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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 "partitionmodel.h"
#include "alignment/superalignment.h"
#include "model/rategamma.h"
PartitionModel::PartitionModel()
: ModelFactory()
{
linked_alpha = -1.0;
}
PartitionModel::PartitionModel(Params ¶ms, PhyloSuperTree *tree, ModelsBlock *models_block)
: ModelFactory()
{
store_trans_matrix = params.store_trans_matrix;
is_storing = false;
joint_optimize = params.optimize_model_rate_joint;
fused_mix_rate = false;
linked_alpha = -1.0;
// create dummy model
model = new ModelSubst(tree->aln->num_states);
site_rate = new RateHeterogeneity();
site_rate->setTree(tree);
// string model_name = params.model_name;
PhyloSuperTree::iterator it;
int part;
if (params.link_alpha) {
params.gamma_shape = fabs(params.gamma_shape);
linked_alpha = params.gamma_shape;
}
for (it = tree->begin(), part = 0; it != tree->end(); it++, part++) {
ASSERT(!((*it)->getModelFactory()));
string model_name = (*it)->aln->model_name;
if (model_name == "") // if empty, take model name from command option
model_name = params.model_name;
(*it)->setModelFactory(new ModelFactory(params, model_name, (*it), models_block));
(*it)->setModel((*it)->getModelFactory()->model);
(*it)->setRate((*it)->getModelFactory()->site_rate);
// params.model_name = model_name;
if ((*it)->aln->getNSeq() < tree->aln->getNSeq() && (*it)->getModel()->freq_type == FREQ_EMPIRICAL && (*it)->aln->seq_type != SEQ_CODON) {
// modify state_freq to account for empty sequences
(*it)->aln->computeStateFreq((*it)->getModel()->state_freq, (*it)->aln->getNSite() * (tree->aln->getNSeq() - (*it)->aln->getNSeq()));
(*it)->getModel()->decomposeRateMatrix();
}
//string taxa_set = ((SuperAlignment*)tree->aln)->getPattern(part);
//(*it)->copyTree(tree, taxa_set);
//(*it)->drawTree(cout);
}
}
void PartitionModel::setCheckpoint(Checkpoint *checkpoint) {
ModelFactory::setCheckpoint(checkpoint);
PhyloSuperTree *tree = (PhyloSuperTree*)site_rate->getTree();
for (PhyloSuperTree::iterator it = tree->begin(); it != tree->end(); it++)
(*it)->getModelFactory()->setCheckpoint(checkpoint);
}
void PartitionModel::startCheckpoint() {
checkpoint->startStruct("PartitionModel");
}
void PartitionModel::saveCheckpoint() {
startCheckpoint();
CKP_SAVE(linked_alpha);
PhyloSuperTree *tree = (PhyloSuperTree*)site_rate->getTree();
int part = 0;
for (PhyloSuperTree::iterator it = tree->begin(); it != tree->end(); it++, part++) {
checkpoint->startStruct((*it)->aln->name);
(*it)->getModelFactory()->saveCheckpoint();
checkpoint->endStruct();
}
endCheckpoint();
CheckpointFactory::saveCheckpoint();
}
void PartitionModel::restoreCheckpoint() {
CheckpointFactory::restoreCheckpoint();
startCheckpoint();
CKP_RESTORE(linked_alpha);
PhyloSuperTree *tree = (PhyloSuperTree*)site_rate->getTree();
int part = 0;
for (PhyloSuperTree::iterator it = tree->begin(); it != tree->end(); it++, part++) {
checkpoint->startStruct((*it)->aln->name);
(*it)->getModelFactory()->restoreCheckpoint();
checkpoint->endStruct();
}
endCheckpoint();
}
int PartitionModel::getNParameters(int brlen_type) {
PhyloSuperTree *tree = (PhyloSuperTree*)site_rate->getTree();
int df = 0;
for (PhyloSuperTree::iterator it = tree->begin(); it != tree->end(); it++) {
df += (*it)->getModelFactory()->getNParameters(brlen_type);
}
if (linked_alpha > 0)
df ++;
return df;
}
double PartitionModel::computeFunction(double shape) {
PhyloSuperTree *tree = (PhyloSuperTree*)site_rate->getTree();
double res = 0.0;
linked_alpha = shape;
for (PhyloSuperTree::iterator it = tree->begin(); it != tree->end(); it++)
if ((*it)->getRate()->isGammaRate()) {
res += (*it)->getRate()->computeFunction(shape);
}
if (res == 0.0)
outError("No partition has Gamma rate heterogeneity!");
return res;
}
double PartitionModel::optimizeLinkedAlpha(bool write_info, double gradient_epsilon) {
if (write_info)
cout << "Optimizing linked gamma shape..." << endl;
double negative_lh;
double current_shape = linked_alpha;
double ferror, optx;
optx = minimizeOneDimen(site_rate->getTree()->params->min_gamma_shape, current_shape, MAX_GAMMA_SHAPE, max(gradient_epsilon, TOL_GAMMA_SHAPE), &negative_lh, &ferror);
if (write_info)
cout << "Linked alpha across partitions: " << linked_alpha << endl;
return site_rate->getTree()->computeLikelihood();
}
double PartitionModel::optimizeParameters(int fixed_len, bool write_info, double logl_epsilon, double gradient_epsilon) {
PhyloSuperTree *tree = (PhyloSuperTree*)site_rate->getTree();
double tree_lh = 0.0;
int ntrees = tree->size();
if (tree->part_order.empty()) tree->computePartitionOrder();
#ifdef _OPENMP
#pragma omp parallel for reduction(+: tree_lh) schedule(dynamic) if(tree->num_threads > 1)
#endif
for (int i = 0; i < ntrees; i++) {
int part = tree->part_order[i];
if (write_info)
#ifdef _OPENMP
#pragma omp critical
#endif
{
cout << "Optimizing " << tree->at(part)->getModelName() <<
" parameters for partition " << tree->at(part)->aln->name <<
" (" << tree->at(part)->getModelFactory()->getNParameters(fixed_len) << " free parameters)" << endl;
}
tree_lh += tree->at(part)->getModelFactory()->optimizeParameters(fixed_len, write_info && verbose_mode >= VB_MED,
logl_epsilon/min(ntrees,10), gradient_epsilon/min(ntrees,10));
}
//return ModelFactory::optimizeParameters(fixed_len, write_info);
if (tree->params->link_alpha) {
tree_lh = optimizeLinkedAlpha(write_info, gradient_epsilon);
}
if (verbose_mode >= VB_MED || write_info)
cout << "Optimal log-likelihood: " << tree_lh << endl;
return tree_lh;
}
double PartitionModel::optimizeParametersGammaInvar(int fixed_len, bool write_info, double logl_epsilon, double gradient_epsilon) {
PhyloSuperTree *tree = (PhyloSuperTree*)site_rate->getTree();
double tree_lh = 0.0;
int ntrees = tree->size();
if (tree->part_order.empty()) tree->computePartitionOrder();
#ifdef _OPENMP
#pragma omp parallel for reduction(+: tree_lh) schedule(dynamic) if(tree->num_threads > 1)
#endif
for (int i = 0; i < ntrees; i++) {
int part = tree->part_order[i];
if (write_info)
#ifdef _OPENMP
#pragma omp critical
#endif
{
cout << "Optimizing " << tree->at(part)->getModelName() <<
" parameters for partition " << tree->at(part)->aln->name <<
" (" << tree->at(part)->getModelFactory()->getNParameters(fixed_len) << " free parameters)" << endl;
}
tree_lh += tree->at(part)->getModelFactory()->optimizeParametersGammaInvar(fixed_len, write_info && verbose_mode >= VB_MED,
logl_epsilon/min(ntrees,10), gradient_epsilon/min(ntrees,10));
}
//return ModelFactory::optimizeParameters(fixed_len, write_info);
if (tree->params->link_alpha) {
tree_lh = optimizeLinkedAlpha(write_info, gradient_epsilon);
}
if (verbose_mode >= VB_MED || write_info)
cout << "Optimal log-likelihood: " << tree_lh << endl;
return tree_lh;
}
PartitionModel::~PartitionModel()
{
}
bool PartitionModel::isUnstableParameters() {
PhyloSuperTree *tree = (PhyloSuperTree*)site_rate->getTree();
for (PhyloSuperTree::iterator it = tree->begin(); it != tree->end(); it++)
if ((*it)->getModelFactory()->isUnstableParameters()) {
return true;
}
return false;
}
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