void NxsTransposeCompressedMatrix(
const std::vector<NxsCharacterPattern> & compressedTransposedMatrix,
ScopedTwoDMatrix<NxsCDiscreteStateSet> & destination,
std::vector<unsigned> * patternCounts,
std::vector<double> * patternWeights)
{
const unsigned npatterns = (unsigned const)compressedTransposedMatrix.size();
if (npatterns == 0)
{
destination.Initialize(0, 0);
return;
}
const unsigned ntaxa = (unsigned const)compressedTransposedMatrix[0].stateCodes.size();
destination.Initialize(ntaxa, npatterns);
NxsCDiscreteStateSet ** matrix = destination.GetAlias(); /** taxa x characters matrix of indices of state sets */
if (patternCounts)
patternCounts->resize(npatterns);
if (patternWeights)
patternWeights->resize(npatterns);
for (unsigned p = 0; p < npatterns; ++p)
{
const NxsCharacterPattern & pattern = compressedTransposedMatrix[p];
const std::vector<NxsCDiscreteState_t> & states = pattern.stateCodes;
for (unsigned t = 0; t < ntaxa; ++t)
matrix[t][p] = states[t];
if (patternCounts)
(*patternCounts)[p] = pattern.count;
if (patternWeights)
(*patternWeights)[p] = pattern.sumOfPatternWeights;
}
}
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;
}
