Esempio n. 1
0
/*! \returns a NxsBlock from `chosenBlockList` with a Title that matches `title`.
    In the event of ties, the most recently read block is returned.
    If `title` is NULL, then any block is considered a match.
    On output *nMatches will be the number of matches (if `nMatches` is not NULL).
    NULL will be returned if there are no matches.
 */
NxsBlock *NxsReader::FindBlockByTitle(const BlockReaderList & chosenBlockList, const char *title, unsigned *nMatches)
{
    BlockReaderList found = FindAllBlocksByTitle(chosenBlockList, title);

    if (found.empty())
    {
        if (nMatches)
        {
            *nMatches = 0;
        }
        return NULL;
    }
    if (nMatches)
    {
        *nMatches = (unsigned)found.size();
    }
    return (NxsBlock *) found.back();
}
Esempio n. 2
0
void BullShell::ExecGetTrees(const GetTreesOpts & gto) {
	errormsg.clear();
	BlockReaderList blocks = getBlocksFromFile(gto.filename, true);
	if (blocks.empty()) {
		errormsg << "No Trees Block found in " << gto.filename;
		throw XBull(errormsg);
	}
	
	unsigned ntreesInFile = 0;
	const unsigned ntreesBlocks = blocks.size();
	vector<NxsTreesBlockAPI *> trBlocks;
	for (BlockReaderList::iterator b = blocks.begin(); b != blocks.end(); ++b) {
		NxsTreesBlockAPI *tb = (NxsTreesBlockAPI *)(*b);
		trBlocks.push_back(tb);
		assert(tb);
		ntreesInFile += tb->GetNumTrees();
	}

	if (ntreesInFile < 1) {
		errormsg << "No Trees found in " << gto.filename;
		throw XBull(errormsg);
	}
	
	const unsigned toTree = (unsigned) (gto.toTree < 0 ? 0 : gto.toTree); 
	const unsigned fromTree = (unsigned) (gto.fromTree < 0 ? ntreesInFile - 1 : gto.fromTree);
	if (fromTree > toTree) {
		errormsg << "Cant get Trees from " << fromTree << " to " << toTree;
		throw XBull( errormsg);
	}

	// Store the specified trees
	// these trees are deleted in the for loop if there is an error, otherwise
	//	they are put under the control of the kernel
	vector<Tree *>	treesToBeAdded; 
	vector<NxsTreesBlockAPI *>::const_iterator tbIt = trBlocks.begin();
	NxsTreesBlockAPI * currTB = *tbIt;
	unsigned nTreesInThisBlock = currTB->GetNumTrees();
	int nleftInThisBlock = (int) nTreesInThisBlock;
	for (unsigned i = 0; i < toTree; i++, --nleftInThisBlock) {
		while (nleftInThisBlock < 1) {
			++tbIt;
			assert(tbIt != trBlocks.end());
			currTB = *tbIt;
			nTreesInThisBlock = currTB->GetNumTrees();
			nleftInThisBlock = (int) nTreesInThisBlock;
		}
		if (i >= fromTree) {
			const std::string newick = currTB->GetTranslatedTreeDescription((unsigned)(nTreesInThisBlock - nleftInThisBlock));
			Tree * temptree = new Tree(newick, gto.storeBrLensFromFile);
			if (!temptree->IsGood()) {
				for (unsigned j = 0; j < i - fromTree; j++)
					delete treesToBeAdded[j];
				errormsg << "Problem Reading Tree Description of " << currTB->GetTreeName(i);
				delete temptree;
				throw XBull(errormsg);
			}
			std::string s = currTB->GetTreeName(i);
			ToUpper(s);
			temptree->SetName(s);
			treesToBeAdded.push_back(temptree);
		}
	}

	ioObject.message.clear();
	ioObject.message << (int)(toTree - fromTree) << " trees read from " << ntreesBlocks << " TREES block(s) in " <<  gto.filename;
	ioObject.printMessage(BullIO::STATUS_MSG_LEVEL);

	assert(gto.mode <= 7 && gto.mode >= 0);
	kernel.updateTrees(treesToBeAdded, UpdateMode(gto.mode));
	for (BlockReaderList::iterator b = blocks.begin(); b != blocks.end(); ++b) {
		if (*b != this)
			delete *b;
	}
}		
Esempio n. 3
0
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;
}