void writeCharactersBlockToStream(
const NxsCharactersBlock & cb,
ostream & outf,
const std::vector<std::string> & taxaNames,
MultiFormatReader::DataFormatType f,
long interleaveLen)
{
const unsigned nt = taxaNames.size();
const unsigned nc = cb.GetNChar();
unsigned nCharsToWrite;
unsigned seqStartColumn = 0;
if (IsRelaxedPhylipType(f))
{
for (unsigned i = 0; i < nt; ++i)
{
const std::string & name = taxaNames[i];
if (name.length() > seqStartColumn)
seqStartColumn = name.length();
}
seqStartColumn += 1;
}
if (IsPhylipType(f) || IsRelaxedPhylipType(f))
{
std::string sep;
outf << nt << ' ' << nc << '\n';
if (IsInterleaveType(f) && interleaveLen > 0)
{
std::vector<std::string> storedSeqs;
storedSeqs.reserve(nt);
std::string *sp;
nCharsToWrite = (nc > (unsigned) interleaveLen ? (unsigned)interleaveLen : nc);
for (unsigned i = 0; i < nt; ++i)
{
const std::string & name = taxaNames[i];
storedSeqs.push_back(cb.GetMatrixRowAsStr(i));
sp = &(storedSeqs[i]);
if (IsRelaxedPhylipType(f))
{
sep.clear();
sep.append(seqStartColumn - name.length(), ' ');
}
outf << name << sep << sp->substr(0, nCharsToWrite) << '\n';
}
for (unsigned currIndex = (unsigned)interleaveLen; currIndex < nc; currIndex += (unsigned)interleaveLen)
{
outf << '\n';
nCharsToWrite = ((nc - currIndex) > (unsigned)interleaveLen ? (unsigned)interleaveLen : (nc - currIndex));
for (unsigned i = 0; i < nt; ++i)
{
sp = &(storedSeqs[i]);
outf << sp->substr(currIndex, nCharsToWrite) << '\n';
}
}
}
else
{
if (interleaveLen > 0)
{
// not interleaved, but wrapping at interleaveLen
for (unsigned i = 0; i < nt; ++i)
{
nCharsToWrite = (nc > (unsigned)interleaveLen ? (unsigned)interleaveLen : nc);
const std::string & name = taxaNames[i];
std::string seq = cb.GetMatrixRowAsStr(i);
if (IsRelaxedPhylipType(f))
{
sep.clear();
sep.append(seqStartColumn - name.length(), ' ');
}
outf << name << sep << seq.substr(0, nCharsToWrite) << '\n';
for (unsigned currIndex = (unsigned)interleaveLen; currIndex < nc; currIndex += (unsigned)interleaveLen)
{
nCharsToWrite = ((nc - currIndex) > (unsigned)interleaveLen ? (unsigned)interleaveLen : (nc - currIndex));
outf << seq.substr(currIndex, nCharsToWrite) << '\n';
}
}
}
else
{
// not interleaved, and not wrapping
for (unsigned i = 0; i < nt; ++i)
{
const std::string & name = taxaNames[i];
std::string seq = cb.GetMatrixRowAsStr(i);
if (IsRelaxedPhylipType(f))
{
sep.clear();
sep.append(seqStartColumn - name.length(), ' ');
}
outf << name << sep << seq << '\n';
}
}
}
}
else if (IsFastaType(f))
{
if (interleaveLen < 1)
interleaveLen = 60; // default FASTA line length
for (unsigned i = 0; i < nt; ++i)
{
nCharsToWrite = (nc > (unsigned)interleaveLen ? (unsigned)interleaveLen : nc);
const std::string & name = taxaNames[i];
std::string seq = cb.GetMatrixRowAsStr(i);
outf << '>' << name << '\n' << seq.substr(0, nCharsToWrite) << '\n';
for (unsigned currIndex = (unsigned)interleaveLen; currIndex < nc; currIndex += (unsigned)interleaveLen)
{
nCharsToWrite = ((nc - currIndex) > (unsigned)interleaveLen ? (unsigned)interleaveLen : (nc - currIndex));
outf << seq.substr(currIndex, nCharsToWrite) << '\n';
}
}
}
else
{
throw NxsException("writeCharactersBlockToStream requested for unsupported format");
}
}
