BlockReaderList NxsReader::FindAllBlocksByTitleNoPrioritization(const BlockReaderList & chosenBlockList, const char *title)
{
BlockReaderList found;
if (chosenBlockList.empty() || title == NULL)
{
found = chosenBlockList;
}
else
{
bool emptyTitle = strlen(title) == 0;
for (BlockReaderList::const_iterator cblIt = chosenBlockList.begin(); cblIt != chosenBlockList.end(); ++cblIt)
{
NxsBlock * b = *cblIt;
std::vector<std::string> v = this->GetAllTitlesForBlock(b);
for (std::vector<std::string>::const_iterator vIt = v.begin(); vIt != v.end(); ++vIt)
{
const std::string & n = *vIt;
if ((emptyTitle && n.empty()) || (NxsString::case_insensitive_equals(title, n.c_str())))
{
found.push_back(b);
break;
}
}
}
}
return found;
}
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);
}
}
void NxsReader::DemoteBlocks(int priorityLevel)
{
BlockReaderList brl = GetUsedBlocksInOrder();
BlockReaderList::iterator brlIt = brl.begin();
for (; brlIt != brl.end(); ++brlIt)
{
NxsBlock * b = *brlIt;
AssignBlockPriority(b, priorityLevel);
}
}
////////////////////////////////////////////////////////////////////////////////
// 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";
}
}
BlockReaderList NxsReader::FindAllBlocksByTitle(const BlockReaderList & chosenBlockList, const char *title)
{
BlockReaderList found = FindAllBlocksByTitleNoPrioritization(chosenBlockList, title);
if (found.empty())
{
return found;
}
map<int, BlockReaderList> byPriority;
for (BlockReaderList::const_iterator fIt = found.begin(); fIt != found.end(); ++fIt)
{
NxsBlock * b = *fIt;
int priority = GetBlockPriority(b);
byPriority[priority].push_back(b);
}
NCL_ASSERT(!byPriority.empty());
return byPriority.rbegin()->second;
}
/*! \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();
}
////////////////////////////////////////////////////////////////////////////////
// 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);
}
}
}
void NxsReader::DeleteBlocksFromFactories()
{
BlockReaderList saved;
std::set<NxsBlock *> todel;
for (BlockReaderList::iterator bIt = blocksInOrder.begin(); bIt != blocksInOrder.end(); ++bIt)
{
NxsBlock * b = *bIt;
if (BlockIsASingeltonReader(b))
saved.push_back(b);
else
todel.insert(b);
}
for (std::set<NxsBlock *>::iterator d = todel.begin(); d != todel.end(); ++d)
{
delete *d;
}
blocksInOrder = saved;
lastExecuteBlocksInOrder = saved;
}
/*! Returns the set of blocks that have been created from factories, and
removes reference to from the NxsReader's collections.
*/
std::set<NxsBlock *> NxsReader::RemoveBlocksFromFactoriesFromUsedBlockLists()
{
std::set<NxsBlock *> todel;
BlockReaderList saved;
for (BlockReaderList::iterator bIt = blocksInOrder.begin(); bIt != blocksInOrder.end(); ++bIt)
{
NxsBlock * b = *bIt;
if (BlockIsASingeltonReader(b))
{
saved.push_back(b);
}
else
{
todel.insert(b);
}
}
for (std::set<NxsBlock *>::iterator d = todel.begin(); d != todel.end(); ++d)
{
RemoveBlockFromUsedBlockList(*d);
}
return todel;
}
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;
}
