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/***************************************************************************
* Copyright (C) 2006 by BUI Quang Minh, Steffen Klaere, Arndt von Haeseler *
* minh.bui@univie.ac.at *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#include "pdtreeset.h"
PDTreeSet::PDTreeSet()
: MTreeSet()
{
}
PDTreeSet::PDTreeSet(Params ¶ms) {
init(params);
}
void PDTreeSet::init(Params ¶ms) {
MTreeSet::init(params.user_file, params.is_rooted, params.tree_burnin, params.tree_max_count);
if (isRootedTrees()) {
params.sub_size++;
params.min_size++;
}
if (isRootedTrees() && params.root != NULL) {
outError(ERR_CONFLICT_ROOT);
}
if (params.sub_size > getNTaxa()) {
ostringstream err;
err << "Subset size k = " << params.sub_size - params.is_rooted <<
" is greater than the number of taxa = " << getNTaxa() - params.is_rooted;
outError(err.str());
}
if (isRootedTrees()) {
char *rname = (char*)ROOT_NAME;
readRootNode(rname);
}
// read the parameter file
if (params.param_file != NULL) {
readParams(params);
}
// identify the root
if (params.root != NULL)
readRootNode(params.root);
// read the initial set of taxa, incoporate info into the split system
if (params.initial_file != NULL) {
readInitialSet(params);
}
}
bool PDTreeSet::isRootedTrees() {
ASSERT(size() > 0);
return front()->rooted;
}
int PDTreeSet::getNTaxa() {
ASSERT(size() > 0);
return front()->leafNum;
}
void PDTreeSet::readRootNode(const char *root_name) {
string name = root_name;
init_taxa.push_back(name);
for (iterator it = begin(); it != end(); it++)
((PDTree*)(*it))->readRootNode(root_name);
}
void PDTreeSet::readParams(Params ¶ms) {
int ntaxa = getNTaxa() - params.is_rooted;
// read parameters from file
double scale;
StrVector tax_name;
DoubleVector ori_weight;
readWeightFile(params, ntaxa, scale, tax_name, ori_weight);
for (iterator it = begin(); it != end(); it++) {
// now convert the weights
PDTree *mytree = (PDTree*)(*it);
LeafMapName lsn;
mytree->buildLeafMapName(lsn);
DoubleVector tax_weight;
tax_weight.resize(ntaxa, 0);
for (int i = 0; i < tax_name.size(); i++) {
LeafMapName::iterator nameit = lsn.find(tax_name[i]);
if (nameit == lsn.end())
outError(ERR_NO_TAXON, tax_name[i]);
tax_weight[(*nameit).second->id] = ori_weight[i];
}
// incoporate them into the tree
mytree->incoporateParams(scale, tax_weight);
}
}
/**
read the initial set of taxa to be included into PD-tree
*/
void PDTreeSet::readInitialSet(Params ¶ms) {
int ntaxa = getNTaxa() - params.is_rooted;
StrVector tax_name;
readInitTaxaFile(params, ntaxa, tax_name);
init_taxa.insert(init_taxa.end(), tax_name.begin(), tax_name.end());
for (iterator itree = begin(); itree != end(); itree++) {
PDTree *mytree = (PDTree*)(*itree);
LeafMapName lsn;
mytree->buildLeafMapName(lsn);
for (StrVector::iterator it = tax_name.begin(); it != tax_name.end(); it++) {
LeafMapName::iterator nameit = lsn.find((*it));
if (nameit == lsn.end()) {
outError(ERR_NO_TAXON, *it);
}
mytree->initialset.push_back((*nameit).second);
}
}
}
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