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87 lines
2.5 KiB
C++
87 lines
2.5 KiB
C++
// $Id: maseFormat.cpp 962 2006-11-07 15:13:34Z privmane $
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#include "maseFormat.h"
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#include "someUtil.h"
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#include "errorMsg.h"
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sequenceContainer maseFormat::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 maseFormat::readUnAligned(istream &infile, const alphabet* alph) {
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if (!infile) {
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errorMsg::reportError("unable to read mase format, could not open file");
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}
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sequenceContainer mySeqData;;
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vector<string> seqFileData;
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putFileIntoVectorStringArray(infile,seqFileData);
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vector<string>::const_iterator it1;
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for (it1 = seqFileData.begin(); it1!= seqFileData.end(); ++it1) {
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if (it1->empty()) continue; // empty line continue
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if (it1->size()>1) {
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if ( ((*it1)[0] == ';') && ((*it1)[1] == ';')) {// general file remarks
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mySeqData.addGeneralRemark(*it1);
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}
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}
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}
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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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if (it1->size()>1) {
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if ( ((*it1)[0] == ';') && ((*it1)[1] == ';')) {// general file remarks
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++it1;continue;
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}
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}
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string remark;
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string name;
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string seqStr;
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if ((*it1)[0] != ';') {
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LOG(5,<<"problem in line: "<<*it1<<endl);
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errorMsg::reportError("Error reading mase file, error finding sequence remark",1);
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}
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if ((*it1)[0] == ';') {remark += *it1;++it1;}
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while ((*it1)[0] == ';') {
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remark += "\n";
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remark += *it1;
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++it1;
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}
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while (it1->empty()) it1++; // empty line continue
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name = *it1;
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++it1;
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while (it1!= seqFileData.end()) {
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if ((*it1)[0] == ';') break;
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// the following lines are taking care of a format which is like "10 aact"
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// in mase format
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string withoutNumberAndSpaces =
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takeCharOutOfString("0123456789 ",*it1);
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seqStr+=withoutNumberAndSpaces;
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++it1;
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}
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mySeqData.add(sequence(seqStr,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 maseFormat::write(ostream &out, const sequenceContainer& sd) {
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vector<string> gfr = sd.getGeneralRemarks();
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if (gfr.empty()) out<<";;\n;;\n";
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for (vector<string>::const_iterator k=gfr.begin() ; k != gfr.end() ; ++k )
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out<<(*k)<<endl;
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for (sequenceContainer::constTaxaIterator it5=sd.constTaxaBegin();it5!=sd.constTaxaEnd();++it5) {
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if ((*it5).remark().size() > 0) out<<";"<<(*it5).remark()<<endl;
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else out<<";\n";
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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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