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;
}
}
