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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 "tree/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::startCheckpoint() {
checkpoint->startStruct("RateHeterogeneity");
}
void RateHeterogeneity::saveCheckpoint() {
startCheckpoint();
// CKP_SAVE(name);
// CKP_SAVE(full_name);
endCheckpoint();
CheckpointFactory::saveCheckpoint();
}
void RateHeterogeneity::restoreCheckpoint() {
startCheckpoint();
// CKP_RESTORE(name);
// CKP_RESTORE(full_name);
endCheckpoint();
}
/*
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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