/*! \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();
}
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;
}
}
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;
}