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75 lines
2.0 KiB
C++
75 lines
2.0 KiB
C++
// $Id: fastaFormat.cpp 10280 2012-02-06 09:45:26Z itaymay $
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#include "fastaFormat.h"
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#include "someUtil.h"
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#include "errorMsg.h"
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#include "ConversionUtils.h"
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#include <algorithm>
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using namespace std;
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sequenceContainer fastaFormat::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 fastaFormat::readUnAligned(istream &infile, const alphabet* alph) {
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sequenceContainer mySeqData;
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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 fasta format");
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}
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vector<string>::const_iterator it1;
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int localid=0;
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for (it1 = seqFileData.begin(); it1!= seqFileData.end(); ) {
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if (it1->empty()) {++it1;continue; }// empty line continue
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string remark;
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string name;
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if ((*it1)[0] == '>') {
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string::const_iterator itstrtmp = (*it1).begin();
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itstrtmp++;
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while (itstrtmp != (*it1).end()) {
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name+= *itstrtmp;
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itstrtmp++;
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}
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//for (string::iterator i = name.begin(); i!=(name.end()-2);++i) {
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// *i=*(i+1); // removing the ">". should be done more elegant...
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//}
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++it1;
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} else {
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LOG(0,<<"problem in line: "<<*it1<<endl);
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errorMsg::reportError("Error reading fasta file, error finding sequence name starting with >",1);
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}
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while (it1->empty()) it1++; // empty line continue
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string str;
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while (it1!= seqFileData.end()) {
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if ((*it1)[0] == '>') break;
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str+=*it1;
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++it1;
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}
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// remove spaces form str;
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str = takeCharOutOfString(" \t", str);
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name = trim(name);
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mySeqData.add(sequence(str,name,remark,localid,alph));
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localid++;
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}
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return mySeqData;
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}
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void fastaFormat::write(ostream &out, const sequenceContainer& sd) {
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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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out<<it5->toString()<<endl;
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}
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}
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