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/*
* modelmorphology.cpp
*
* Created on: Apr 15, 2014
* Author: minh
*/
#include "modelmorphology.h"
ModelMorphology::ModelMorphology(const char *model_name, string model_params, StateFreqType freq, string freq_params, PhyloTree *tree)
: ModelGTR(tree, false)
{
init(model_name, model_params, freq, freq_params);
}
void ModelMorphology::init(const char *model_name, string model_params, StateFreqType freq, string freq_params)
{
name = model_name;
full_name = model_name;
freq = FREQ_EQUAL;
if (name == "MK") {
// all were initialized
} else if (name == "ORDERED") {
int k = 0;
// only allow for substitution from state i to state i+1 and back.
for (int i = 0; i < num_states-1; i++) {
rates[k++] = 1.0;
for (int j = i+2; j < num_states; j++, k++)
rates[k] = 0.0;
}
} else {
outError("Unknown morphological model name");
}
ModelGTR::init(freq);
}
ModelMorphology::~ModelMorphology() {
}
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