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iqtree.cpp
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iqtree.cpp
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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 "iqtree.h"
#include "phylosupertree.h"
#include "phylosupertreeplen.h"
#include "mexttree.h"
#include "timeutil.h"
extern double t_begin;
IQTree::IQTree() :
PhyloTree() {
init();
}
void IQTree::init() {
k_represent = 0;
k_delete = k_delete_min = k_delete_max = k_delete_stay = 0;
dist_matrix = NULL;
var_matrix = NULL;
nni_count_est = 0.0;
nni_delta_est = 0;
curScore = 0.0; // Current score of the tree
bestScore = 0.0; // Best score found so far
curIQPIter = 1;
cur_pars_score = -1;
enable_parsimony = false;
enableHeuris = true; // This is set true when the heuristic started (after N iterations)
linRegModel = NULL;
estimate_nni_cutoff = false;
nni_steps = 0;
nni_cutoff = -1e6;
nni_sort = false;
testNNI = false;
print_tree_lh = false;
write_intermediate_trees = 0;
max_candidate_trees = 0;
logl_cutoff = 0.0;
len_scale = 10000;
save_all_br_lens = false;
duplication_counter = 0;
phyloTree = NULL;
//boot_splits = new SplitGraph;
//initLeafFrequency();
nnicut.num_delta = 0;
nnicut.delta_min = DBL_MAX;
}
IQTree::IQTree(Alignment *aln) :
PhyloTree(aln) {
init();
}
double IQTree::computeParsimonyTreePhylolib() {
allocateParsimonyDataStructures(phyloTree);
makeParsimonyTreeFast(phyloTree);
freeParsimonyDataStructures(phyloTree);
treeEvaluate(phyloTree, 32);
return phyloTree->likelihood;
/*
int printBranchLengths = TRUE;
Tree2String(iqtree.raxmlTree->tree_string, iqtree.raxmlTree,
iqtree.raxmlTree->start->back, printBranchLengths, TRUE, 0, 0, 0,
SUMMARIZE_LH, 0, 0);
string parsimony_tree_file = params.out_prefix;
parsimony_tree_file += ".parsimonyTree";
printString2File(string(iqtree.raxmlTree->tree_string),
parsimony_tree_file);
*/
}
void IQTree::setParams(Params ¶ms) {
if (params.min_iterations == -1) {
if (!params.gbo_replicates) {
if (aln->getNSeq() < 100)
params.min_iterations = 200;
else
params.min_iterations = aln->getNSeq() * 2;
if (params.iteration_multiple > 1)
params.min_iterations = aln->getNSeq() * params.iteration_multiple;
} else {
params.min_iterations = 100;
}
}
if (params.gbo_replicates)
params.max_iterations = max(params.max_iterations, max(params.min_iterations, 1000));
k_represent = params.k_representative;
if (params.p_delete == -1.0) {
if (aln->getNSeq() < 51)
params.p_delete = 0.5;
else if (aln->getNSeq() < 100)
params.p_delete = 0.3;
else if (aln->getNSeq() < 200)
params.p_delete = 0.2;
else if (aln->getNSeq() < 400)
params.p_delete = 0.1;
else
params.p_delete = 0.05;
}
//tree.setProbDelete(params.p_delete);
if (params.p_delete != -1.0) {
k_delete = k_delete_min = k_delete_max = ceil(params.p_delete * leafNum);
} else {
k_delete = k_delete_min = 10;
k_delete_max = leafNum / 2;
if (k_delete_max > 100)
k_delete_max = 100;
if (k_delete_max < 20)
k_delete_max = 20;
k_delete_stay = ceil(leafNum / k_delete);
}
//tree.setIQPIterations(params.stop_condition, params.stop_confidence, params.min_iterations, params.max_iterations);
stop_rule.setStopCondition(params.stop_condition);
stop_rule.setConfidenceValue(params.stop_confidence);
stop_rule.setIterationNum(params.min_iterations, params.max_iterations);
//tree.setIQPAssessQuartet(params.iqp_assess_quartet);
iqp_assess_quartet = params.iqp_assess_quartet;
estimate_nni_cutoff = params.estimate_nni_cutoff;
nni_cutoff = params.nni_cutoff;
nni_sort = params.nni_sort;
testNNI = params.testNNI;
this->params = ¶ms;
write_intermediate_trees = params.write_intermediate_trees;
if (write_intermediate_trees > 2 || params.gbo_replicates > 0) {
save_all_trees = 1;
}
if (params.gbo_replicates > 0) {
if (params.iqp_assess_quartet != IQP_BOOTSTRAP) {
save_all_trees = 2;
}
}
if (params.gbo_replicates > 0 && params.do_compression)
save_all_br_lens = true;
print_tree_lh = params.print_tree_lh;
max_candidate_trees = params.max_candidate_trees;
if (max_candidate_trees == 0)
max_candidate_trees = aln->getNSeq() * stop_rule.getNumIterations();
setRootNode(params.root);
if (params.online_bootstrap && params.gbo_replicates > 0) {
cout << "Generating " << params.gbo_replicates << " samples for ultrafast bootstrap..." << endl;
boot_samples.resize(params.gbo_replicates);
boot_logl.resize(params.gbo_replicates, -DBL_MAX);
boot_trees.resize(params.gbo_replicates, -1);
boot_counts.resize(params.gbo_replicates, 0);
for (int i = 0; i < params.gbo_replicates; i++) {
aln->createBootstrapAlignment(boot_samples[i], params.bootstrap_spec);
}
cout << "Max candidate trees (tau): " << max_candidate_trees << endl;
}
nnicut.doNNICut = params.estimate_nni_cutoff;
if (params.root_state) {
if (strlen(params.root_state) != 1)
outError("Root state must have exactly 1 character");
root_state = aln->convertState(params.root_state[0]);
if (root_state < 0 || root_state >= aln->num_states)
outError("Invalid root state");
}
}
IQTree::~IQTree() {
//if (bonus_values)
//delete bonus_values;
//bonus_values = NULL;
if (dist_matrix)
delete[] dist_matrix;
dist_matrix = NULL;
if (var_matrix)
delete[] var_matrix;
var_matrix = NULL;
for (vector<double*>::reverse_iterator it = treels_ptnlh.rbegin(); it != treels_ptnlh.rend(); it++)
delete[] (*it);
treels_ptnlh.clear();
for (vector<SplitGraph*>::reverse_iterator it2 = boot_splits.rbegin(); it2 != boot_splits.rend(); it2++)
delete (*it2);
//if (boot_splits) delete boot_splits;
if (phyloTree)
delete phyloTree;
}
double IQTree::getProbDelete() {
return (double) k_delete / leafNum;
}
void IQTree::resetKDelete() {
k_delete = k_delete_min;
k_delete_stay = ceil(leafNum / k_delete);
}
void IQTree::increaseKDelete() {
if (k_delete >= k_delete_max)
return;
k_delete_stay--;
if (k_delete_stay > 0)
return;
k_delete++;
k_delete_stay = ceil(leafNum / k_delete);
if (verbose_mode >= VB_MED)
cout << "Increase k_delete to " << k_delete << endl;
}
void IQTree::setIQPIterations(STOP_CONDITION stop_condition, double stop_confidence, int min_iterations,
int max_iterations) {
stop_rule.setStopCondition(stop_condition);
stop_rule.setConfidenceValue(stop_confidence);
stop_rule.setIterationNum(min_iterations, max_iterations);
}
RepresentLeafSet* IQTree::findRepresentLeaves(vector<RepresentLeafSet*> &leaves_vec, int nei_id, PhyloNode *dad) {
PhyloNode *node = (PhyloNode*) (dad->neighbors[nei_id]->node);
int set_id = dad->id * 3 + nei_id;
if (leaves_vec[set_id])
return leaves_vec[set_id];
RepresentLeafSet *leaves = new RepresentLeafSet;
RepresentLeafSet * leaves_it[2] = { NULL, NULL };
leaves_vec[set_id] = leaves;
RepresentLeafSet::iterator last;
RepresentLeafSet::iterator cur_it;
int i, j;
//double admit_height = 1000000;
leaves->clear();
if (node->isLeaf()) {
// set the depth to zero
//node->height = 0.0;
leaves->insert(new RepLeaf(node, 0));
} else {
for (i = 0, j = 0; i < node->neighbors.size(); i++)
if (node->neighbors[i]->node != dad) {
leaves_it[j++] = findRepresentLeaves(leaves_vec, i, node);
}
assert(j == 2 && leaves_it[0] && leaves_it[1]);
if (leaves_it[0]->empty() && leaves_it[1]->empty()) {
cout << "wrong";
}
RepresentLeafSet::iterator lit[2] = { leaves_it[0]->begin(), leaves_it[1]->begin() };
while (leaves->size() < k_represent) {
int id = -1;
if (lit[0] != leaves_it[0]->end() && lit[1] != leaves_it[1]->end()) {
if ((*lit[0])->height < (*lit[1])->height)
id = 0;
else if ((*lit[0])->height > (*lit[1])->height)
id = 1;
else { // tie, choose at random
id = random_int(2);
}
} else if (lit[0] != leaves_it[0]->end())
id = 0;
else if (lit[1] != leaves_it[1]->end())
id = 1;
else
break;
assert(id < 2 && id >= 0);
leaves->insert(new RepLeaf((*lit[id])->leaf, (*lit[id])->height + 1));
lit[id]++;
}
}
assert(!leaves->empty());
/*
if (verbose_mode >= VB_MAX) {
for (cur_it = leaves->begin(); cur_it != leaves->end(); cur_it++)
cout << (*cur_it)->leaf->name << " ";
cout << endl;
}*/
return leaves;
}
/*
void IQPTree::clearRepresentLeaves(vector<RepresentLeafSet*> &leaves_vec, Node *node, Node *dad) {
int nei_id;
for (nei_id = 0; nei_id < node->neighbors.size(); nei_id++)
if (node->neighbors[nei_id]->node == dad) break;
assert(nei_id < node->neighbors.size());
int set_id = node->id * 3 + nei_id;
if (leaves_vec[set_id]) {
for (RepresentLeafSet::iterator rlit = leaves_vec[set_id]->begin(); rlit != leaves_vec[set_id]->end(); rlit++)
delete (*rlit);
delete leaves_vec[set_id];
leaves_vec[set_id] = NULL;
}
FOR_NEIGHBOR_IT(node, dad, it) {
clearRepresentLeaves(leaves_vec, (*it)->node, node);
}
}*/
void IQTree::initLeafFrequency(PhyloNode *node, PhyloNode *dad) {
if (!node)
node = (PhyloNode*) root;
if (node->isLeaf()) {
LeafFreq leaf_freq;
leaf_freq.leaf_id = node->id;
leaf_freq.freq = 0;
leaf_freqs.push_back(leaf_freq);
}
for (NeighborVec::iterator it = node->neighbors.begin(); it != node->neighbors.end(); it++)
if ((*it)->node != dad) {
initLeafFrequency((PhyloNode*) (*it)->node, node);
}
}
void IQTree::clearLeafFrequency() {
for (vector<LeafFreq>::iterator it = leaf_freqs.begin(); it != leaf_freqs.end(); it++) {
(*it).freq = 0;
}
}
void IQTree::deleteNonCherryLeaves(PhyloNodeVector &del_leaves) {
NodeVector cherry_taxa;
NodeVector noncherry_taxa;
// get the vector of non cherry taxa
getNonCherryLeaves(noncherry_taxa, cherry_taxa);
root = NULL;
int num_taxa = aln->getNSeq();
int num_delete = k_delete;
if (num_delete > num_taxa - 4)
num_delete = num_taxa - 4;
if (verbose_mode >= VB_DEBUG) {
cout << "Deleting " << num_delete << " leaves" << endl;
}
vector<unsigned int> indices_noncherry(noncherry_taxa.size());
//iota(indices_noncherry.begin(), indices_noncherry.end(), 0);
unsigned int startValue = 0;
for (vector<unsigned int>::iterator it = indices_noncherry.begin(); it != indices_noncherry.end(); ++it) {
(*it) = startValue;
++startValue;
}
random_shuffle(indices_noncherry.begin(), indices_noncherry.end());
int i;
for (i = 0; i < num_delete && i < noncherry_taxa.size(); i++) {
PhyloNode *taxon = (PhyloNode*) noncherry_taxa[indices_noncherry[i]];
del_leaves.push_back(taxon);
deleteLeaf(taxon);
//cout << taxon->id << ", ";
}
int j = 0;
if (i < num_delete) {
vector<unsigned int> indices_cherry(cherry_taxa.size());
//iota(indices_cherry.begin(), indices_cherry.end(), 0);
startValue = 0;
for (vector<unsigned int>::iterator it = indices_cherry.begin(); it != indices_cherry.end(); ++it) {
(*it) = startValue;
++startValue;
}
random_shuffle(indices_cherry.begin(), indices_cherry.end());
while (i < num_delete) {
PhyloNode *taxon = (PhyloNode*) cherry_taxa[indices_cherry[j]];
del_leaves.push_back(taxon);
deleteLeaf(taxon);
i++;
j++;
}
}
root = cherry_taxa[j];
}
void IQTree::deleteNonTabuLeaves(PhyloNodeVector &del_leaves) {
// sort node frequency
sort(leaf_freqs.begin(), leaf_freqs.end());
NodeVector taxa;
// get the vector of taxa
getTaxa(taxa);
// shuffle the sorted list first so that leaves with the same frequency have the same
// chance of being removed
int cur_freq = leaf_freqs[0].freq;
//cout << "size: " << leaf_freqs.size() << endl;
//cout << "Before randomize" << endl;
/*
for (size_t i = 0; i < leaf_freqs.size(); i++) {
cout << leaf_freqs[i].leaf_id << ":" << leaf_freqs[i].freq << " ";
}
cout << endl;
*/
int startIndex = 0;
int endIndex = 0;
while (true) {
while (leaf_freqs[endIndex].freq == cur_freq && endIndex < leaf_freqs.size()) {
endIndex++;
}
random_shuffle(leaf_freqs.begin() + startIndex, leaf_freqs.begin() + endIndex);
if (endIndex == leaf_freqs.size())
break;
startIndex = endIndex;
cur_freq = leaf_freqs[endIndex].freq;
}
/*
cout << "After randomize" << endl;
for (size_t i = 0; i < leaf_freqs.size(); i++) {
cout << leaf_freqs[i].leaf_id << ":" << leaf_freqs[i].freq << " ";
}
cout << endl;
*/
int leafCnt = 0;
while (leafCnt < k_delete) {
PhyloNode *taxon = (PhyloNode*) taxa[leaf_freqs[leafCnt].leaf_id];
del_leaves.push_back(taxon);
leaf_freqs[leafCnt].freq++;
leafCnt++;
deleteLeaf(taxon);
}
root = taxa[leaf_freqs[leafCnt].leaf_id];
}
void IQTree::deleteLeaves(PhyloNodeVector &del_leaves) {
NodeVector taxa;
// get the vector of taxa
getTaxa(taxa);
root = NULL;
//int num_delete = floor(p_delete * taxa.size());
int num_delete = k_delete;
int i;
if (num_delete > taxa.size() - 4)
num_delete = taxa.size() - 4;
if (verbose_mode >= VB_DEBUG) {
cout << "Deleting " << num_delete << " leaves" << endl;
}
// now try to randomly delete some taxa of the probability of p_delete
for (i = 0; i < num_delete;) {
int id = random_int(taxa.size());
if (!taxa[id])
continue;
else
i++;
PhyloNode *taxon = (PhyloNode*) taxa[id];
del_leaves.push_back(taxon);
deleteLeaf(taxon);
taxa[id] = NULL;
}
// set root to the first taxon which was not deleted
for (i = 0; i < taxa.size(); i++)
if (taxa[i]) {
root = taxa[i];
break;
}
}
int IQTree::assessQuartet(Node *leaf0, Node *leaf1, Node *leaf2, Node *del_leaf) {
assert(dist_matrix);
int nseq = aln->getNSeq();
//int id0 = leaf0->id, id1 = leaf1->id, id2 = leaf2->id;
double dist0 = dist_matrix[leaf0->id * nseq + del_leaf->id] + dist_matrix[leaf1->id * nseq + leaf2->id];
double dist1 = dist_matrix[leaf1->id * nseq + del_leaf->id] + dist_matrix[leaf0->id * nseq + leaf2->id];
double dist2 = dist_matrix[leaf2->id * nseq + del_leaf->id] + dist_matrix[leaf0->id * nseq + leaf1->id];
if (dist0 < dist1 && dist0 < dist2)
return 0;
if (dist1 < dist2)
return 1;
return 2;
}
int IQTree::assessQuartetParsimony(Node *leaf0, Node *leaf1, Node *leaf2, Node *del_leaf) {
int score[3] = { 0, 0, 0 };
for (Alignment::iterator it = aln->begin(); it != aln->end(); it++) {
char ch0 = (*it)[leaf0->id];
char ch1 = (*it)[leaf1->id];
char ch2 = (*it)[leaf2->id];
char chd = (*it)[del_leaf->id];
if (ch0 >= aln->num_states || ch1 >= aln->num_states || ch2 >= aln->num_states || chd >= aln->num_states)
continue;
if (chd == ch0 && ch1 == ch2)
score[0] += (*it).frequency;
if (chd == ch1 && ch0 == ch2)
score[1] += (*it).frequency;
if (chd == ch2 && ch0 == ch1)
score[2] += (*it).frequency;
}
if (score[0] == score[1] && score[0] == score[2]) {
int id = random_int(3);
return id;
}
if (score[0] > score[1] && score[0] > score[2])
return 0;
if (score[1] < score[2])
return 2;
return 1;
}
void IQTree::initializeBonus(PhyloNode *node, PhyloNode *dad) {
if (!node)
node = (PhyloNode*) root;
if (dad) {
PhyloNeighbor *node_nei = (PhyloNeighbor*) node->findNeighbor(dad);
PhyloNeighbor *dad_nei = (PhyloNeighbor*) dad->findNeighbor(node);
node_nei->lh_scale_factor = 0.0;
node_nei->partial_lh_computed = 0;
dad_nei->lh_scale_factor = 0.0;
dad_nei->partial_lh_computed = 0;
}
FOR_NEIGHBOR_IT(node, dad, it){
initializeBonus((PhyloNode*) ((*it)->node), node);
}
}
void IQTree::raiseBonus(Neighbor *nei, Node *dad, double bonus) {
((PhyloNeighbor*) nei)->lh_scale_factor += bonus;
if (verbose_mode >= VB_DEBUG)
cout << dad->id << " - " << nei->node->id << " : " << bonus << endl;
// FOR_NEIGHBOR_IT(nei->node, dad, it)
// raiseBonus((*it), nei->node, bonus);
}
double IQTree::computePartialBonus(Node *node, Node* dad) {
PhyloNeighbor *node_nei = (PhyloNeighbor*) node->findNeighbor(dad);
if (node_nei->partial_lh_computed)
return node_nei->lh_scale_factor;
FOR_NEIGHBOR_IT(node, dad, it){
node_nei->lh_scale_factor += computePartialBonus((*it)->node, node);
}
node_nei->partial_lh_computed = 1;
return node_nei->lh_scale_factor;
}
double IQTree::doVNS() {
curScore = optimizeNNI(false);
return curScore;
}
/*
bool IQTree::containPosNNI(vector<NNIMove> posNNIs) {
for (vector<NNIMove>::iterator iter = posNNIs.begin(); iter != posNNIs.end(); iter++) {
if (iter->newloglh > iter->oldloglh)
return true;
}
return false;
}
*/
void IQTree::findBestBonus(double &best_score, NodeVector &best_nodes, NodeVector &best_dads, Node *node, Node *dad) {
double score;
if (!node)
node = root;
if (!dad) {
best_score = 0;
} else {
score = computePartialBonus(node, dad) + computePartialBonus(dad, node);
if (score >= best_score) {
if (score > best_score) {
best_score = score;
best_nodes.clear();
best_dads.clear();
}
best_nodes.push_back(node);
best_dads.push_back(dad);
}
//cout << node->id << " - " << dad->id << " : " << best_score << endl;
}
FOR_NEIGHBOR_IT(node, dad, it){
findBestBonus(best_score, best_nodes, best_dads, (*it)->node, node);
}
}
void IQTree::assessQuartets(vector<RepresentLeafSet*> &leaves_vec, PhyloNode *cur_root, PhyloNode *del_leaf) {
const int MAX_DEGREE = 3;
RepresentLeafSet * leaves[MAX_DEGREE];
double bonus[MAX_DEGREE];
memset(bonus, 0, MAX_DEGREE * sizeof(double));
int cnt = 0;
// only work for birfucating tree
assert(cur_root->degree() == MAX_DEGREE);
// find the representative leaf set for three subtrees
FOR_NEIGHBOR_IT(cur_root, NULL, it){
leaves[cnt] = findRepresentLeaves(leaves_vec, cnt, cur_root);
cnt++;
}
for (RepresentLeafSet::iterator i0 = leaves[0]->begin(); i0 != leaves[0]->end(); i0++)
for (RepresentLeafSet::iterator i1 = leaves[1]->begin(); i1 != leaves[1]->end(); i1++)
for (RepresentLeafSet::iterator i2 = leaves[2]->begin(); i2 != leaves[2]->end(); i2++) {
int best_id;
if (iqp_assess_quartet == IQP_DISTANCE)
best_id = assessQuartet((*i0)->leaf, (*i1)->leaf, (*i2)->leaf, del_leaf);
else
best_id = assessQuartetParsimony((*i0)->leaf, (*i1)->leaf, (*i2)->leaf, del_leaf);
bonus[best_id] += 1.0;
}
for (cnt = 0; cnt < MAX_DEGREE; cnt++)
if (bonus[cnt] > 0.0)
raiseBonus(cur_root->neighbors[cnt], cur_root, bonus[cnt]);
}
void IQTree::reinsertLeavesByParsimony(PhyloNodeVector &del_leaves) {
PhyloNodeVector::iterator it_leaf;
assert(root->isLeaf());
for (it_leaf = del_leaves.begin(); it_leaf != del_leaves.end(); it_leaf++) {
//cout << "Add leaf " << (*it_leaf)->id << " to the tree" << endl;
initializeAllPartialPars();
clearAllPartialLH();
Node *target_node = NULL;
Node *target_dad = NULL;
Node *added_node = (*it_leaf)->neighbors[0]->node;
Node *node1 = NULL;
Node *node2 = NULL;
//Node *leaf;
for (int i = 0; i < 3; i++) {
if (added_node->neighbors[i]->node->id == (*it_leaf)->id) {
//leaf = added_node->neighbors[i]->node;
} else if (!node1) {
node1 = added_node->neighbors[i]->node;
} else {
node2 = added_node->neighbors[i]->node;
}
}
//cout << "(" << node1->id << ", " << node2->id << ")" << "----" << "(" << added_node->id << "," << leaf->id << ")" << endl;
added_node->updateNeighbor(node1, (Node*) 1);
added_node->updateNeighbor(node2, (Node*) 2);
addTaxonMPFast(added_node, target_node, target_dad, root->neighbors[0]->node, root);
target_node->updateNeighbor(target_dad, added_node, -1.0);
target_dad->updateNeighbor(target_node, added_node, -1.0);
added_node->updateNeighbor((Node*) 1, target_node, -1.0);
added_node->updateNeighbor((Node*) 2, target_dad, -1.0);
}
}
void IQTree::reinsertLeaves(PhyloNodeVector &del_leaves) {
PhyloNodeVector::iterator it_leaf;
//int num_del_leaves = del_leaves.size();
assert(root->isLeaf());
for (it_leaf = del_leaves.begin(); it_leaf != del_leaves.end(); it_leaf++) {
if (verbose_mode >= VB_DEBUG)
cout << "Reinserting " << (*it_leaf)->name << " (" << (*it_leaf)->id << ")" << endl;
vector<RepresentLeafSet*> leaves_vec;
leaves_vec.resize(nodeNum * 3, NULL);
initializeBonus();
NodeVector nodes;
getInternalNodes(nodes);
if (verbose_mode >= VB_DEBUG)
drawTree(cout, WT_BR_SCALE | WT_INT_NODE | WT_TAXON_ID | WT_NEWLINE | WT_BR_ID);
//printTree(cout, WT_BR_LEN | WT_INT_NODE | WT_TAXON_ID | WT_NEWLINE);
for (NodeVector::iterator it = nodes.begin(); it != nodes.end(); it++) {
assessQuartets(leaves_vec, (PhyloNode*) (*it), (*it_leaf));
}
NodeVector best_nodes, best_dads;
double best_bonus;
findBestBonus(best_bonus, best_nodes, best_dads);
if (verbose_mode >= VB_DEBUG)
cout << "Best bonus " << best_bonus << " " << best_nodes[0]->id << " " << best_dads[0]->id << endl;
assert(best_nodes.size() == best_dads.size());
int node_id = random_int(best_nodes.size());
if (best_nodes.size() > 1 && verbose_mode >= VB_DEBUG)
cout << best_nodes.size() << " branches show the same best bonus, branch nr. " << node_id << " is chosen"
<< endl;
reinsertLeaf(*it_leaf, best_nodes[node_id], best_dads[node_id]);
//clearRepresentLeaves(leaves_vec, *it_node, *it_leaf);
/*if (verbose_mode >= VB_DEBUG) {
printTree(cout);
cout << endl;
}*/
for (vector<RepresentLeafSet*>::iterator rit = leaves_vec.begin(); rit != leaves_vec.end(); rit++)
if ((*rit)) {
RepresentLeafSet *tit = (*rit);
for (RepresentLeafSet::iterator rlit = tit->begin(); rlit != tit->end(); rlit++)
delete (*rlit);
delete (*rit);
}
}
initializeTree(); // BQM: re-index nodes and branches s.t. ping-pong neighbors have the same ID
if (verbose_mode >= VB_DEBUG)
drawTree(cout, WT_BR_SCALE | WT_INT_NODE | WT_TAXON_ID | WT_NEWLINE | WT_BR_ID);
}
void IQTree::doParsimonyReinsertion() {
PhyloNodeVector del_leaves;
if (params->tabu) {
deleteNonTabuLeaves(del_leaves);
} else {
deleteLeaves(del_leaves);
}
reinsertLeavesByParsimony(del_leaves);
fixNegativeBranch(false);
}
double IQTree::doIQP() {
if (verbose_mode >= VB_DEBUG)
drawTree(cout, WT_BR_SCALE | WT_INT_NODE | WT_TAXON_ID | WT_NEWLINE | WT_BR_ID);
//double time_begin = getCPUTime();
PhyloNodeVector del_leaves;
if (params->tabu) {
deleteNonTabuLeaves(del_leaves);
} else if (params->cherry) {
// delete all leaves of a subtree
deleteNonCherryLeaves(del_leaves);
} else {
deleteLeaves(del_leaves);
}
/*
for (int i = 0; i < del_leaves.size(); i++)
cout << del_leaves[i]->id << " ";
cout << endl;
*/
reinsertLeaves(del_leaves);
if (!params->phylolib) {
// just to make sure IQP does it right
setAlignment(aln);
clearAllPartialLH();
if (params->gbo_replicates)
//curScore = optimizeAllBranches(3, 1.0);
curScore = optimizeAllBranches(params->numSmoothTree);
else {
// optimize branches at the reinsertion point
/*
for (PhyloNodeVector::iterator dit = del_leaves.begin(); dit != del_leaves.end(); dit++) {
PhyloNode *adj_node = (PhyloNode*) (*dit)->neighbors[0]->node;
FOR_NEIGHBOR_IT(adj_node, (*dit), it)
curScore = optimizeOneBranch(adj_node, (PhyloNode*) (*it)->node);
curScore = optimizeOneBranch(adj_node, (PhyloNode*)(*dit));
}
*/
curScore = optimizeAllBranches(params->numSmoothTree);
}
}
//cout << "IQP log-likelihood: " << curScore << endl;
//cout << "computeLikelihood(): " << computeLikelihood() << endl;
if (enable_parsimony) {
cur_pars_score = computeParsimony();
if (verbose_mode >= VB_MAX) {
cout << "IQP Likelihood = " << curScore << " Parsimony = " << cur_pars_score << endl;
}
}
//double time_end = getCPUTime();
//cout << "IQP Time: " << (time_end - time_begin) << endl;
return curScore;
}
double IQTree::swapTaxa(PhyloNode *node1, PhyloNode *node2) {
assert(node1->isLeaf());
assert(node2->isLeaf());
PhyloNeighbor *node1nei = (PhyloNeighbor*) *(node1->neighbors.begin());
PhyloNeighbor *node2nei = (PhyloNeighbor*) *(node2->neighbors.begin());
node2nei->node->updateNeighbor(node2, node1);
node1nei->node->updateNeighbor(node1, node2);
// Update the new neightbors of the 2 nodes
node1->updateNeighbor(node1->neighbors.begin(), node2nei);
node2->updateNeighbor(node2->neighbors.begin(), node1nei);
PhyloNeighbor *node1NewNei = (PhyloNeighbor*) *(node1->neighbors.begin());
PhyloNeighbor *node2NewNei = (PhyloNeighbor*) *(node2->neighbors.begin());
// Reoptimize the branch lengths
optimizeOneBranch(node1, (PhyloNode*) node1NewNei->node);
this->curScore = optimizeOneBranch(node2, (PhyloNode*) node2NewNei->node);
//drawTree(cout, WT_BR_SCALE | WT_INT_NODE | WT_TAXON_ID | WT_NEWLINE);
return this->curScore;
}
double IQTree::perturb(int times) {
while (times > 0) {
NodeVector taxa;
// get the vector of taxa
getTaxa(taxa);
int taxonid1 = random_int(taxa.size());
PhyloNode *taxon1 = (PhyloNode*) taxa[taxonid1];
PhyloNode *taxon2;
int *dists = new int[taxa.size()];
int minDist = 1000000;
for (int i = 0; i < taxa.size(); i++) {
if (i == taxonid1)
continue;
taxon2 = (PhyloNode*) taxa[i];
int dist = taxon1->calDist(taxon2);
dists[i] = dist;
if (dist >= 7 && dist < minDist)
minDist = dist;
}
int taxonid2 = -1;
for (int i = 0; i < taxa.size(); i++) {
if (dists[i] == minDist)
taxonid2 = i;
}
taxon2 = (PhyloNode*) taxa[taxonid2];
cout << "Swapping node " << taxon1->id << " and node " << taxon2->id << endl;
cout << "Distance " << minDist << endl;
curScore = swapTaxa(taxon1, taxon2);
//taxa.erase( taxa.begin() + taxaID1 );
//taxa.erase( taxa.begin() + taxaID2 -1 );
times--;
delete[] dists;
}
curScore = optimizeAllBranches(1);
return curScore;
}
//double IQPTree::doILS(Params ¶ms, int perturbLevel) {
//
// string tree_file_name = params.aln_file;
// tree_file_name += ".treefile";
// // keep the best tree into a string
// stringstream best_tree_string;
// printTree(best_tree_string, WT_TAXON_ID + WT_BR_LEN);
// bestScore = curScore;PhyloNode* node1 = vec_nonconf_nni.at(i).node1;
//
// int numIter = params.min_iterations;
// for (int i=1 ; i <= numIter; i++) {
//
// if (i > speedUpFromIter) {
// enableHeuris = true;
// nbNNI95 = estimateNumNNI();
// deltaNNI95 = estimateDeltaNNI();
// }
//
// cout.precision(10);
// perturb(perturbLevel);
//
// optimizeNNI();
//
// cout.precision(15);
// cout << "Iteration " << i << " / Log-Likelihood: "
// << curScore << endl;
// if (curScore > bestScore + TOL_LIKELIHOOD) {
// //nni_score = optimizeNNI(true);
// //curScore = optimizeAllBranches();
// cout << "BETTER TREE FOUND: " << curScore << endl;
// bestScore = curScore;
// best_tree_string.seekp(0);
// printTree(best_tree_string, WT_TAXON_ID + WT_BR_LEN);
// printTree(tree_file_name.c_str());
// } else {
// /* take back the current best tree */
// best_tree_string.seekg(0);
// freeNode();
// readTree(best_tree_string, rooted);
// assignLeafNames();
// initializeAllPartialLh();
// }
// }
//
// return bestScore;
//}
void IQTree::doRandomRestart() {
int curIQPIter;
setRootNode(params->root);
// keep the best tree into a string
stringstream best_tree_string;
printTree(best_tree_string, WT_TAXON_ID + WT_BR_LEN);
stringstream best_tree_topo_ss;
printTree(best_tree_topo_ss, WT_TAXON_ID + WT_SORT_TAXA);
string best_tree_topo = best_tree_topo_ss.str();
for (curIQPIter = 2; curIQPIter < params->min_iterations; curIQPIter++) {
double min_elapsed = (getCPUTime() - params->startTime) / 60;
if (min_elapsed > params->maxtime) {
break;
}
double parsimonyLH = computeParsimonyTreePhylolib();
cout << "Parsimony score: " << parsimonyLH << endl;
curScore = optimizeNNIRax();
if (curScore > bestScore) {
curScore = optimizeAllBranches();
stringstream cur_tree_topo_ss;
printTree(cur_tree_topo_ss, WT_TAXON_ID | WT_SORT_TAXA);
if (cur_tree_topo_ss.str() != best_tree_topo) {
cout << "BETTER TREE FOUND: " << curScore << endl;
bestScore = curScore;
best_tree_string.seekp(0, ios::beg);
printTree(best_tree_string, WT_TAXON_ID + WT_BR_LEN);
printResultTree();
} else {
// higher likelihood but the same tree topology
bestScore = curScore;
cout << "UPDATE BEST LOG-LIKELIHOOD: " << bestScore << endl;
}
}
double cputime_secs = getCPUTime() - params->startTime;
cout << "Iteration " << curIQPIter << " / LogL: " << curScore << " / CPU time: "
<< (int) round(cputime_secs) << "s" << endl;
;
}
// read in new tree
int printBranchLengths = TRUE;
Tree2String(phyloTree->tree_string, phyloTree, phyloTree->start->back, printBranchLengths, TRUE, 0, 0, 0,
SUMMARIZE_LH, 0, 0);
stringstream mytree;
mytree << phyloTree->tree_string;
freeNode();
readTree(mytree, rooted);
setAlignment(aln);
}
double IQTree::doIQPNNI() {
//double bestIQPScore = -DBL_MAX + 100;
if (testNNI) {
string str = params->out_prefix;
str += ".nni";
outNNI.open(str.c_str());
outNNI << "cur_lh\tzero_lh\tnni_lh1\tnni_lh2\topt_len\tnnilen1\tnnilen2\tnni_round" << endl;
}
time_t begin_time, cur_time;
time(&begin_time);
string tree_file_name = params->out_prefix;
tree_file_name += ".treefile";
bestScore = curScore;
//printResultTree(params);
string treels_name = params->out_prefix;
treels_name += ".treels";
string out_lh_file = params->out_prefix;
out_lh_file += ".treelh";
string site_lh_file = params->out_prefix;
site_lh_file += ".sitelh";
if (params->print_tree_lh) {
out_treelh.open(out_lh_file.c_str());
out_sitelh.open(site_lh_file.c_str());
}
if (params->write_intermediate_trees)
out_treels.open(treels_name.c_str());
if (params->write_intermediate_trees && save_all_trees != 2) {
printIntermediateTree(WT_NEWLINE | WT_APPEND | WT_SORT_TAXA | WT_BR_LEN);
}
//printTree(treels_name.c_str(), WT_NEWLINE | WT_BR_LEN);
setRootNode(params->root);
// keep the best tree into a string
stringstream best_tree_string;
printTree(best_tree_string, WT_TAXON_ID + WT_BR_LEN);
stringstream best_tree_topo_ss;
printTree(best_tree_topo_ss, WT_TAXON_ID + WT_SORT_TAXA);
string best_tree_topo = best_tree_topo_ss.str();
// write tree's loglikelihood to a file (if nni_lh option is enabled)
ofstream lh_file;
if (params->nni_lh) {
// Remove the .treefile ending and add iq-tree.lh ending to the file name
string aln_file_name;
aln_file_name.assign(tree_file_name).erase(tree_file_name.size() - 9);
string lh_file_name = aln_file_name + ".iq-tree.lh";
lh_file.open((lh_file_name).c_str());
if (lh_file.is_open()) {
lh_file.precision(15);
lh_file << 1;
lh_file << "\t";
lh_file << bestScore;
lh_file << endl;