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//
// C++ Implementation: substmodel
//
// Description:
//
//
// Author: BUI Quang Minh, Steffen Klaere, Arndt von Haeseler <minh.bui@univie.ac.at>, (C) 2008
//
// Copyright: See COPYING file that comes with this distribution
//
//
#include "modelsubst.h"
#include "tools.h"
ModelSubst::ModelSubst(int nstates) : Optimization(), CheckpointFactory()
{
num_states = nstates;
name = "JC";
full_name = "JC (Juke and Cantor, 1969)";
state_freq = new double[num_states];
for (int i = 0; i < num_states; i++)
state_freq[i] = 1.0 / num_states;
freq_type = FREQ_EQUAL;
}
void ModelSubst::saveCheckpoint() {
checkpoint->startStruct("ModelSubst");
// CKP_SAVE(num_states);
CKP_SAVE(name);
// CKP_SAVE(full_name);
// CKP_SAVE(freq_type);
if (freq_type == FREQ_EMPIRICAL || freq_type == FREQ_ESTIMATE)
CKP_ARRAY_SAVE(num_states, state_freq);
checkpoint->endStruct();
CheckpointFactory::saveCheckpoint();
}
/**
restore object from the checkpoint
@param ckp checkpoint to restore from
*/
void ModelSubst::restoreCheckpoint() {
CheckpointFactory::restoreCheckpoint();
checkpoint->startStruct("ModelSubst");
// CKP_RESTORE(num_states);
CKP_RESTORE(name);
// CKP_RESTORE(full_name);
// int freq_type = this->freq_type;
// CKP_RESTORE(freq_type);
// this->freq_type = (StateFreqType)freq_type;
if (freq_type == FREQ_EMPIRICAL || freq_type == FREQ_ESTIMATE)
CKP_ARRAY_RESTORE(num_states, state_freq);
checkpoint->endStruct();
decomposeRateMatrix();
}
// here the simplest Juke-Cantor model is implemented, valid for all kind of data (DNA, AA,...)
void ModelSubst::computeTransMatrix(double time, double *trans_matrix) {
double non_diagonal = (1.0 - exp(-time*num_states/(num_states - 1))) / num_states;
double diagonal = 1.0 - non_diagonal * (num_states - 1);
int nstates_sqr = num_states * num_states;
for (int i = 0; i < nstates_sqr; i++)
if (i % (num_states+1) == 0)
trans_matrix[i] = diagonal;
else
trans_matrix[i] = non_diagonal;
}
void ModelSubst::computeTransMatrixFreq(double time, double* trans_matrix)
{
computeTransMatrix(time, trans_matrix);
for (int state1 = 0; state1 < num_states; state1++) {
double *trans_mat_state = trans_matrix + (state1 * num_states);
for (int state2 = 0; state2 < num_states; state2++)
trans_mat_state[state2] /= num_states;
}
}
double ModelSubst::computeTrans(double time, int state1, int state2) {
double expt = exp(-time * num_states / (num_states-1));
if (state1 != state2) {
return (1.0 - expt) / num_states;
}
return (1.0 + (num_states-1)*expt) / num_states;
/* double non_diagonal = (1.0 - exp(-time*num_states/(num_states - 1))) / num_states;
if (state1 != state2)
return non_diagonal;
return 1.0 - non_diagonal * (num_states - 1);*/
}
double ModelSubst::computeTrans(double time, int model_id, int state1, int state2) {
return computeTrans(time, state1, state2);
}
double ModelSubst::computeTrans(double time, int state1, int state2, double &derv1, double &derv2) {
double coef = -double(num_states) / (num_states-1);
double expt = exp(time * coef);
if (state1 != state2) {
derv1 = expt / (num_states-1);
derv2 = derv1 * coef;
return (1.0 - expt) / num_states;
}
derv1 = -expt;
derv2 = derv1 * coef;
return (1.0 + (num_states-1)*expt) / num_states;
}
double ModelSubst::computeTrans(double time, int model_id, int state1, int state2, double &derv1, double &derv2) {
return computeTrans(time, state1, state2, derv1, derv2);
}
void ModelSubst::getRateMatrix(double *rate_mat) {
int nrate = getNumRateEntries();
for (int i = 0; i < nrate; i++)
rate_mat[i] = 1.0;
}
void ModelSubst::getQMatrix(double *q_mat) {
int i, j, k;
for (i = 0, k = 0; i < num_states; i++)
for (j = 0; j < num_states; j++, k++)
if (i == j) q_mat[k] = -1.0; else q_mat[k] = 1.0/3;
}
void ModelSubst::getStateFrequency(double *state_freq) {
double freq = 1.0 / num_states;
for (int i = 0; i < num_states; i++)
state_freq[i] = freq;
}
void ModelSubst::computeTransDerv(double time, double *trans_matrix,
double *trans_derv1, double *trans_derv2)
{
double expf = exp(-time*num_states/(num_states - 1));
double non_diag = (1.0 - expf) / num_states;
double diag = 1.0 - non_diag * (num_states - 1);
double derv1_non_diag = expf / (num_states-1);
double derv1_diag = -expf;
double derv2_non_diag = -derv1_non_diag*num_states/(num_states-1);
double derv2_diag = -derv1_diag*num_states/(num_states-1);
int nstates_sqr = num_states * num_states;
int i;
for (i = 0; i < nstates_sqr; i++)
if (i % (num_states+1) == 0) {
trans_matrix[i] = diag;
trans_derv1[i] = derv1_diag;
trans_derv2[i] = derv2_diag;
} else {
trans_matrix[i] = non_diag;
trans_derv1[i] = derv1_non_diag;
trans_derv2[i] = derv2_non_diag;
}
// DEBUG
/*int j;
if (verbose_mode == VB_DEBUG) {
cout.precision(4);
cout << "time = " << time << endl;
for (i = 0; i < num_states; i++, cout << endl) {
for (j = 0; j < num_states; j++) {
cout.width(8);
cout << right << trans_matrix[i*num_states+j] << " ";
}
cout << "| ";
for (j = 0; j < num_states; j++) {
cout << right << trans_derv1[i*num_states+j] << " ";
cout.width(8);
}
cout << "| ";
for (j = 0; j < num_states; j++) {
cout.width(8);
cout << right << trans_derv2[i*num_states+j] << " ";
}
}
cout.precision(10);
}*/
}
void ModelSubst::computeTransDervFreq(double time, double rate_val, double* trans_matrix, double* trans_derv1, double* trans_derv2)
{
int nstates = num_states;
double rate_sqr = rate_val*rate_val;
computeTransDerv(time * rate_val, trans_matrix, trans_derv1, trans_derv2);
for (int state1 = 0; state1 < nstates; state1++) {
double *trans_mat_state = trans_matrix + (state1 * nstates);
double *trans_derv1_state = trans_derv1 + (state1 * nstates);
double *trans_derv2_state = trans_derv2 + (state1 * nstates);
for (int state2 = 0; state2 < nstates; state2++) {
trans_mat_state[state2] /= num_states;
trans_derv1_state[state2] *= (rate_val/num_states);
trans_derv2_state[state2] *= (rate_sqr/num_states);
}
}
}
double *ModelSubst::newTransMatrix() {
return new double[num_states * num_states];
}
ModelSubst::~ModelSubst()
{
if (state_freq) delete [] state_freq;
}
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