//---------------------------------------------------------------------
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// vector<sequenceContainer::sequenceDatum*> vec;
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// seqDataPtr->getSequenceDatumPtrVectorNonConst(vec);
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int localID=-1;
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vector<string>::const_iterator it1 = seqFileData.begin();
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++it1; //skipping the first line that was read already.
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while (it1!= seqFileData.end()) {
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localID++;
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if (it1->empty()) {
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it1++;
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continue; // empty line continue
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}
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// read the name.
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string name(*it1);
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it1++;
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string tmpString;
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while (it1 != seqFileData.end()) {
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if (tmpString.size() < f_seqLength) {
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tmpString+=*it1;
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++it1;
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}
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else break;
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}
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mySeqData.add(sequence(tmpString,name,"",localID,alph));
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}
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return mySeqData;
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}
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void molphyFormat::write(ostream &out, const sequenceContainer& sd) {
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out<<sd.numberOfSeqs()<<" "<<sd.seqLen()<<endl;
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for (sequenceContainer::constTaxaIterator it5=sd.constTaxaBegin();it5!=sd.constTaxaEnd();++it5) {
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out<<it5->name()<<endl;
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string seqString = it5->toString();
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int k=0;
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for (string::const_iterator cPos=seqString.begin() ; cPos != seqString.end() ; cPos ++,k++ ) {
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if (k>0 && ((k%60)==0)) out<<endl;
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out<<*cPos;
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}
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out<<endl;
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}
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}
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