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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 "modelbin.h"
ModelBIN::ModelBIN(const char *model_name, string model_params, StateFreqType freq, string freq_params, PhyloTree *tree)
: ModelMarkov(tree)
{
init(model_name, model_params, freq, freq_params);
}
void ModelBIN::init(const char *model_name, string model_params, StateFreqType freq, string freq_params)
{
ASSERT(num_states == 2); // make sure that you create model for Binary data
StateFreqType def_freq = FREQ_UNKNOWN;
name = model_name;
full_name = model_name;
if (name == "JC2") {
def_freq = FREQ_EQUAL;
} else if (name == "GTR2") {
def_freq = FREQ_ESTIMATE;
} else {
readParameters(model_name);
}
if (freq_params != "") {
readStateFreq(freq_params);
}
if (model_params != "") {
readRates(model_params);
}
if (freq == FREQ_UNKNOWN || def_freq == FREQ_EQUAL) freq = def_freq;
ModelMarkov::init(freq);
}
void ModelBIN::startCheckpoint() {
checkpoint->startStruct("ModelBIN");
}
string ModelBIN::getNameParams() {
//if (num_params == 0) return name;
ostringstream retname;
retname << name;
// if (!fixed_parameters) {
// retname << '{';
// int nrates = getNumRateEntries();
// for (int i = 0; i < nrates; i++) {
// if (i>0) retname << ',';
// retname << rates[i];
// }
// retname << '}';
// }
// getNameParamsFreq(retname);
retname << freqTypeString(freq_type, phylo_tree->aln->seq_type, true);
if (freq_type == FREQ_EMPIRICAL || freq_type == FREQ_ESTIMATE ||
(freq_type == FREQ_USER_DEFINED)) {
retname << "{" << state_freq[0];
for (int i = 1; i < num_states; i++)
retname << "," << state_freq[i];
retname << "}";
}
return retname.str();
}
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