int processContent(PublicNexusReader & nexusReader,
const char *gFilename,
std::ostream *os,
INIReader & iniReader) {
BlockReaderList blocks = nexusReader.GetUsedBlocksInOrder();
if (blocks.size() == 0) {
cerr << "Error:\n No understandable content was found.\n";
exit(1);
}
const unsigned numTaxaBlocks = nexusReader.GetNumTaxaBlocks();
if (numTaxaBlocks != 1) {
std::cerr << "Expecting a file with exactly 1 TAXA block, but found " << numTaxaBlocks << " in the file " << gFilename << ".\n";
return 2;
}
NxsTaxaBlock * taxaBlock = nexusReader.GetTaxaBlock(0);
const unsigned nCharBlocks = nexusReader.GetNumCharactersBlocks(taxaBlock);
if (nCharBlocks != 1) {
std::cerr << "Expecting a file with exactly 1 CHARACTERS/DATA block, but found " << nCharBlocks << " in the file " << gFilename << ".\n";
return 3;
}
const unsigned nTreesBlocks = nexusReader.GetNumTreesBlocks(taxaBlock);
if (nTreesBlocks != 1) {
std::cerr << "Expecting a file with exactly 1 TREES block, but found " << nTreesBlocks << " in the file " << gFilename << ".\n";
return 3;
}
const NxsCharactersBlock * charBlock = nexusReader.GetCharactersBlock(taxaBlock, 0);
std::vector<const NxsDiscreteDatatypeMapper *> mappers = charBlock->GetAllDatatypeMappers();
if (mappers.size() != 1) {
std::cerr << "Expecting an unmixed characters block, but found a matrix with datatype = mixed or a datatype with augmented symbols\n";
return 4;
}
const NxsDiscreteDatatypeMapper * dm = mappers[0];
ScopedTwoDMatrix<NxsCDiscreteStateSet> compressedMatrix;
std::vector<unsigned> patternCounts;
std::vector<double> patternWeights;
bool hasWeights = true;
std::vector<NxsCharacterPattern> compressedTransposedMatrix;
std::vector<std::set<unsigned> > compressedIndexToOriginal;
std::vector<int> originalIndexToCompressed;
if (true) {
if (true) {
NxsCXXDiscreteMatrix cxxMat(*charBlock, false, 0L, false);
hasWeights = cxxMat.hasWeights();
NxsCompressDiscreteMatrix(cxxMat, compressedTransposedMatrix, &originalIndexToCompressed, &compressedIndexToOriginal);
}
std::vector<double> * wtsPtr = (hasWeights ? &patternWeights : 0L);
NxsTransposeCompressedMatrix(compressedTransposedMatrix, compressedMatrix, &patternCounts, wtsPtr);
patternWeights.clear();
for (auto i : patternCounts) {
patternWeights.push_back(double(i));
}
}
_DEBUG_VEC(patternWeights);
NxsCDiscreteStateSet ** matrixAlias = compressedMatrix.GetAlias();
const unsigned ntaxTotal = charBlock->GetNTaxTotal();
const NxsTreesBlock * treesBlock = nexusReader.GetTreesBlock(taxaBlock, 0);
//mt::ModelDescription md(mt::ModelDescription::VAR_ONLY_NO_MISSING_ASC_BIAS); //@TODO should be run-time setting
mt::ModelDescription md(mt::ModelDescription::NO_ASC_BIAS); //@TODO should be run-time setting
mt::NCL2MT ncl2mt;
for (unsigned nti = 0; nti < treesBlock->GetNumTrees(); ++nti) {
const NxsSimpleTree nst(treesBlock->GetFullTreeDescription(nti), 1, 0.1, true);
ncl2mt.processTree(os,
ntaxTotal,
charBlock,
dm,
(const NxsCDiscreteStateSet **) matrixAlias,
patternWeights,
originalIndexToCompressed,
nst,
md,
iniReader);
}
return 0;
}
void exportCharacters(
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 nCharBlocks = nexusReader.GetNumCharactersBlocks(tb);
if (nCharBlocks == 0)
continue;
NxsString tbSpecificPrefix;
if (t > 0)
tbSpecificPrefix << (1 + t);
tbSpecificPrefix << prefix;
typedef std::pair<const NxsCharactersBlock *, std::string> PairCBAndString;
typedef std::vector< PairCBAndString > VecPairCBAndString;
VecPairCBAndString cbToWrite;
for (unsigned i = 0; i < nCharBlocks; ++i)
{
NxsString fn = tbSpecificPrefix;
if (i > 0)
fn << (1 + i);
fn << getFileExtension(f);
const NxsCharactersBlock * cb = nexusReader.GetCharactersBlock(tb, i);
NxsCharactersBlock::DataTypesEnum dt = cb->GetDataType();
bool writeBlock = false;
if ((dt == NxsCharactersBlock::standard)
&& (f == MultiFormatReader::PHYLIP_DISC_FORMAT
|| f == MultiFormatReader::INTERLEAVED_PHYLIP_DISC_FORMAT
|| f == MultiFormatReader::RELAXED_PHYLIP_DISC_FORMAT
|| f == MultiFormatReader::INTERLEAVED_RELAXED_PHYLIP_DISC_FORMAT))
writeBlock = true;
else if ((dt == NxsCharactersBlock::dna || dt == NxsCharactersBlock::nucleotide)
&& (f == MultiFormatReader::PHYLIP_DNA_FORMAT
|| f == MultiFormatReader::INTERLEAVED_PHYLIP_DNA_FORMAT
|| f == MultiFormatReader::FASTA_DNA_FORMAT
|| f == MultiFormatReader::RELAXED_PHYLIP_DNA_FORMAT
|| f == MultiFormatReader::INTERLEAVED_RELAXED_PHYLIP_DNA_FORMAT))
writeBlock = true;
else if ((dt == NxsCharactersBlock::rna)
&& (f == MultiFormatReader::PHYLIP_RNA_FORMAT
|| f == MultiFormatReader::INTERLEAVED_PHYLIP_RNA_FORMAT
|| f == MultiFormatReader::FASTA_RNA_FORMAT
|| f == MultiFormatReader::RELAXED_PHYLIP_RNA_FORMAT
|| f == MultiFormatReader::INTERLEAVED_RELAXED_PHYLIP_RNA_FORMAT))
writeBlock = true;
else if ((dt == NxsCharactersBlock::protein)
&& (f == MultiFormatReader::PHYLIP_AA_FORMAT
|| f == MultiFormatReader::INTERLEAVED_PHYLIP_AA_FORMAT
|| f == MultiFormatReader::FASTA_AA_FORMAT
|| f == MultiFormatReader::RELAXED_PHYLIP_AA_FORMAT
|| f == MultiFormatReader::INTERLEAVED_RELAXED_PHYLIP_AA_FORMAT))
writeBlock = true;
if (writeBlock)
cbToWrite.push_back(std::pair<const NxsCharactersBlock *, std::string>(cb, fn));
}
if (!cbToWrite.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 (VecPairCBAndString::const_iterator vIt = cbToWrite.begin(); vIt != cbToWrite.end(); ++vIt)
{
const NxsCharactersBlock * cbP = vIt->first;
std::string fn = vIt->second;
ofstream outf;
if (fp == 0L)
{
openOrThrow(outf, fn);
fpToUse = &outf;
}
writeCharactersBlockToStream(*cbP, *fpToUse, namesToPrint, f, interleaveLen);
}
}
}
}
