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// $Id: phylipFormat.cpp 962 2006-11-07 15:13:34Z privmane $
#include "phylipSequentialFormat.h"
#include "someUtil.h"
#include "errorMsg.h"
#include "logFile.h"
sequenceContainer phylipSequentialFormat::read(istream &infile, const alphabet* alph){
sequenceContainer mySeqData = readUnAligned(infile, alph);
mySeqData.makeSureAllSeqAreSameLengthAndGetLen();
return mySeqData;
}
sequenceContainer phylipSequentialFormat::readUnAligned(istream &infile, const alphabet* alph){
sequenceContainer mySeqData;
vector<string> seqFileData;
putFileIntoVectorStringArray(infile,seqFileData);
vector<string>::const_iterator currentLinePosition = seqFileData.begin();
string::const_iterator itStr = seqFileData.begin()->begin();
string::const_iterator itStrEnd = seqFileData.begin()->end();
int f_numSeq;
bool readSeqNum= fromStringIterToInt(itStr,itStrEnd,f_numSeq);
if (readSeqNum == false) errorMsg::reportError("Error reading number of sequences while reading PHYLIP sequence format");
int f_seqLength;
bool readSeqLen= fromStringIterToInt(itStr,itStrEnd,f_seqLength);
if (readSeqLen == false) errorMsg::reportError("Error reading the sequences length while reading PHYLIP sequence format");
currentLinePosition++; // we read the first line.
int localid=0;
for (; currentLinePosition != seqFileData.end() ; ) {
if (currentLinePosition->empty()) {++currentLinePosition;continue;} // empty line continue
string stringSeq1;
string name1;
while (stringSeq1.length() < f_seqLength ) { // adding a new seq
string::const_iterator it2 = (currentLinePosition)->begin();
if ((*it2)==' ') { // line without seq. name, read seq. content only
for (; it2 != (currentLinePosition)->end();++it2) {
if ((*it2)==' ') continue;
else stringSeq1+=(*it2);
}
}
else { // first read sequence name, then read seq itself
for (; it2 != (currentLinePosition)->end();++it2) {
if ((*it2)==' ') break;
else name1+=(*it2);
}
for (; it2 != (currentLinePosition)->end();++it2) {
if ((*it2)==' ') continue;
else stringSeq1+=(*it2);
}
}
currentLinePosition++;
}
mySeqData.add(sequence(stringSeq1,name1,"",localid,alph));
localid++;
}
return mySeqData;
}
void phylipSequentialFormat::write(ostream &out, const sequenceContainer& sd,
const int numOfPositionInLine,
const int spaceEvery) {
sequenceContainer::constTaxaIterator it5=sd.constTaxaBegin();
for (;it5!=sd.constTaxaEnd();++it5) {
if (it5->name().size() > 10) break;
}
if (it5 != sd.constTaxaEnd()) {
LOG(1,<<"you asked to print in phylip format\n");
LOG(1,<<"however, the names in phylip format\n");
LOG(1,<<"must be no more than 10 characters.\n");
LOG(1,<<"Names are hence trancated to ten \n");
LOG(1,<<"characters. Notice, that this might\n");
LOG(1,<<"result in a two or more sequences \n");
LOG(1,<<"having the same name \n");
}
// vector<const sequenceContainer::sequenceDatum*> vec;
// sd.getSequenceDatumPtrVector(vec);
out<<sd.numberOfSeqs()<<" "<<sd.seqLen();
if (sd.constTaxaBegin()==sd.constTaxaEnd()) return;
int maxLengthOfSeqName =0;
maxLengthOfSeqName=10; // all this maxLengthOfSeqName is the
for (sequenceContainer::constTaxaIterator it5=sd.constTaxaBegin();it5!=sd.constTaxaEnd();++it5) {
int currentPosition = 0;
out<<endl;
out.flush();
// first - print name of sequence
for (int iName = 0 ;iName<maxLengthOfSeqName; ++iName) {
if (iName<it5->name().size()) {
if (currentPosition<numOfPositionInLine) {
out<<it5->name()[iName];
}
else out<<" ";
out.flush();
}
else out<<" ";
}
out.flush();
out<<" ";
// next - print sequence itself
while (currentPosition < sd.seqLen() ) {
if (it5->seqLen()<numOfPositionInLine)
out<<it5->toString()<<endl;
else {
for (int k=currentPosition; k < currentPosition+numOfPositionInLine; ++k) {
if (k>=it5->seqLen()) break;
out<<it5->toString(k);
if (((k+1)%spaceEvery==0) && (((k+1)%numOfPositionInLine!=0))) out<<" ";
}
out<<endl;
if (currentPosition+numOfPositionInLine < sd.seqLen()) {
for (int i = 0; i < spaceEvery +1; i++) // creates spaces to align properly
out << " ";
}
}
currentPosition +=numOfPositionInLine;
}
}
}
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