void writeAsNexus(PublicNexusReader & nexusReader, ostream & os) { BlockReaderList blocks = nexusReader.GetUsedBlocksInOrder(); os << "#NEXUS\n"; for (BlockReaderList::const_iterator bIt = blocks.begin(); bIt != blocks.end(); ++bIt) { NxsBlock * b = *bIt; if (b) b->WriteAsNexus(os); } }
//////////////////////////////////////////////////////////////////////////////// // Takes NxsReader that has successfully read a file, and processes the // information stored in the reader. // // The caller is responsibel for calling DeleteBlocksFromFactories() to clean // up (if the reader uses the factory API). //////////////////////////////////////////////////////////////////////////////// void processContent(PublicNexusReader & nexusReader, ostream *out) { if (!out) return; BlockReaderList blocks = nexusReader.GetUsedBlocksInOrder(); *out << "#NEXUS\n"; for (BlockReaderList::const_iterator bIt = blocks.begin(); bIt != blocks.end(); ++bIt) { NxsBlock * b = *bIt; if (b->GetID() == "TAXA") b->WriteAsNexus(*out); } TreesToSplits::TaxaBlockToSplitsMap::const_iterator tbtsm = gTreesToSplitsB->taxaBlockToSplitsMap.begin(); for (; tbtsm != gTreesToSplitsB->taxaBlockToSplitsMap.end(); ++tbtsm) { *out << "Begin Trees;\n"; NxsTaxaBlockAPI * tb = tbtsm->first; if (tb && gTreesToSplitsB->taxaBlockToSplitsMap.size() > 1) *out << "Link Taxa = " << NxsString::GetEscaped(tb->GetTitle()) << ";\n"; writeTranslateCommand(tb, *out); const TreesToSplits::NTreesSplitsMap & ntsm = tbtsm->second; const unsigned nt = ntsm.first; const TreesToSplits::SplitsMap & sm = ntsm.second; unsigned n = 1; writeStarTreeCommand(tb, *out); for (TreesToSplits::SplitsMap::const_iterator smIt = sm.begin(); smIt != sm.end(); ++smIt, ++n) { const SplitInfo & si = smIt->second; *out << "Tree split_" << n << " = " << " [&"; *out << (gTreesToSplitsB->treatAsRooted ? 'R' : 'U'); *out << "] ["; if (gTreesToSplitsB->trackFreq || gTreesToSplitsB->trackEdgeLenSummary || gTreesToSplitsB->trackEdgeLen) *out << "&W " << ((double)si.nTimes)/((double)nt) << " ] ["; if (gTreesToSplitsB->trackHeightSummary) { *out << "meanH =" << ((double)si.heightSum)/((double)si.nTimes); } *out << "] "; if (gTreesToSplitsB->trackEdgeLenSummary) smIt->first.writeNewick(*out, si.edgeLenSum/((double)si.nTimes), true); else smIt->first.writeNewick(*out, true); *out << ";\n"; } *out << "End;\n"; } }
//////////////////////////////////////////////////////////////////////////////// // Takes NxsReader that has successfully read a file, and processes the // information stored in the reader. // // The caller is responsibel for calling DeleteBlocksFromFactories() to clean // up (if the reader uses the factory API). //////////////////////////////////////////////////////////////////////////////// void processContent(PublicNexusReader & nexusReader, ostream *out) { if (!out) return; BlockReaderList blocks = nexusReader.GetUsedBlocksInOrder(); *out << "#NEXUS\n"; for (BlockReaderList::const_iterator bIt = blocks.begin(); bIt != blocks.end(); ++bIt) { NxsBlock * b = *bIt; if (b->GetID() == "TAXA") b->WriteAsNexus(*out); else if (b->GetID() == "CHARACTERS" || b->GetID() == "DATA" ) { NxsCharactersBlock * charactersBPtr = (NxsCharactersBlock *) b; writeCharactersAsGapped(*out, charactersBPtr); } } }
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; }
//////////////////////////////////////////////////////////////////////////////// // Takes NxsReader that has successfully read a file, and processes the // information stored in the reader. // // The caller is responsibel for calling DeleteBlocksFromFactories() to clean // up (if the reader uses the factory API). //////////////////////////////////////////////////////////////////////////////// void processContent(PublicNexusReader & nexusReader, ostream *os, ProcessActionsEnum currentAction) { BlockReaderList blocks = nexusReader.GetUsedBlocksInOrder(); writeAsNexus(nexusReader, *os); }