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 exportTrees(
PublicNexusReader & nexusReader,
MultiFormatReader::DataFormatType f,
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 nTreesBlocks = nexusReader.GetNumTreesBlocks(tb);
if (nTreesBlocks == 0)
continue;
NxsString tbSpecificPrefix;
if (t > 0)
tbSpecificPrefix << (1 + t);
tbSpecificPrefix << prefix;
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 (unsigned i = 0; i < nTreesBlocks; ++i)
{
NxsString fn = tbSpecificPrefix;
if (i > 0)
fn << (1 + i);
fn << getFileExtension(f);
const NxsTreesBlock * trb = nexusReader.GetTreesBlock(tb, i);
ofstream outf;
if (fp == 0L)
{
openOrThrow(outf, fn);
fpToUse = &outf;
}
trb->ProcessAllTrees();
for (unsigned j = 0; j < trb->GetNumTrees(); ++j)
{
const NxsFullTreeDescription & ftd = trb->GetFullTreeDescription(j);
NxsSimpleTree tree(ftd, -1, -1.0);
std::vector<NxsSimpleNode *> & leaves = tree.GetLeavesRef();
for (std::vector<NxsSimpleNode *>::const_iterator leafIt = leaves.begin(); leafIt != leaves.end(); ++leafIt)
{
NxsSimpleNode * leaf = *leafIt;
if (leaf)
{
const std::string name = namesToPrint[leaf->GetTaxonIndex()];
if (!gQuietMode)
std::cerr << "Setting name=" << name << '\n';
leaf->SetName(name);
}
}
tree.WriteAsNewick(*fpToUse, true, true, false, tb, true);
*fpToUse << ";\n";
}
}
}
}
