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/***************************************************************************
* Copyright (C) 2009 by BUI Quang Minh *
* 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 "phylotree.h"
#include "rateheterogeneity.h"
RateHeterogeneity::RateHeterogeneity()
: Optimization(), CheckpointFactory()
{
name = "";
full_name = "Uniform";
phylo_tree = NULL;
}
void RateHeterogeneity::setTree(PhyloTree *tree) {
phylo_tree = tree;
}
RateHeterogeneity::~RateHeterogeneity()
{
}
void RateHeterogeneity::saveCheckpoint() {
checkpoint->startStruct("RateHeterogeneity");
// CKP_SAVE(name);
// CKP_SAVE(full_name);
checkpoint->endStruct();
CheckpointFactory::saveCheckpoint();
}
void RateHeterogeneity::restoreCheckpoint() {
checkpoint->startStruct("RateHeterogeneity");
// CKP_RESTORE(name);
// CKP_RESTORE(full_name);
checkpoint->endStruct();
}
void RateHeterogeneity::writeSiteRates(ostream &out, DoubleVector &pattern_rates, IntVector &pattern_cat, int ncategory) {
int nsite = phylo_tree->aln->getNSite();
int i;
out.setf(ios::fixed,ios::floatfield);
out.precision(5);
out << "Site\tRate";
if (!pattern_cat.empty()) out << "\tCategory\tCategorized_rate";
out << endl;
//cout << __func__ << endl;
IntVector count;
count.resize(ncategory, 0);
for (i = 0; i < nsite; i++) {
int ptn = phylo_tree->aln->getPatternID(i);
out << i+1 << "\t";
if (pattern_rates[ptn] >= MAX_SITE_RATE) out << "100.0"; else out << pattern_rates[ptn];
//cout << i << " "<< ptn << " " << pattern_cat[ptn] << endl;
if (!pattern_cat.empty()) {
int site_cat;
double cat_rate;
if (getPInvar() == 0.0) {
site_cat = pattern_cat[ptn]+1;
cat_rate = getRate(pattern_cat[ptn]);
} else {
site_cat = pattern_cat[ptn];
if (site_cat == 0)
cat_rate = 0.0;
else
cat_rate = getRate(pattern_cat[ptn]-1);
}
out << "\t" << site_cat << "\t" << cat_rate;
count[pattern_cat[ptn]]++;
}
out << endl;
}
cout << "Empirical proportions for each category:";
for (i = 0; i < count.size(); i++)
cout << " " << ((double)count[i])/nsite;
cout << endl;
}
void RateHeterogeneity::writeSiteRates(ostream &out) {
DoubleVector pattern_rates;
IntVector pattern_cat;
int ncategory = computePatternRates(pattern_rates, pattern_cat);
if (pattern_rates.empty()) return;
writeSiteRates(out, pattern_rates, pattern_cat, ncategory);
}
void RateHeterogeneity::writeSiteRates(const char *file_name) {
DoubleVector pattern_rates;
IntVector pattern_cat;
int ncategory = computePatternRates(pattern_rates, pattern_cat);
if (pattern_rates.empty()) return;
try {
ofstream out;
out.exceptions(ios::failbit | ios::badbit);
out.open(file_name);
writeSiteRates(out, pattern_rates, pattern_cat, ncategory);
out.close();
cout << "Site rates printed to " << file_name << endl;
} catch (ios::failure) {
outError(ERR_WRITE_OUTPUT, file_name);
}
}
double RateHeterogeneity::targetFunk(double x[]) {
return -phylo_tree->computeLikelihood();
}
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