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