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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 "alignmentpairwise.h"
#include "tree/phylosupertree.h"
AlignmentPairwise::AlignmentPairwise()
: Alignment(), Optimization()
{
pair_freq = NULL;
}
AlignmentPairwise::AlignmentPairwise(PhyloTree *atree, int seq1, int seq2) : Alignment(), Optimization() {
tree = atree;
seq_id1 = seq1;
seq_id2 = seq2;
num_states = tree->aln->num_states;
STATE_UNKNOWN = tree->aln->STATE_UNKNOWN;
pair_freq = NULL;
if (tree->getRate()->isSiteSpecificRate() || tree->getModel()->isSiteSpecificModel()) return;
// categorized rates
if (tree->getRate()->getPtnCat(0) >= 0) {
int size_sqr = num_states * num_states;
int total_size = size_sqr * tree->getRate()->getNDiscreteRate();
pair_freq = new double[total_size];
memset(pair_freq, 0, sizeof(double)*total_size);
int i = 0;
for (Alignment::iterator it = tree->aln->begin(); it != tree->aln->end(); it++, i++) {
int state1 = tree->aln->convertPomoState((*it)[seq_id1]);
int state2 = tree->aln->convertPomoState((*it)[seq_id2]);
addPattern(state1, state2, it->frequency, tree->getRate()->getPtnCat(i));
/*
if (state1 < num_states && state2 < num_states)
pair_freq[tree->getRate()->getPtnCat(i)*size_sqr + state1*num_states + state2] += it->frequency;*/
}
return;
}
pair_freq = new double[num_states * num_states];
memset(pair_freq, 0, sizeof(double) * num_states * num_states);
for (Alignment::iterator it = tree->aln->begin(); it != tree->aln->end(); it++) {
int state1 = tree->aln->convertPomoState((*it)[seq_id1]);
int state2 = tree->aln->convertPomoState((*it)[seq_id2]);
addPattern(state1, state2, it->frequency);
/* if (state1 < num_states && state2 < num_states)
pair_freq[state1 * num_states + state2] += it->frequency;*/
}
}
bool AlignmentPairwise::addPattern(int state1, int state2, int freq, int cat) {
int i;
if (state1 == STATE_UNKNOWN || state2 == STATE_UNKNOWN) return true;
double *pair_pos = pair_freq + (cat*num_states*num_states);
// unambiguous case
if (state1 < num_states && state2 < num_states) {
pair_pos[state1*num_states + state2] += freq;
return false;
}
return true;
if (state1 < num_states) {
// ambiguous character, for DNA, RNA
state2 = state2 - (num_states - 1);
for (i = 0; i < num_states; i++)
if (state2 & (1 << i))
pair_pos[state1*num_states + i] += freq;
return false;
}
if (state2 < num_states) {
// ambiguous character, for DNA, RNA
state1 = state1 - (num_states - 1);
for (i = 0; i < num_states; i++)
if (state1 & (1 << i))
pair_pos[i*num_states + state2] += freq;
return false;
}
return true;
}
double AlignmentPairwise::computeFunction(double value) {
RateHeterogeneity *site_rate = tree->getRate();
int ncat = site_rate->getNDiscreteRate();
ModelSubst *model = tree->getModel();
int trans_size = tree->getModel()->getTransMatrixSize();
int cat, i;
int nptn = tree->aln->getNPattern();
double lh = 0.0;
// site-specific rates
if (site_rate->isSiteSpecificRate()) {
for (i = 0; i < nptn; i++) {
int state1 = tree->aln->at(i)[seq_id1];
int state2 = tree->aln->at(i)[seq_id2];
if (state1 >= num_states || state2 >= num_states) continue;
double trans = tree->getModelFactory()->computeTrans(value * site_rate->getPtnRate(i), state1, state2);
lh -= log(trans) * tree->aln->at(i).frequency;
}
return lh;
}
if (tree->getModel()->isSiteSpecificModel()) {
for (i = 0; i < nptn; i++) {
int state1 = tree->aln->at(i)[seq_id1];
int state2 = tree->aln->at(i)[seq_id2];
if (state1 >= num_states || state2 >= num_states) continue;
double trans = tree->getModel()->computeTrans(value, model->getPtnModelID(i), state1, state2);
lh -= log(trans) * tree->aln->at(i).frequency;
}
return lh;
}
double *trans_mat = new double[trans_size];
// categorized rates
if (site_rate->getPtnCat(0) >= 0) {
for (cat = 0; cat < ncat; cat++) {
tree->getModelFactory()->computeTransMatrix(value*site_rate->getRate(cat), trans_mat);
double *pair_pos = pair_freq + cat*trans_size;
for (i = 0; i < trans_size; i++) if (pair_pos[i] > Params::getInstance().min_branch_length) {
if (trans_mat[i] <= 0) throw "Negative transition probability";
lh -= pair_pos[i] * log(trans_mat[i]);
}
}
delete [] trans_mat;
return lh;
}
double *sum_trans_mat = new double[trans_size];
if (tree->getModelFactory()->site_rate->getGammaShape() == 0.0)
tree->getModelFactory()->computeTransMatrix(value, sum_trans_mat);
else {
tree->getModelFactory()->computeTransMatrix(value * site_rate->getRate(0), sum_trans_mat);
for (cat = 1; cat < ncat; cat++) {
tree->getModelFactory()->computeTransMatrix(value * site_rate->getRate(cat), trans_mat);
for (i = 0; i < trans_size; i++)
sum_trans_mat[i] += trans_mat[i];
}
}
for (i = 0; i < trans_size; i++) {
lh -= pair_freq[i] * log(sum_trans_mat[i]);
}
delete [] sum_trans_mat;
delete [] trans_mat;
// negative log-likelihood (for minimization)
return lh;
}
void AlignmentPairwise::computeFuncDerv(double value, double &df, double &ddf) {
RateHeterogeneity *site_rate = tree->getRate();
int ncat = site_rate->getNDiscreteRate();
ModelSubst *model = tree->getModel();
int trans_size = tree->getModel()->getTransMatrixSize();
int cat, i;
int nptn = tree->aln->getNPattern();
// double lh = 0.0;
df = 0.0;
ddf = 0.0;
if (site_rate->isSiteSpecificRate()) {
for (i = 0; i < nptn; i++) {
int state1 = tree->aln->at(i)[seq_id1];
int state2 = tree->aln->at(i)[seq_id2];
if (state1 >= num_states || state2 >= num_states) continue;
double rate_val = site_rate->getPtnRate(i);
double rate_sqr = rate_val * rate_val;
double derv1, derv2;
double trans = tree->getModelFactory()->computeTrans(value * rate_val, state1, state2, derv1, derv2);
// lh -= log(trans) * tree->aln->at(i).frequency;
double d1 = derv1 / trans;
df -= rate_val * d1 * tree->aln->at(i).frequency;
ddf -= rate_sqr * (derv2/trans - d1*d1) * tree->aln->at(i).frequency;
}
// return lh;
return;
}
if (tree->getModel()->isSiteSpecificModel()) {
for (i = 0; i < nptn; i++) {
int state1 = tree->aln->at(i)[seq_id1];
int state2 = tree->aln->at(i)[seq_id2];
if (state1 >= num_states || state2 >= num_states) continue;
double rate_val = site_rate->getPtnRate(i);
double rate_sqr = rate_val * rate_val;
double derv1, derv2;
double trans = tree->getModel()->computeTrans(value * rate_val,model->getPtnModelID(i), state1, state2, derv1, derv2);
// lh -= log(trans) * tree->aln->at(i).frequency;
double d1 = derv1 / trans;
df -= rate_val * d1 * tree->aln->at(i).frequency;
ddf -= rate_sqr * (derv2/trans - d1*d1) * tree->aln->at(i).frequency;
}
// return lh;
return;
}
double *trans_mat = new double[trans_size];
double *trans_derv1 = new double[trans_size];
double *trans_derv2 = new double[trans_size];
// categorized rates
if (site_rate->getPtnCat(0) >= 0) {
for (cat = 0; cat < ncat; cat++) {
double rate_val = site_rate->getRate(cat);
double derv1 = 0.0, derv2 = 0.0;
tree->getModelFactory()->computeTransDerv(value*rate_val, trans_mat, trans_derv1, trans_derv2);
double *pair_pos = pair_freq + cat*trans_size;
for (i = 0; i < trans_size; i++) if (pair_pos[i] > 0) {
if (trans_mat[i] <= 0) throw "Negative transition probability";
double d1 = trans_derv1[i] / trans_mat[i];
derv1 += pair_pos[i] * d1;
derv2 += pair_pos[i] * (trans_derv2[i]/trans_mat[i] - d1 * d1);
// lh -= pair_pos[i] * log(trans_mat[i]);
}
df -= derv1 * rate_val;
ddf -= derv2 * rate_val * rate_val;
}
delete [] trans_derv2;
delete [] trans_derv1;
delete [] trans_mat;
// return lh;
return;
}
double *sum_trans = new double[trans_size];
double *sum_derv1 = new double[trans_size];
double *sum_derv2 = new double[trans_size];
memset(sum_trans, 0, sizeof(double) * trans_size);
memset(sum_derv1, 0, sizeof(double) * trans_size);
memset(sum_derv2, 0, sizeof(double) * trans_size);
for (cat = 0; cat < ncat; cat++) {
double rate_val = site_rate->getRate(cat);
double prop_val = site_rate->getProp(cat);
if (tree->getModelFactory()->site_rate->getGammaShape() == 0.0)
rate_val = 1.0;
double coeff1 = rate_val * prop_val;
double coeff2 = rate_val * coeff1;
tree->getModelFactory()->computeTransDerv(value * rate_val, trans_mat, trans_derv1, trans_derv2);
for (i = 0; i < trans_size; i++) {
sum_trans[i] += trans_mat[i] * prop_val;
sum_derv1[i] += trans_derv1[i] * coeff1;
sum_derv2[i] += trans_derv2[i] * coeff2;
}
}
// 2019-07-03: incorporate p_invar
double p_invar = site_rate->getPInvar();
if (p_invar > 0.0)
for (i = 0; i < num_states; i++)
sum_trans[i*num_states+i] += p_invar;
for (i = 0; i < trans_size; i++)
if (pair_freq[i] > Params::getInstance().min_branch_length && sum_trans[i] > 0.0) {
// lh -= pair_freq[i] * log(sum_trans[i]);
double d1 = sum_derv1[i] / sum_trans[i];
df -= pair_freq[i] * d1;
ddf -= pair_freq[i] * (sum_derv2[i]/sum_trans[i] - d1 * d1);
}
delete [] sum_derv2;
delete [] sum_derv1;
delete [] sum_trans;
delete [] trans_derv2;
delete [] trans_derv1;
delete [] trans_mat;
// negative log-likelihood (for minimization)
// return lh;
return;
}
double AlignmentPairwise::optimizeDist(double initial_dist, double &d2l) {
// initial guess of the distance using Juke-Cantor correction
double dist = initial_dist;
d2l = -1.0;
// if no model or rate is specified, return the JC distance and set variance to const
if (!tree->getModelFactory() || !tree->getRate()) return dist;
double negative_lh, ferror;
double max_genetic_dist = MAX_GENETIC_DIST;
if (tree->aln->seq_type == SEQ_POMO) {
int N = tree->aln->virtual_pop_size;
max_genetic_dist *= N*N;
}
if (tree->optimize_by_newton) // Newton-Raphson method
dist = minimizeNewton(Params::getInstance().min_branch_length, dist, max_genetic_dist, Params::getInstance().min_branch_length, d2l);
else // Brent method
dist = minimizeOneDimen(Params::getInstance().min_branch_length, dist, max_genetic_dist, Params::getInstance().min_branch_length, &negative_lh, &ferror);
return dist;
}
double AlignmentPairwise::optimizeDist(double initial_dist) {
double d2l;
return optimizeDist(initial_dist, d2l);
}
AlignmentPairwise::~AlignmentPairwise()
{
if (pair_freq) delete [] pair_freq;
}
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