void exportUnalignedBlocks(
PublicNexusReader & nexusReader,
MultiFormatReader::DataFormatType f,
long interleaveLen,
std::string prefix,
std::ostream * fp)
{
std::ostream * fpToUse = fp;
const unsigned nTaxaBlocks = nexusReader.GetNumTaxaBlocks();
for (unsigned t = 0; t < nTaxaBlocks; ++t)
{
const NxsTaxaBlock * tb = nexusReader.GetTaxaBlock(t);
const unsigned nUnalignedBlocks = nexusReader.GetNumUnalignedBlocks(tb);
if (nUnalignedBlocks == 0)
continue;
NxsString tbSpecificPrefix;
if (t > 0)
tbSpecificPrefix << (1 + t);
tbSpecificPrefix << prefix << "-unaligned";
typedef std::pair<const NxsUnalignedBlock *, std::string> PairUBAndString;
typedef std::vector< PairUBAndString > VecPairUBAndString;
VecPairUBAndString ubToWrite;
for (unsigned i = 0; i < nUnalignedBlocks; ++i)
{
NxsString fn = tbSpecificPrefix;
if (i > 0)
fn << (1 + i);
fn << getFileExtension(f);
const NxsUnalignedBlock * ub = nexusReader.GetUnalignedBlock(tb, i);
NxsCharactersBlock::DataTypesEnum dt = ub->GetDataType();
bool writeBlock = false;
if ((dt == NxsCharactersBlock::dna || dt == NxsCharactersBlock::nucleotide) && (f == MultiFormatReader::FASTA_DNA_FORMAT))
writeBlock = true;
else if ((dt == NxsCharactersBlock::rna) && (f == MultiFormatReader::FASTA_RNA_FORMAT))
writeBlock = true;
else if ((dt == NxsCharactersBlock::protein) && (f == MultiFormatReader::FASTA_AA_FORMAT))
writeBlock = true;
if (writeBlock)
ubToWrite.push_back(std::pair<const NxsUnalignedBlock *, std::string>(ub, fn));
}
if (!ubToWrite.empty())
{
std::vector<std::string> namesToPrint(tb->GetAllLabels());
std::vector<NxsNameToNameTrans> nameTrans = nameTranslationDict(namesToPrint, f);
if (!nameTrans.empty())
{
namesToPrint.clear();
for (std::vector<NxsNameToNameTrans>::const_iterator nIt = nameTrans.begin(); nIt != nameTrans.end(); ++nIt)
namesToPrint.push_back(nIt->second);
if (nexusReader.conversionOutputRecord.writeNameTranslationFile)
nexusReader.conversionOutputRecord.writeNameTranslation(nameTrans, tb);
}
for (VecPairUBAndString::const_iterator vIt = ubToWrite.begin(); vIt != ubToWrite.end(); ++vIt)
{
const NxsUnalignedBlock * ubP = vIt->first;
std::string fn = vIt->second;
ofstream outf;
if (fp == 0L)
{
openOrThrow(outf, fn);
fpToUse = &outf;
}
writeUnalignedBlockToStream(*ubP, *fpToUse, namesToPrint, f, interleaveLen);
}
}
}
}
