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/*
* phylosupertreeplen.cpp
*
* Created on: Aug 5, 2013
* Author: olga
*/
#include "phylosupertreeplen.h"
#include "alignment/superalignmentpairwiseplen.h"
#include "model/partitionmodelplen.h"
#include <string.h>
#include "utils/timeutil.h"
/**********************************************************
* class PhyloSuperTreePlen
**********************************************************/
PhyloSuperTreePlen::PhyloSuperTreePlen()
: PhyloSuperTree()
{
memset(allNNIcases_computed, 0, 5*sizeof(int));
fixed_rates = false;
}
/*
PhyloSuperTreePlen::PhyloSuperTreePlen(SuperAlignment *alignment)
: PhyloSuperTree(alignment)
{
memset(allNNIcases_computed, 0, 5*sizeof(int));
fixed_rates = (params->partition_type == BRLEN_FIX) ? true : false;
int part = 0;
for (iterator it = begin(); it != end(); it++, part++) {
part_info[part].part_rate = 1.0;
part_info[part].evalNNIs = 0.0;
if ((*it)->aln->seq_type == SEQ_CODON && rescale_codon_brlen)
part_info[part].part_rate = 3.0;
}
}
*/
PhyloSuperTreePlen::PhyloSuperTreePlen(SuperAlignment *alignment, int partition_type)
: PhyloSuperTree(alignment)
{
memset(allNNIcases_computed, 0, 5*sizeof(int));
// fixed_rates = false;
fixed_rates = (partition_type == BRLEN_FIX) ? true : false;
int part = 0;
for (iterator it = begin(); it != end(); it++, part++) {
part_info[part].part_rate = 1.0;
part_info[part].evalNNIs = 0.0;
if ((*it)->aln->seq_type == SEQ_CODON && rescale_codon_brlen)
part_info[part].part_rate = 3.0;
}
}
PhyloSuperTreePlen::PhyloSuperTreePlen(SuperAlignment *alignment, PhyloSuperTree *super_tree)
: PhyloSuperTree(alignment,super_tree)
{
memset(allNNIcases_computed, 0, 5*sizeof(int));
fixed_rates = false;
int part = 0;
for (iterator it = begin(); it != end(); it++, part++) {
part_info[part].part_rate = 1.0;
part_info[part].evalNNIs = 0.0;
if ((*it)->aln->seq_type == SEQ_CODON && rescale_codon_brlen)
part_info[part].part_rate = 3.0;
}
}
void PhyloSuperTreePlen::deleteAllPartialLh() {
for (iterator it = begin(); it != end(); it++) {
// reset these pointers so that they are not deleted
(*it)->central_partial_lh = NULL;
(*it)->central_scale_num = NULL;
// (*it)->central_partial_pars = NULL;
(*it)->_pattern_lh = NULL;
(*it)->_pattern_lh_cat = NULL;
(*it)->theta_all = NULL;
(*it)->buffer_scale_all = NULL;
(*it)->buffer_partial_lh = NULL;
(*it)->ptn_freq = NULL;
(*it)->ptn_freq_computed = false;
(*it)->ptn_invar = NULL;
(*it)->nni_partial_lh = NULL;
(*it)->nni_scale_num = NULL;
}
PhyloTree::deleteAllPartialLh();
}
PhyloSuperTreePlen::~PhyloSuperTreePlen()
{
for (iterator it = begin(); it != end(); it++) {
// reset these pointers so that they are not deleted
(*it)->central_partial_lh = NULL;
(*it)->central_scale_num = NULL;
// (*it)->central_partial_pars = NULL;
(*it)->_pattern_lh = NULL;
(*it)->_pattern_lh_cat = NULL;
(*it)->theta_all = NULL;
(*it)->buffer_scale_all = NULL;
(*it)->buffer_partial_lh = NULL;
(*it)->ptn_freq = NULL;
(*it)->ptn_freq_computed = false;
(*it)->ptn_invar = NULL;
(*it)->nni_partial_lh = NULL;
(*it)->nni_scale_num = NULL;
}
}
void PhyloSuperTreePlen::saveCheckpoint() {
// bypass PhyloSuperTree
IQTree::saveCheckpoint();
}
void PhyloSuperTreePlen::restoreCheckpoint() {
// bypass PhyloSuperTree
IQTree::restoreCheckpoint();
}
// -------------------------------------------------------------------------------------------------------------
double PhyloSuperTreePlen::computeDist(int seq1, int seq2, double initial_dist, double &var) {
// if no model or site rate is specified, return JC distance
if (initial_dist == 0.0)
initial_dist = aln->computeDist(seq1, seq2);
if (initial_dist == MAX_GENETIC_DIST) return initial_dist;
if (!model_factory || !site_rate) return initial_dist;
// now optimize the distance based on the model and site rate
SuperAlignmentPairwisePlen aln_pair(this, seq1, seq2);
return aln_pair.optimizeDist(initial_dist, var);
}
void PhyloSuperTreePlen::mapTrees() {
ASSERT(root);
int part = 0;
// this is important: rescale branch length of codon partitions to be compatible with other partitions.
// since for codon models, branch lengths = # nucleotide subst per codon site!
bool noncodon_present = false;
iterator it;
for (it = begin(); it != end(); it++)
if ((*it)->aln->seq_type != SEQ_CODON) {
noncodon_present = true;
break;
}
for (it = begin(); it != end(); it++, part++) {
string taxa_set;
Pattern taxa_pat = ((SuperAlignment*)aln)->getPattern(part);
taxa_set.insert(taxa_set.begin(), taxa_pat.begin(), taxa_pat.end());
(*it)->copyTree(this, taxa_set);
// the only difference with PhyloSuperTree::mapTrees()
(*it)->scaleLength(part_info[part].part_rate);
// if ((*it)->getModel())
// (*it)->initializeAllPartialLh();
NodeVector my_taxa, part_taxa;
(*it)->getOrderedTaxa(my_taxa);
part_taxa.resize(leafNum, NULL);
int i;
for (i = 0; i < leafNum; i++) {
int id = ((SuperAlignment*)aln)->taxa_index[i][part];
if (id >=0) part_taxa[i] = my_taxa[id];
}
linkTree(part, part_taxa);
}
if (getModel())
initializeAllPartialLh();
}
void PhyloSuperTreePlen::linkTrees() {
mapTrees();
}
double PhyloSuperTreePlen::optimizeAllBranches(int my_iterations, double tolerance, int maxNRStep) {
//initPartitionInfo(); // OLGA: not needed here
//cout<<"Optimizing all branches"<<endl;
for(int part = 0; part < size(); part++){
part_info[part].cur_score = 0.0;
}
return PhyloTree::optimizeAllBranches(my_iterations,tolerance, maxNRStep);
}
void PhyloSuperTreePlen::optimizeOneBranch(PhyloNode *node1, PhyloNode *node2, bool clearLH, int maxNRStep) {
SuperNeighbor *nei1 = (SuperNeighbor*)node1->findNeighbor(node2);
SuperNeighbor *nei2 = (SuperNeighbor*)node2->findNeighbor(node1);
int part;
current_it = (PhyloNeighbor*) node1->findNeighbor(node2);
current_it_back = (PhyloNeighbor*) node2->findNeighbor(node1);
for (part = 0; part < size(); part++) {
if (((SuperNeighbor*)current_it)->link_neighbors[part]) {
at(part)->current_it = ((SuperNeighbor*)current_it)->link_neighbors[part];
at(part)->current_it_back = ((SuperNeighbor*)current_it_back)->link_neighbors[part];
}
}
double current_len = current_it->length;
for (part = 0; part < size(); part++) {
at(part)->theta_computed = false;
}
//this->clearAllPartialLH();
PhyloTree::optimizeOneBranch(node1, node2, false, maxNRStep);
if (part_order.empty()) computePartitionOrder();
// bug fix: assign cur_score into part_info
#ifdef _OPENMP
#pragma omp parallel for private(part) schedule(dynamic) if(num_threads > 1)
#endif
for (int partid = 0; partid < size(); partid++) {
part = part_order_by_nptn[partid];
if (((SuperNeighbor*)current_it)->link_neighbors[part]) {
part_info[part].cur_score = at(part)->computeLikelihoodFromBuffer();
}
}
if(clearLH && current_len != current_it->length){
for (int part = 0; part < size(); part++) {
PhyloNeighbor *nei1_part = nei1->link_neighbors[part];
PhyloNeighbor *nei2_part = nei2->link_neighbors[part];
if(nei1_part){
((PhyloNode*)nei1_part->node)->clearReversePartialLh(((PhyloNode*)nei2_part->node));
((PhyloNode*)nei2_part->node)->clearReversePartialLh(((PhyloNode*)nei1_part->node));
}
}
}
// return tree_lh;
}
double PhyloSuperTreePlen::computeFunction(double value) {
double tree_lh = 0.0;
int ntrees = size();
if (!central_partial_lh) initializeAllPartialLh();
double lambda = value-current_it->length;
current_it->length = value;
current_it_back->length = value;
SuperNeighbor *nei1 = (SuperNeighbor*)current_it_back->node->findNeighbor(current_it->node);
SuperNeighbor *nei2 = (SuperNeighbor*)current_it->node->findNeighbor(current_it_back->node);
ASSERT(nei1 && nei2);
if (part_order.empty()) computePartitionOrder();
#ifdef _OPENMP
#pragma omp parallel for reduction(+: tree_lh) schedule(dynamic) if(num_threads > 1)
#endif
for (int partid = 0; partid < ntrees; partid++) {
int part = part_order_by_nptn[partid];
PhyloNeighbor *nei1_part = nei1->link_neighbors[part];
PhyloNeighbor *nei2_part = nei2->link_neighbors[part];
if (nei1_part && nei2_part) {
at(part)->current_it = nei1_part;
at(part)->current_it_back = nei2_part;
nei1_part->length += lambda*part_info[part].part_rate;
nei2_part->length += lambda*part_info[part].part_rate;
part_info[part].cur_score = at(part)->computeLikelihoodBranch(nei2_part,(PhyloNode*)nei1_part->node);
tree_lh += part_info[part].cur_score;
} else {
if (part_info[part].cur_score == 0.0)
part_info[part].cur_score = at(part)->computeLikelihood();
tree_lh += part_info[part].cur_score;
}
}
return -tree_lh;
}
double PhyloSuperTreePlen::computeLikelihoodBranch(PhyloNeighbor *dad_branch, PhyloNode *dad) {
current_it = dad_branch;
current_it_back = (PhyloNeighbor*)dad_branch->node->findNeighbor(dad);
return -computeFunction(dad_branch->length);
}
double PhyloSuperTreePlen::computeLikelihoodFromBuffer() {
//return -computeFunction(current_it->length);
double score = 0.0;
int part, ntrees = size();
for (part = 0; part < ntrees; part++) {
// assert(part_info[part].cur_score != 0.0);
score += part_info[part].cur_score;
}
return score;
}
void PhyloSuperTreePlen::computeFuncDerv(double value, double &df_ret, double &ddf_ret) {
// double tree_lh = 0.0;
double df = 0.0;
double ddf = 0.0;
int ntrees = size();
if (!central_partial_lh) initializeAllPartialLh();
double lambda = value-current_it->length;
current_it->length = value;
current_it_back->length = value;
SuperNeighbor *nei1 = (SuperNeighbor*)current_it_back->node->findNeighbor(current_it->node);
SuperNeighbor *nei2 = (SuperNeighbor*)current_it->node->findNeighbor(current_it_back->node);
ASSERT(nei1 && nei2);
if (part_order.empty()) computePartitionOrder();
#ifdef _OPENMP
#pragma omp parallel for reduction(+: df, ddf) schedule(dynamic) if(num_threads > 1)
#endif
for (int partid = 0; partid < ntrees; partid++) {
int part = part_order_by_nptn[partid];
double df_aux, ddf_aux;
PhyloNeighbor *nei1_part = nei1->link_neighbors[part];
PhyloNeighbor *nei2_part = nei2->link_neighbors[part];
if (nei1_part && nei2_part) {
at(part)->current_it = nei1_part;
at(part)->current_it_back = nei2_part;
nei1_part->length += lambda*part_info[part].part_rate;
nei2_part->length += lambda*part_info[part].part_rate;
if(nei1_part->length<-1e-4){
cout<<"lambda = "<<lambda<<endl;
cout<<"NEGATIVE BRANCH len = "<<nei1_part->length<<endl<<" rate = "<<part_info[part].part_rate<<endl;
ASSERT(0);
outError("shit!! ",__func__);
}
at(part)->computeLikelihoodDerv(nei2_part,(PhyloNode*)nei1_part->node, &df_aux, &ddf_aux);
df += part_info[part].part_rate*df_aux;
ddf += part_info[part].part_rate*part_info[part].part_rate*ddf_aux;
}
else {
if (part_info[part].cur_score == 0.0)
part_info[part].cur_score = at(part)->computeLikelihood();
}
}
df_ret = -df;
ddf_ret = -ddf;
}
NNIMove PhyloSuperTreePlen::getBestNNIForBran(PhyloNode *node1, PhyloNode *node2, NNIMove *nniMoves)
{
ASSERT(node1->degree() == 3 && node2->degree() == 3);
double backupScore = curScore;
SwapNNIParam nni_param;
// nni_param.node1/2_nei tell swapNNIBranch what to swap first
// ------------------------------------------------------------------
int cnt;
//NNIMove nniMoves[2];
bool newNNIMoves = false;
if (!nniMoves) {
// Initialize the 2 NNI moves
newNNIMoves = true;
nniMoves = new NNIMove[2];
nniMoves[0].ptnlh = nniMoves[1].ptnlh = NULL;
nniMoves[0].node1 = NULL;
}
if (nniMoves[0].node1) {
// assuming that node1Nei_it and node2Nei_it are defined in nniMoves structure
for (cnt = 0; cnt < 2; cnt++) {
// sanity check
if (!node1->findNeighbor((*nniMoves[cnt].node1Nei_it)->node)) outError(__func__);
if (!node2->findNeighbor((*nniMoves[cnt].node2Nei_it)->node)) outError(__func__);
}
} else {
FOR_NEIGHBOR_IT(node1, node2, node1_it) {
cnt = 0;
FOR_NEIGHBOR_IT(node2, node1, node2_it) {
// Initialize the 2 NNI moves
nniMoves[cnt].node1Nei_it = node1_it; // the same neighbor of node1 for cnt = 0 and cnt = 1
nniMoves[cnt].node2Nei_it = node2_it;
cnt++;
}
break;
}
}
// Initialize node1 and node2 in nniMoves
nniMoves[0].node1 = nniMoves[1].node1 = node1;
nniMoves[0].node2 = nniMoves[1].node2 = node2;
nniMoves[0].newloglh = nniMoves[1].newloglh = -DBL_MAX;
// check for compatibility with constraint
// check for consistency with constraint tree
for (cnt = 0; cnt < 2; cnt++) {
if (!constraintTree.isCompatible(nniMoves[cnt])) {
nniMoves[cnt].node1 = nniMoves[cnt].node2 = NULL;
}
}
//--------------------------------------------------------------------------
if (nniMoves[0].node1 || nniMoves[1].node1)
this->swapNNIBranch(0.0, node1, node2, &nni_param, nniMoves);
// restore curScore
curScore = backupScore;
NNIMove myMove;
if (nniMoves[0].newloglh > nniMoves[1].newloglh) {
myMove = nniMoves[0];
myMove.swap_id = 1;
} else {
myMove = nniMoves[1];
myMove.swap_id = 2;
}
if (newNNIMoves) {
delete [] nniMoves;
}
return myMove;
}
void PhyloSuperTreePlen::doNNIs(vector<NNIMove> &compatibleNNIs, bool changeBran) {
IQTree::doNNIs(compatibleNNIs, changeBran);
mapBranchLen();
//clearAllPartialLH();
}
void PhyloSuperTreePlen::getNNIType(PhyloNode *node1, PhyloNode *node2, vector<NNIType> &nni_type) {
int epsilon_cnt, part, ntrees=size();
nni_type.resize(ntrees, NNI_NO_EPSILON);
for(part=0; part<ntrees;part++){
totalNNIs++;
nni_type[part] = NNI_NO_EPSILON;
epsilon_cnt = 0;
FOR_NEIGHBOR_DECLARE(node1,NULL,nit){
if(!((SuperNeighbor*)*nit)->link_neighbors[part]) { epsilon_cnt++; }
}
FOR_NEIGHBOR(node2, node1, nit) {
if(!((SuperNeighbor*)*nit)->link_neighbors[part]) { epsilon_cnt++; }
}
if(epsilon_cnt == 0){
nni_type[part]=NNI_NO_EPSILON;
}else if(epsilon_cnt == 1){
nni_type[part] = NNI_ONE_EPSILON;
}else if(epsilon_cnt == 2){
nni_type[part]=NNI_TWO_EPSILON;
}else if(epsilon_cnt == 3){
nni_type[part]=NNI_THREE_EPSILON;
}else {
nni_type[part] = NNI_MANY_EPSILON;
}
}
}
void PhyloSuperTreePlen::doNNI(NNIMove &move, bool clearLH)
{
//checkBranchLen();
SuperNeighbor *nei1 = (SuperNeighbor*)move.node1->findNeighbor(move.node2);
SuperNeighbor *nei2 = (SuperNeighbor*)move.node2->findNeighbor(move.node1);
SuperNeighbor *node1_nei = (SuperNeighbor*)*move.node1Nei_it;
SuperNeighbor *node2_nei = (SuperNeighbor*)*move.node2Nei_it;
int part = 0, ntrees = size();
iterator it;
vector<NNIMove> part_move;
vector<NNIType> is_nni;
part_move.resize(ntrees);
getNNIType(move.node1, move.node2, is_nni);
for (it = begin(), part = 0; it != end(); it++, part++) {
if(is_nni[part] == NNI_NO_EPSILON){
PhyloNeighbor *nei1_part = nei1->link_neighbors[part];
PhyloNeighbor *nei2_part = nei2->link_neighbors[part];
part_move[part].node1 = (PhyloNode*)nei2_part->node;
part_move[part].node2 = (PhyloNode*)nei1_part->node;
part_move[part].node1Nei_it = part_move[part].node1->findNeighborIt(node1_nei->link_neighbors[part]->node);
part_move[part].node2Nei_it = part_move[part].node2->findNeighborIt(node2_nei->link_neighbors[part]->node);
}
}
// PhyloTree::doNNI(move,clearLH);
PhyloTree::doNNI(move,false);
PhyloNode *node1, *node2;
for (it = begin(), part = 0; it != end(); it++, part++) {
switch (is_nni[part]) {
case NNI_NO_EPSILON:
(*it)->doNNI(part_move[part],clearLH);
break;
case NNI_ONE_EPSILON:
linkBranch(part, nei1, nei2);
if (clearLH) {
// clear partial likelihood vector
node1 = (PhyloNode*)nei2->link_neighbors[part]->node;
node2 = (PhyloNode*)nei1->link_neighbors[part]->node;
nei1->link_neighbors[part]->clearPartialLh();
nei2->link_neighbors[part]->clearPartialLh();
node2->clearReversePartialLh(node1);
node1->clearReversePartialLh(node2);
}
break;
case NNI_TWO_EPSILON:
node1 = (PhyloNode*)nei2->link_neighbors[part]->node;
node2 = (PhyloNode*)nei1->link_neighbors[part]->node;
linkBranch(part, nei1, nei2);
if(clearLH){
// the check "&& !(PhyloNode*)nei2->link_neighbors[part]" is not needed,
// since the branch lengths are changed during the optimization
// and we anyway have to clearReversePartialLh
node2->clearReversePartialLh(node1);
node1->clearReversePartialLh(node2);
}
break;
case NNI_THREE_EPSILON:
linkBranch(part, nei1, nei2);
if (clearLH) {
// clear partial likelihood vector
node1 = (PhyloNode*)nei2->link_neighbors[part]->node;
node2 = (PhyloNode*)nei1->link_neighbors[part]->node;
node2->clearReversePartialLh(node1);
node1->clearReversePartialLh(node2);
}
break;
case NNI_MANY_EPSILON:
break;
}
}
}
double PhyloSuperTreePlen::swapNNIBranch(double cur_score, PhyloNode *node1, PhyloNode *node2, SwapNNIParam *nni_param, NNIMove *nniMoves) {
int i = 0, id = 0;
int part, ntrees = size();
uint64_t total_block_size = 0, total_scale_block_size = 0;
for (int j = 0; j < ntrees; j++) {
total_block_size += block_size[j];
total_scale_block_size += scale_block_size[j];
}
/*===========================================================================================
* Identify NNIType for partitions
*===========================================================================================*/
vector<NNIType> is_nni;
getNNIType(node1, node2, is_nni);
if(verbose_mode >= VB_MED){
for (part = 0; part < ntrees; part++)
switch (is_nni[part]) {
case NNI_NO_EPSILON:
allNNIcases_computed[0]++;
break;
case NNI_ONE_EPSILON:
allNNIcases_computed[1]++;
break;
case NNI_TWO_EPSILON:
allNNIcases_computed[2]++;
break;
case NNI_THREE_EPSILON:
allNNIcases_computed[3]++;
break;
case NNI_MANY_EPSILON:
allNNIcases_computed[4]++;
break;
}
}
//==================================================================================================
// SuperTREE: saving Neighbors and allocating new ones; assign which nodes/neighbors to be swapped.
//==================================================================================================
double old_brlen = node1->findNeighbor(node2)->length; // length of the branch between node1 and node2 on SuperTree before NNI
int IT_NUM = (params->nni5) ? 6 : 2;
NeighborVec::iterator it, saved_it[6], node_nei_it[4];
Node* neighbor_nodes[4];
saved_it[id++] = node1->findNeighborIt(node2);
saved_it[id++] = node2->findNeighborIt(node1);
//if (params->nni5) {
FOR_NEIGHBOR(node1, node2, it){
saved_it[id++] = (*it)->node->findNeighborIt(node1);
node_nei_it[i++] = it;
neighbor_nodes[i-1] = (*it)->node;
}
FOR_NEIGHBOR(node2, node1, it){
saved_it[id++] = (*it)->node->findNeighborIt(node2);
node_nei_it[i++] = it;
neighbor_nodes[i-1] = (*it)->node;
}
//}
// cout<<"------NODE_id check-----------------------------------"<<endl;
// for(part=0; part<ntrees; part++){
// cout<<"PART = "<<part<<endl;
// for(id=2; id<6; id++){
// if(node1->isNeighbor(neighbor_nodes[id-2])){
// if(((SuperNeighbor*)(node1->findNeighbor(neighbor_nodes[id-2])))->link_neighbors[part]){
// cout<<"node1: "<<"id = "<<id<<"; node_id = "<<
// ((SuperNeighbor*)(node1->findNeighbor(neighbor_nodes[id-2])))->link_neighbors[part]->node->id<<";"<<endl;
// } else {
// cout<<"node1: "<<"id = "<<id<<"; no neighbor;"<<endl;
// }
// } else if(node2->isNeighbor(neighbor_nodes[id-2])){
// if(((SuperNeighbor*)(node2->findNeighbor(neighbor_nodes[id-2])))->link_neighbors[part]){
// cout<<"node2: "<<"id = "<<id<<"; node_id = "<<
// ((SuperNeighbor*)(node2->findNeighbor(neighbor_nodes[id-2])))->link_neighbors[part]->node->id<<";"<<endl;
// } else {
// cout<<"node2: "<<"id = "<<id<<"; no neighbor;"<<endl;
// }
// }
// }
// cout<<"------"<<endl;
// for(id=2; id<6; id++){
// if(((SuperNeighbor*)(*node_nei_it[id-2]))->link_neighbors[part]){
// cout<<"id = "<<id<<"; node_id = "<<((SuperNeighbor*)(*node_nei_it[id-2]))->link_neighbors[part]->node->id<<";"<<endl;
// }
// }
// }
// cout<<"------------------------------------------------------"<<endl;
// reorient partial_lh in case of nni1
if (!params->nni5) {
reorientPartialLh((PhyloNeighbor*)node1->findNeighbor(node2), node1);
reorientPartialLh((PhyloNeighbor*)node2->findNeighbor(node1), node2);
}
/*------------------------------------------------------------------------------------
* Saving original neighbors:
* saved_nei[0] - node2 as a neighbor of node1
* saved_nei[1] - node1 as a neighbor of node2
* IF(nni5Branches)
* saved_nei[2(3)] - node1 as a neighbor of its nei1(nei2) different from node2
* saved_nei[4(5)] - node2 as a neighbor of its nei1(nei2) different from node1
*------------------------------------------------------------------------------------*/
SuperNeighbor *saved_nei[6];
// allocate new Super Neighbor pointers
for (id = 0; id < IT_NUM; id++) {
saved_nei[id] = (SuperNeighbor*)(*saved_it[id]);
*saved_it[id] = new SuperNeighbor(saved_nei[id]->node, saved_nei[id]->length);
(*saved_it[id])->id = saved_nei[id]->id;
for(part = 0; part < ntrees; part++)
((SuperNeighbor*)*saved_it[id])->link_neighbors.push_back(NULL);
}
// Getting NEW Neighbors: get the Neighbors again since they were saved for restoring purpose and replaced by new
SuperNeighbor *nei1_new = (SuperNeighbor*) node1->findNeighbor(node2);
SuperNeighbor *nei2_new = (SuperNeighbor*) node2->findNeighbor(node1);
// /* -------------------------------------------------------------------------------------------
// * NNI details: assigning nodes to be swapped on SuperTree
// * -------------------------------------------------------------------------------------------*/
//
// // node1_nei - one of the node1 neighbors, which is not node2
// NeighborVec::iterator node1_it = node1->findNeighborIt(nni_param->node1_nei->node);
// Neighbor *node1_nei = *node1_it;
//
// // *node2_its[0] - one of the node2 neighbors, which is not node1
// // *node2_its[1] - second neighbor of node2, which is not node1
// vector<NeighborVec::iterator> node2_its;
// node2_its.push_back(node2->findNeighborIt(nni_param->node2_nei->node));
//
// FOR_NEIGHBOR_DECLARE(node2, node1, node2_it){
// FOR_NEIGHBOR_DECLARE(node2,(*node2_it)->node,node2_it2)
// node2_its.push_back(node2_it2);
// }
// assert(node2_its.size() == 2);
/* =================================================================================================
* SubTREEs: saving Neighbors and allocating new ones.
* =================================================================================================*/
/*------------------------------------------------------------------------------------
* Variables to be used for saving/restoring purposes on SubTrees
*------------------------------------------------------------------------------------*/
vector<PhyloNeighbor*> sub_saved_nei1,sub_saved_nei2,sub_saved_nei;
vector<NeighborVec::iterator> sub_saved_it;
// Saving linked neighbor of node1->findNei(node2)
sub_saved_nei1.resize(ntrees);
// Saving linked neighbor of node2->findNei(node1)
sub_saved_nei2.resize(ntrees);
sub_saved_nei.resize(6*ntrees);
sub_saved_it.resize(6*ntrees);
/*---------------------------------------------------------
* For Restoring: saving branch lengths on SubTrees
*---------------------------------------------------------*/
/* NO_EPS: one/five branches need to be restored in nni1/nni5 cases respectively,
* but these branches are saved in saved_nei->link_neighbors, we won't store them again
* ONE_EPS: three branches need to be restored (stick to ids: 0,...,5)
* TWO_EPS: the image of central branch needs to be restored (the id for restoring [6*part+0])
* THREE_EPS: one branch needs to be restored: which the central is relinked to after NNI (the id for restoring [6*part+0])
* MANY_EPS: nothing to be restored
*/
double *sub_saved_branch = new double[6*ntrees];
/* ---------------------------------------------------------
* For Restoring: saving current likelihoods for SubTree
* ---------------------------------------------------------*/
double *saved_cur_score = new double[part_info.size()];
for (i = 0; i < part_info.size(); i++)
saved_cur_score[i] = part_info[i].cur_score;
/* -------------------------------------------------------------------------------------------------------------------
* Allocate new PhyloNeighbors:
* NO_EPS: 2 or 6 for nni1 and nni5 respectively; update link_neighbors for corresponding SuperNeighbors.
* ONE_EPS: 1 or 3 for nni1 and nni5 respectively; update link_neighbors for corresponding SuperNeighbors LATER
* (since it depends on particular NNI).
* -------------------------------------------------------------------------------------------------------------------*/
// Auxiliary variables: we allocate new PhyloNeighbor for [node_link->findNeighbor(nei_link)]
Node *node_link, *nei_link;
SuperNeighbor *nei;
// For ONE_epsilon case: saves "id" of the neighbors that have an empty image
int id_eps[part];
uint64_t lh_addr = 0, scale_addr = 0;
for(int partid = 0; partid < ntrees; partid++){
part = part_order[partid];
if(is_nni[part]==NNI_NO_EPSILON){
//evalNNIs++;
//part_info[part].evalNNIs++;
int mem_id = 0;
// one branch optimization ------------------------------------------------------------------
for(id = 0; id < 2; id++){
/*
for id=0, nei_link = node1->find(node2)->link->node = node2_link
for id=0, node_link = node2->find(node1)->link->node = node1_link
for id=0, saving iterator of neighbor of node1_link, that is node2_link;
then on this place we'll create a new PhyloNei
*/
nei_link = saved_nei[id]->link_neighbors[part]->node;
node_link = saved_nei[1-id]->link_neighbors[part]->node;
sub_saved_it[part*6 + id] = node_link->findNeighborIt(nei_link);
// Create a new PhyloNeighbor, with new partial lhs, scale number and set the branch id as before
*sub_saved_it[part*6 + id] = new PhyloNeighbor(nei_link, saved_nei[id]->link_neighbors[part]->length);
if (saved_nei[id]->link_neighbors[part]->partial_lh) {
((PhyloNeighbor*) (*sub_saved_it[part*6 + id]))->partial_lh = nni_partial_lh + (mem_id*total_block_size + lh_addr);
((PhyloNeighbor*) (*sub_saved_it[part*6 + id]))->scale_num = nni_scale_num + (mem_id*total_scale_block_size + scale_addr);
mem_id++;
}
(*sub_saved_it[part*6 + id])->id = saved_nei[id]->link_neighbors[part]->id;
// update link_neighbor[part]: for New SuperNeighbor we set the corresponding new PhyloNeighbor on partition part
((SuperNeighbor*)*saved_it[id])->link_neighbors[part] = (PhyloNeighbor*)*sub_saved_it[part*6 + id];
}
// optimization on 5 branches ------------------------------------------------------------------
if(params->nni5){
for(id = 2; id < 6; id ++){
nei_link = saved_nei[id]->link_neighbors[part]->node;
node_link = ((SuperNeighbor*)(*node_nei_it[id-2]))->link_neighbors[part]->node;
sub_saved_it[part*6 + id] = node_link->findNeighborIt(nei_link);
*sub_saved_it[part*6 + id] = new PhyloNeighbor(nei_link, saved_nei[id]->link_neighbors[part]->length);
if (saved_nei[id]->link_neighbors[part]->partial_lh) {
((PhyloNeighbor*) (*sub_saved_it[part*6 + id]))->partial_lh = nni_partial_lh + (mem_id*total_block_size + lh_addr);
((PhyloNeighbor*) (*sub_saved_it[part*6 + id]))->scale_num = nni_scale_num + (mem_id*total_scale_block_size + scale_addr);
mem_id++;
}
(*sub_saved_it[part*6 + id])->id = saved_nei[id]->link_neighbors[part]->id;
// update link_neighbor[part]
((SuperNeighbor*)*saved_it[id])->link_neighbors[part] = (PhyloNeighbor*)*sub_saved_it[part*6 + id];
}
ASSERT(mem_id == 2);
}
} else if(is_nni[part]==NNI_ONE_EPSILON){
int mem_id = 0;
// Make sure to update all the necessary link_neighbors and take care of branch lengths
// (increase/decrease by central branch where necessary).
nei1_new->link_neighbors[part] = saved_nei[0]->link_neighbors[part];
nei2_new->link_neighbors[part] = saved_nei[1]->link_neighbors[part];
// Change the length of branch, (node1,node2) WAS linked to (-=)
nei1_new->link_neighbors[part]->length -= old_brlen * part_info[part].part_rate;
nei2_new->link_neighbors[part]->length -= old_brlen * part_info[part].part_rate;
ASSERT(nei1_new->link_neighbors[part]->length >= 0.0);
// Allocate three new PhyloNeighbors.
// For nni1 only one of it will be actually used and which one depends on the NNI.
// We have this if condition, since saved_nei will be newly allocated neis in nni5 case,
// while saved_it are the actual neighbors and we don't want to mess them up
for(id = 2; id < 6; id++){
if(params->nni5){
nei = saved_nei[id];
} else {
nei = (SuperNeighbor*)(*saved_it[id]);
}
if(nei->link_neighbors[part]){
// nei_link is either node1 or node2 on SubTrees
nei_link = nei->link_neighbors[part]->node;
// node_link are nodes neighbors of node1 and node2 on SubTrees
node_link = ((SuperNeighbor*)(*node_nei_it[id-2]))->link_neighbors[part]->node;
sub_saved_it[part*6 + id] = node_link->findNeighborIt(nei_link);
// Saving branch lengths
sub_saved_branch[6*part + id] = nei->link_neighbors[part]->length;
*sub_saved_it[part*6 + id] = new PhyloNeighbor(nei_link, nei->link_neighbors[part]->length);
if (nei->link_neighbors[part]->partial_lh) {
((PhyloNeighbor*) (*sub_saved_it[part*6 + id]))->partial_lh = nni_partial_lh + (mem_id*total_block_size + lh_addr);
((PhyloNeighbor*) (*sub_saved_it[part*6 + id]))->scale_num = nni_scale_num + (mem_id*total_scale_block_size + scale_addr);
mem_id++;
}
(*sub_saved_it[part*6 + id])->id = nei->link_neighbors[part]->id;
// If nni5 we update the link neighbors already here, otherwise
// they will be updated for each NNI within the loop.
if(params->nni5){
((SuperNeighbor*)*saved_it[id])->link_neighbors[part] = (PhyloNeighbor*)*sub_saved_it[part*6 + id];
}
//cout<<"saved_it["<<id<<"]; neighbor->node->id = "<<(*sub_saved_it[part*6 + id])->node->id<<endl;
//cout<<"saved_it["<<id<<"]; node->id = "<<node_link->id<<endl;
} else {
id_eps[part] = id;
}
}
ASSERT(mem_id == 1);
}else if(is_nni[part]==NNI_THREE_EPSILON && params->nni5){
// you fill out link neighbors vector for newly allocated SuperNeighbors
for(id = 2; id < 6; id++){
if(saved_nei[id]->link_neighbors[part]){
((SuperNeighbor*)*saved_it[id])->link_neighbors[part] = saved_nei[id]->link_neighbors[part];
}
}
}else if(is_nni[part]==NNI_TWO_EPSILON && params->nni5){
// you fill out link neighbors vector for newly allocated SuperNeighbors
for(id = 2; id < 6; id++){
if(saved_nei[id]->link_neighbors[part]){
((SuperNeighbor*)*saved_it[id])->link_neighbors[part] = saved_nei[id]->link_neighbors[part];
}
}
}
lh_addr += block_size[part];
scale_addr += scale_block_size[part];
}
/* -------------------------------------------------------------------
* Variables to store the information about which nodes/neighbors
* to be swapped on SubTrees for the corresponding NNI on SuperTree
*
* node1 -> node1_link[part]
* node2 -> node2_link[part]
* node1_nei -> node1_link_nei[part]
* node2_nei -> node2_link_nei[part]
* -------------------------------------------------------------------*/
vector<PhyloNode*> node1_link,node2_link;
vector<PhyloNeighbor*> node1_link_nei,node2_link_nei;
vector<NeighborVec::iterator> node1_link_it, node2_link_it;
// Nodes which correspond to node1 and node2 on partitions
node1_link.resize(ntrees);
node2_link.resize(ntrees);
// Neighbors of node1_link and node2_link to be swapped during NNI
node1_link_nei.resize(ntrees);
node2_link_nei.resize(ntrees);
// iterators for the neighbors of node1_link and node2_link to be swapped
node1_link_it.resize(ntrees);
node2_link_it.resize(ntrees);
/*===========================================================================================
* MAIN:
* - do the NNI swap on SuperTree and perform the corresponding actions on SubTrees;
* - compute the likelihood of swapped topology;
* - swap back;
* - restore if necessary.
*===========================================================================================*/
int cnt;
for (cnt = 0; cnt < 2; cnt++) if (nniMoves[cnt].node1) // only if nniMove satisfy constraint
{
//cout<<"NNI Loop-----------------------------NNI."<<cnt<<endl;
NeighborVec::iterator node1_it = nniMoves[cnt].node1Nei_it;
NeighborVec::iterator node2_it = nniMoves[cnt].node2Nei_it;
Neighbor *node1_nei = *node1_it;
Neighbor *node2_nei = *node2_it;
//node2_it = node2_its[cnt];
//Neighbor *node2_nei = *node2_it;
// Define which nodes/neighbors to be swapped on SubTree ----------------------------
for(part=0; part<ntrees; part++)
if(is_nni[part]==NNI_NO_EPSILON){
node1_link[part] = (PhyloNode*) nei2_new->link_neighbors[part]->node;
node2_link[part] = (PhyloNode*) nei1_new->link_neighbors[part]->node;
node1_link_nei[part] = ((SuperNeighbor*)node1_nei)->link_neighbors[part];
node1_link_it[part] = node1_link[part]->findNeighborIt(node1_link_nei[part]->node);
node2_link_nei[part] = ((SuperNeighbor*)node2_nei)->link_neighbors[part];
node2_link_it[part] = node2_link[part]->findNeighborIt(node2_link_nei[part]->node);
}
// Do the NNI swap on SuperTrees ----------------------------------------------------
node1->updateNeighbor(node1_it, node2_nei);
node2_nei->node->updateNeighbor(node2, node1);
node2->updateNeighbor(node2_it, node1_nei);
node1_nei->node->updateNeighbor(node1, node2);
// Perform actions in accordance with the type of NNI for a given partition ---------
for(part = 0; part < ntrees; part++){
//cout<<"Partition: "<<part<<endl;
if(is_nni[part]==NNI_NO_EPSILON){
//cout<<part<<"- NO_EPS: do NNI swap"<<endl;
//allNNIcases_computed[0] += 1;
// reorient partial_lh before swap
at(part)->reorientPartialLh((PhyloNeighbor*)node1_link[part]->findNeighbor(node2_link[part]), node1_link[part]);
at(part)->reorientPartialLh((PhyloNeighbor*)node2_link[part]->findNeighbor(node1_link[part]), node2_link[part]);
// Do NNI swap on partition
node1_link[part]->updateNeighbor(node1_link_it[part], node2_link_nei[part]);
node2_link_nei[part]->node->updateNeighbor(node2_link[part], node1_link[part]);
node2_link[part]->updateNeighbor(node2_link_it[part], node1_link_nei[part]);
node1_link_nei[part]->node->updateNeighbor(node1_link[part], node2_link[part]);
for(id=0; id<IT_NUM; id++){
((PhyloNeighbor*)(*sub_saved_it[part*6+id]))->clearPartialLh();
}
//checkBranchLen();
} else if(is_nni[part]==NNI_MANY_EPSILON){
//cout<<part<<"- MANY_EPS: do nothing"<<endl;
// the NNI on SuperTree does not change anything on SubTree
} else if(is_nni[part]==NNI_THREE_EPSILON){
//cout<<part<<"- THREE_EPS: relink"<<endl;
// The central branch had no image before the NNI.
// Relink the central branch and take care of branch lengths.
// In the end restore one branch (valid for both nni1 and nni5).
linkBranch(part, nei1_new, nei2_new);
ASSERT(nei1_new->link_neighbors[part]);
// Save the branch length
if(cnt == 0)
sub_saved_branch[6*part] = nei1_new->link_neighbors[part]->length;
nei1_new->link_neighbors[part]->length += old_brlen * part_info[part].part_rate;
nei2_new->link_neighbors[part]->length += old_brlen * part_info[part].part_rate;
// since the branch length was changed we have to recompute the likelihood of the branch
part_info[part].cur_score = at(part)->computeLikelihoodBranch(nei1_new->link_neighbors[part],
(PhyloNode*)nei2_new->link_neighbors[part]->node);
}else if(is_nni[part]==NNI_TWO_EPSILON){
//cout<<part<<"- TWO_EPS: relink"<<endl;
/* In fact, before relinking the image of central branch is NULL (because we allocated
* new SuperNeighbor and filled the link_neighbors with NULL for all partitions).
* After relinking it can be either NULL or it should relink to the same branch as before.
* In the end restore one branch (valid for both nni1 and nni5).*/
// Save the branch length
if(cnt == 0)
sub_saved_branch[6*part] = saved_nei[0]->link_neighbors[part]->length;
linkBranch(part, nei1_new, nei2_new);
if(!nei1_new->link_neighbors[part]){
saved_nei[0]->link_neighbors[part]->length -= old_brlen * part_info[part].part_rate;
saved_nei[1]->link_neighbors[part]->length -= old_brlen * part_info[part].part_rate;
part_info[part].cur_score = at(part)->computeLikelihoodBranch(saved_nei[0]->link_neighbors[part],
(PhyloNode*)saved_nei[1]->link_neighbors[part]->node);
}
}else if(is_nni[part] == NNI_ONE_EPSILON){
//cout<<part<<"- ONE_EPS: relink, update the link_neighbors"<<endl;
/* The crazy case, which absorbs most of the bugs:(
* Lets say on SuperTree there are five branches, a,b,c,d and central e, and d has an empty image.
* The corresponding SubTree has 3 branches, a',b',c'.
* Before NNI central branch, e, has an image. Lets say it maps to a'.
* After NNI it will be remapped either to b' or c', depending on which nodes will be swapped.
* Update the corresponding link_neighbors. Make sure that link_neighbors for central branch e
* and for the one it is now mapped to (b' or c'), are the same.
* Decrease a' (done before). Increase b' or c' depending on the NNI. Restore three branches.*/
linkBranch(part, nei1_new, nei2_new);
ASSERT(nei1_new->link_neighbors[part]);
//cout<<"nei1_new->link_nei["<<part<<"]->node->id"<<nei1_new->link_neighbors[part]->node->id<<endl;
//cout<<"nei2_new->link_nei["<<part<<"]->node->id"<<nei2_new->link_neighbors[part]->node->id<<endl;
ASSERT(nei1_new->link_neighbors[part]->node->findNeighbor(nei2_new->link_neighbors[part]->node));
ASSERT(nei2_new->link_neighbors[part]->node->findNeighbor(nei1_new->link_neighbors[part]->node));
// nni1:
// - you need to update only one link_neighbor with new PhyloNeighbor
// (either node1->findNeighbor(node2) or node2->findNeighbor(node1))
// - the second is already linked to some existing PhyloNeighbor after linkBranch().
for(id=2; id<6; id++){
if(node2->isNeighbor(neighbor_nodes[id-2])){
// nei2_new should be updated
if(((SuperNeighbor*)node2->findNeighbor(neighbor_nodes[id-2]))->link_neighbors[part]){
//cout<<"node2: "<<"id = "<<id<<"; node_id = "<<((SuperNeighbor*)(node2->findNeighbor(neighbor_nodes[id-2])))->link_neighbors[part]->node->id<<";"<<endl;
if(((SuperNeighbor*)node2->findNeighbor(neighbor_nodes[id-2]))->link_neighbors[part]->node
== nei1_new->link_neighbors[part]->node){
//assert(((SuperNeighbor*)node2->findNeighbor(neighbor_nodes[id-2]))->link_neighbors[part]->node->id
// == (*sub_saved_it[part*6 + id])->node->id);
nei2_new->link_neighbors[part] = (PhyloNeighbor*)(*sub_saved_it[part*6 + id]);
//cout<<" nei id = "<<id<<"; node_id = "<<((SuperNeighbor*)(*node_nei_it[id-2]))->link_neighbors[part]->node->id<<";"<<endl;
//cout<<" sub "<<"id = "<<id<<"; node_id = "<<(*sub_saved_it[part*6 + id])->node->id<<";"<<endl;
break;
}
}
} else {
// nei1_new should be updated
ASSERT(node1->isNeighbor(neighbor_nodes[id-2]));
if(((SuperNeighbor*)node1->findNeighbor(neighbor_nodes[id-2]))->link_neighbors[part]){
//cout<<"node1: "<<"id = "<<id<<"; node_id = "<<((SuperNeighbor*)(node1->findNeighbor(neighbor_nodes[id-2])))->link_neighbors[part]->node->id<<";"<<endl;
if(((SuperNeighbor*)node1->findNeighbor(neighbor_nodes[id-2]))->link_neighbors[part]->node
== nei2_new->link_neighbors[part]->node){
//assert(((SuperNeighbor*)node1->findNeighbor(neighbor_nodes[id-2]))->link_neighbors[part]->node->id
// == (*sub_saved_it[part*6 + id])->node->id);
nei1_new->link_neighbors[part] = (PhyloNeighbor*)(*sub_saved_it[part*6 + id]);
//cout<<" nei id = "<<id<<"; node_id = "<<((SuperNeighbor*)(*node_nei_it[id-2]))->link_neighbors[part]->node->id<<";"<<endl;
//cout<<" sub "<<"id = "<<id<<"; node_id = "<<(*sub_saved_it[part*6 + id])->node->id<<";"<<endl;
break;
}
}
}
}
// Clear partial likelihoods for all three neighbors nei1/2->find(node1/2)
if(params->nni5 && cnt == 1){
for(id=2; id<6; id++){
if(id != id_eps[part]){
((PhyloNeighbor*)(*sub_saved_it[part*6 + id]))->clearPartialLh();
}
}
}
//cout<<"nei1_new->link_nei["<<part<<"]->node->id"<<nei1_new->link_neighbors[part]->node->id<<endl;
//cout<<"nei2_new->link_nei["<<part<<"]->node->id"<<nei2_new->link_neighbors[part]->node->id<<endl;
ASSERT(nei1_new->link_neighbors[part]->node->findNeighbor(nei2_new->link_neighbors[part]->node));
ASSERT(nei2_new->link_neighbors[part]->node->findNeighbor(nei1_new->link_neighbors[part]->node));
// Increase the branch to which the central is relinked.
nei1_new->link_neighbors[part]->length += old_brlen * part_info[part].part_rate;
nei2_new->link_neighbors[part]->length += old_brlen * part_info[part].part_rate;
} // end of else ONE_EPS case
} // end of part loop
/*===============================================================================================================================*
* Compute the score of the swapped topology *
*===============================================================================================================================*/
//cout<<"Before optimization"<<endl;
//mapBranchLen();
//checkBranchLen();
optimizeOneBranch(node1, node2, false, NNI_MAX_NR_STEP);
// double score = computeLikelihoodFromBuffer();
node1->findNeighbor(node2)->getLength(nniMoves[cnt].newLen[0]);
// if (verbose_mode >= VB_MED) {
// cout << "After_nni1 [" << score << "] ";
// printTree(cout);
// cout << endl;
// //for(part = 0; part < ntrees; part++)
// // cout << is_nni[part] << " ";
// //cout << endl;
// //cout<<"NNI count = "<<cnt<<endl;
// }
//cout<<"After optimization"<<endl;
//checkBranchLen();
// %%%%%%%%%%%%%%%%%%%%%%%% FIVE BRANCH OPTIMIZATION %%%%%%%%%%%%%%%%%%%%%%%%
i=1;
if (params->nni5) {
// ------ Optimization of branches incident to node1 ---------------
FOR_NEIGHBOR(node1, node2, it){
// Clear the partial likelihood of node1 neighbor: only for NO or ONE epsilon cases
for(part = 0; part < ntrees; part++)
if(((SuperNeighbor*)(*it))->link_neighbors[part] && (is_nni[part]==NNI_NO_EPSILON || is_nni[part]==NNI_ONE_EPSILON)){
node_link = ((SuperNeighbor*)(*it))->link_neighbors[part]->node;
nei_link = nei2_new->link_neighbors[part]->node; // this should be node 1 on subtree
// the problem is that for ONE_epsilon case node1 on subtree is equal to its neighbor node on subtree
// in this case we have to set nei_link to node2 on subtree
if(node_link->id == nei_link->id){
nei_link = nei1_new->link_neighbors[part]->node;
}
//cout<<"HERE it is: "<<((SuperNeighbor*)(*it))->link_neighbors[part]->node->id<<endl;
//cout<<nei2_new->link_neighbors[part]->node->id<<endl;
((PhyloNeighbor*)node_link->findNeighbor(nei_link))->clearPartialLh();
//cout<<"CASE:"<<is_nni[part]<<"Cleared partial likelihood"<<endl;
}
// Optimize the branch incident to node1
//cout<<"NNI5 : node1 : Before optimization"<<endl;
//checkBranchLen();
optimizeOneBranch(node1, (PhyloNode*) (*it)->node, false, NNI_MAX_NR_STEP);
node1->findNeighbor((*it)->node)->getLength(nniMoves[cnt].newLen[i]);
i++;
//cout<<"NNI5 : node1 : After optimization"<<endl;
//checkBranchLen();
}
// ------ Clear the partial likelihood on the central branch -------
for(part = 0; part < ntrees; part++)
if(((SuperNeighbor*)node2->findNeighbor(node1))->link_neighbors[part] && (is_nni[part]==NNI_NO_EPSILON || is_nni[part]==NNI_ONE_EPSILON)){
((SuperNeighbor*)node2->findNeighbor(node1))->link_neighbors[part]->clearPartialLh();
}
// ------ Optimization of branches incident to node2 ---------------
FOR_NEIGHBOR(node2, node1, it){
// Clear the partial likelihood of node2 neighbor: only for NO or ONE epsilon cases
for(part = 0; part < ntrees; part++){
if(((SuperNeighbor*)(*it))->link_neighbors[part] && (is_nni[part]==NNI_NO_EPSILON || is_nni[part]==NNI_ONE_EPSILON)){
node_link = ((SuperNeighbor*)(*it))->link_neighbors[part]->node;
nei_link = nei1_new->link_neighbors[part]->node;
if(node_link->id == nei_link->id){
nei_link = nei2_new->link_neighbors[part]->node;
}
((PhyloNeighbor*)node_link->findNeighbor(nei_link))->clearPartialLh();
//cout<<"CASE:"<<is_nni[part]<<"Cleared partial likelihood"<<endl;
}
}
// Optimize the branch incident to node2
optimizeOneBranch(node2, (PhyloNode*) (*it)->node, false, NNI_MAX_NR_STEP);
node2->findNeighbor((*it)->node)->getLength(nniMoves[cnt].newLen[i]);
i++;
}
}
double score = computeLikelihoodFromBuffer();
if (verbose_mode >= VB_DEBUG)
cout << "Log-likelihood: " << score << endl;
// %%%%%%%%%%%%%%%%%%%%%%%%%%% END of nni5branch %%%%%%%%%%%%%%%%%%%%%%%%%%%%
nniMoves[cnt].newloglh = score;
// if (verbose_mode >= VB_MED) {
// //this->clearAllPartialLH();
// //for(part = 0; part<ntrees; part++){
// // at(part)->clearAllPartialLH();
// //}
// //cout << "[" << this->computeLikelihood() << "] ";
// cout << "After_nni5 " << score << " ";
// printTree(cout);
// cout << endl;
// for(part = 0; part < ntrees; part++)
// cout << is_nni[part] << " ";
// cout << endl;
// }
// FOR SH-aLRT test
if (nniMoves[cnt].ptnlh)
computePatternLikelihood(nniMoves[cnt].ptnlh, &score);
// Save current tree for ufboot analysis
if (save_all_trees == 2) {
saveCurrentTree(score);
}
// // *************************** STORE INFO ABOUT NNI ***************************
//
// // Store information about this NNI for NNImove for SuperTree
// if (nni_param) {
//// if (verbose_mode >= VB_MAX)
//// printTree(cout, WT_BR_LEN + WT_NEWLINE);
// if (cnt == 0) {
// nni_param->nni1_score = score;
// nni_param->nni1_brlen = nei1_new->length;
// } else {
// nni_param->nni2_score = score;
// nni_param->nni2_brlen = nei1_new->length;
// }
// }
// // ***************************************************************************
// =============================== RESTORE INFO ==============================
// Restore the cur_score for partitions
for (i = 0; i < part_info.size(); i++)
part_info[i].cur_score = saved_cur_score[i];
//Restoring branch length on Super Tree
nei1_new->length = old_brlen;
nei2_new->length = old_brlen;
// Swap back on SuperTree --------------------------------------------------------------------------------------------------------------
node1->updateNeighbor(node1_it, node1_nei);
node1_nei->node->updateNeighbor(node2, node1);
node2->updateNeighbor(node2_it, node2_nei);
node2_nei->node->updateNeighbor(node1, node2);
//Restoring 4 branches around central?
if(params->nni5){
for(id=2;id<6;id++){
(*saved_it[id])->length = saved_nei[id]->length;
(*node_nei_it[id-2])->length = saved_nei[id]->length;
}
}
// Swap back or relink back on SubTrees------------------------------------------------------------------------------------------------
for(part = 0; part < ntrees; part++){
if(is_nni[part]==NNI_NO_EPSILON){
// reorient partial_lh before swap
at(part)->reorientPartialLh((PhyloNeighbor*)node1_link[part]->findNeighbor(node2_link[part]), node1_link[part]);
at(part)->reorientPartialLh((PhyloNeighbor*)node2_link[part]->findNeighbor(node1_link[part]), node2_link[part]);
node1_link[part]->updateNeighbor(node1_link_it[part], node1_link_nei[part]);
node1_link_nei[part]->node->updateNeighbor(node2_link[part], node1_link[part]);
node2_link[part]->updateNeighbor(node2_link_it[part], node2_link_nei[part]);
node2_link_nei[part]->node->updateNeighbor(node1_link[part], node2_link[part]);
//Restoring the branch length on the SubTree
node1_link[part]->findNeighbor(node2_link[part])->length = saved_nei[0]->link_neighbors[part]->length;
node2_link[part]->findNeighbor(node1_link[part])->length = saved_nei[0]->link_neighbors[part]->length;
if(params->nni5){
for(id = 2; id < 6; id++){
((SuperNeighbor*)(*saved_it[id]))->link_neighbors[part]->length = saved_nei[id]->link_neighbors[part]->length;
((SuperNeighbor*)(*node_nei_it[id-2]))->link_neighbors[part]->length = saved_nei[id]->link_neighbors[part]->length;
}
}
//mapBranchLen();
} else if(is_nni[part]==NNI_ONE_EPSILON){
//linkCheckRe(part,node1,node2,sub_saved_nei2[part],sub_saved_nei1[part]);
//linkCheckRe(part,node2,node1,sub_saved_nei1[part],sub_saved_nei2[part]);
// Relink back
linkBranch(part, nei1_new, nei2_new);
ASSERT(nei1_new->link_neighbors[part]->node == saved_nei[0]->link_neighbors[part]->node);
ASSERT(nei2_new->link_neighbors[part]->node == saved_nei[1]->link_neighbors[part]->node);
// Restore three branches
for(id=2; id<6; id++){
if(((SuperNeighbor*)*saved_it[id])->link_neighbors[part]){
(*sub_saved_it[part*6+id])->length = sub_saved_branch[6*part + id];
((SuperNeighbor*)*saved_it[id])->link_neighbors[part]->length = sub_saved_branch[6*part + id];
((SuperNeighbor*)*node_nei_it[id-2])->link_neighbors[part]->length = sub_saved_branch[6*part + id];
}
}
} else if(is_nni[part]==NNI_THREE_EPSILON){
nei1_new->link_neighbors[part]->length = sub_saved_branch[6*part];
nei2_new->link_neighbors[part]->length = sub_saved_branch[6*part];
//linkBranch(part, nei1_new, nei2_new);
} else if(is_nni[part]==NNI_TWO_EPSILON){
//linkBranch(part, nei1_new, nei2_new);
saved_nei[0]->link_neighbors[part]->length = sub_saved_branch[6*part];
saved_nei[1]->link_neighbors[part]->length = sub_saved_branch[6*part];
nei1_new->link_neighbors[part] = NULL;
nei2_new->link_neighbors[part] = NULL;
} else if(is_nni[part]==NNI_MANY_EPSILON){
// There is no need to restore anything
}
}
//cout<<"in NNI1end ---- logL = "<<this->computeLikelihood()<<endl;
} // end of for(cnt)
//=============================================================================================================================================================
// Restoring after 2 NNIs
//=============================================================================================================================================================
// Restoring information for SuperTree ------------------------------------------------------------------------------------------------------------
// restore the Neighbors*
for (id = IT_NUM-1; id >= 0; id--) {
if (*saved_it[id] == current_it) current_it = (SuperNeighbor*) saved_nei[id];
if (*saved_it[id] == current_it_back) current_it_back = (SuperNeighbor*) saved_nei[id];
delete (*saved_it[id]);
(*saved_it[id]) = saved_nei[id];
}
// restore the length of 4 branches around node1, node2
// since you have restored the neighbors and by this also the correct branch lengths,
// now just restore branch lengths of the second corresponding neighbors
FOR_NEIGHBOR(node1, node2, it)
(*it)->length = (*it)->node->findNeighbor(node1)->length;
FOR_NEIGHBOR(node2, node1, it)
(*it)->length = (*it)->node->findNeighbor(node2)->length;
// Restoring information for SubTrees ------------------------------------------------------------------------------------------------------------
for(part = 0; part < ntrees; part++){
if(is_nni[part] == NNI_NO_EPSILON){
// restore the Neighbors*
for (i = IT_NUM-1; i >= 0; i--) {
if((*sub_saved_it[part*6+i])){
// aligned_free(((PhyloNeighbor*) *sub_saved_it[part*6+i])->scale_num);
// aligned_free(((PhyloNeighbor*) *sub_saved_it[part*6+i])->partial_lh);
if (*sub_saved_it[part*6+i] == at(part)->current_it) at(part)->current_it = saved_nei[i]->link_neighbors[part];
if (*sub_saved_it[part*6+i] == at(part)->current_it_back) at(part)->current_it_back = saved_nei[i]->link_neighbors[part];
delete (*sub_saved_it[part*6+i]);
(*sub_saved_it[part*6+i]) = saved_nei[i]->link_neighbors[part];
}
}
// restore the length of 4 branches around node1_link[part], node2_link[part]
node1_link[part] = (PhyloNode*)(saved_nei[1]->link_neighbors[part]->node);
node2_link[part] = (PhyloNode*)(saved_nei[0]->link_neighbors[part]->node);
FOR_NEIGHBOR(node1_link[part], node2_link[part], it)
(*it)->length = (*it)->node->findNeighbor(node1_link[part])->length;
FOR_NEIGHBOR(node2_link[part], node1_link[part], it)
(*it)->length = (*it)->node->findNeighbor(node2_link[part])->length;
} else if(is_nni[part] == NNI_ONE_EPSILON){
// Delete the allocated neighbors and restore from saved neighbors
for (id = 5; id >= 2; id--) {
//if((*sub_saved_it[part*6+id])){
if(((SuperNeighbor*)(*node_nei_it[id-2]))->link_neighbors[part]){
// aligned_free(((PhyloNeighbor*) *sub_saved_it[part*6+id])->scale_num);
// aligned_free(((PhyloNeighbor*) *sub_saved_it[part*6+id])->partial_lh);
// It was commented, not sure why.. Just keep in mind------------------
if (*sub_saved_it[part*6+id] == at(part)->current_it)
at(part)->current_it = saved_nei[id]->link_neighbors[part];
if (*sub_saved_it[part*6+id] == at(part)->current_it_back)
at(part)->current_it_back = saved_nei[id]->link_neighbors[part];
//---------------------------------------------------------------------
delete (*sub_saved_it[part*6+id]);
(*sub_saved_it[part*6+id]) = ((SuperNeighbor*)(*saved_it[id]))->link_neighbors[part];
}
}
// Increase the central branch, since the length that was saved, was decreased
saved_nei[0]->link_neighbors[part]->length += old_brlen * part_info[part].part_rate;
saved_nei[1]->link_neighbors[part]->length += old_brlen * part_info[part].part_rate;
}
}
//mapBranchLen();
//cout<<"In the end of swap NNI"<<endl;
//checkBranchLen();
//------------------------------------------------------------------------------------------------------------------------------------------------
//if(score_mine != this->computeLikelihood())
// cout<<"Something weird happens during NNI evaluation..." << score_mine << " " << computeLikelihood() <<endl;
delete [] saved_cur_score;
delete [] sub_saved_branch;
return cur_score;
}
void PhyloSuperTreePlen::linkCheck(int part,Node* node, Node* dad, PhyloNeighbor* saved_link_dad_nei){
NeighborVec::iterator it;
SuperNeighbor *dad_nei = (SuperNeighbor*)dad->findNeighbor(node);
SuperNeighbor *node_nei = (SuperNeighbor*)node->findNeighbor(dad);
FOR_NEIGHBOR(node, dad, it){
if(((SuperNeighbor*)(*it))->link_neighbors[part] == saved_link_dad_nei){
((SuperNeighbor*)(*it))->link_neighbors[part] = dad_nei->link_neighbors[part];
((SuperNeighbor*)((*it)->node->findNeighbor(node)))->link_neighbors[part] = node_nei->link_neighbors[part];
linkCheck(part, (*it)->node, node, saved_link_dad_nei);
}
}
}
void PhyloSuperTreePlen::linkCheckRe(int part,Node* node, Node* dad, PhyloNeighbor* saved_link_dad_nei,PhyloNeighbor* saved_link_node_nei){
NeighborVec::iterator it;
FOR_NEIGHBOR(node, dad, it){
if(((SuperNeighbor*)(*it))->link_neighbors[part] == ((SuperNeighbor*)dad->findNeighbor(node))->link_neighbors[part]){
linkCheckRe(part, (*it)->node, node, saved_link_dad_nei, saved_link_node_nei);
((SuperNeighbor*)(*it))->link_neighbors[part] = saved_link_dad_nei;
((SuperNeighbor*)((*it)->node->findNeighbor(node)))->link_neighbors[part] = saved_link_node_nei;
}
}
}
//void PhyloSuperTreePlen::restoreAllBrans(PhyloNode *node, PhyloNode *dad) {
// IQTree::restoreAllBrans(node,dad);
// mapTrees();
//}
bool PhyloSuperTreePlen::checkBranchLen(){
// NodeVector nodes1,nodes2;
// int i;
// getBranches(nodes1, nodes2);
// double *checkVAL = new double[branchNum];
// for(int part = 0; part < size(); part++){
// memset(checkVAL, 0, at(part)->branchNum*sizeof(double));
// for (i = 0; i < nodes1.size(); i++){
// if(((SuperNeighbor*)nodes1[i]->findNeighbor(nodes2[i]))->link_neighbors[part])
// checkVAL[((SuperNeighbor*)nodes1[i]->findNeighbor(nodes2[i]))->link_neighbors[part]->id] += nodes1[i]->findNeighbor(nodes2[i])->length * part_info[part].part_rate;
// }
// NodeVector nodes1_sub, nodes2_sub;
// at(part)->getBranches(nodes1_sub, nodes2_sub);
// for(int j = 0; j<nodes1_sub.size();j++)
// if(fabs(nodes1_sub[j]->findNeighbor(nodes2_sub[j])->length-checkVAL[nodes1_sub[j]->findNeighbor(nodes2_sub[j])->id])>0.0001){
// //drawTree(cout, WT_BR_SCALE + WT_INT_NODE + WT_BR_LEN);
// printMapInfo();
// cout<<endl;
// cout<<"Partition = "<<part<<", Branch id = "<<nodes1_sub[j]->findNeighbor(nodes2_sub[j])->id<<endl;
// outError("Branches on SuperTree and SubTree do not match!!",__func__);
// }
//
// }
// delete [] checkVAL;
return true;
}
void PhyloSuperTreePlen::mapBranchLen()
{
NodeVector nodes1,nodes2;
int i;
getBranches(nodes1, nodes2);
double *checkVAL = new double[branchNum];
for(int part = 0; part < size(); part++){
memset(checkVAL,0,at(part)->branchNum*sizeof(double));
for (i = 0; i < nodes1.size(); i++){
if(((SuperNeighbor*)nodes1[i]->findNeighbor(nodes2[i]))->link_neighbors[part])
checkVAL[((SuperNeighbor*)nodes1[i]->findNeighbor(nodes2[i]))->link_neighbors[part]->id] +=
nodes1[i]->findNeighbor(nodes2[i])->length * part_info[part].part_rate;
}
NodeVector nodes1_sub, nodes2_sub;
at(part)->getBranches(nodes1_sub, nodes2_sub);
for(int j = 0; j<nodes1_sub.size();j++){
nodes1_sub[j]->findNeighbor(nodes2_sub[j])->length = checkVAL[nodes1_sub[j]->findNeighbor(nodes2_sub[j])->id];
nodes2_sub[j]->findNeighbor(nodes1_sub[j])->length = checkVAL[nodes1_sub[j]->findNeighbor(nodes2_sub[j])->id];
}
}
delete [] checkVAL;
}
void PhyloSuperTreePlen::mapBranchLen(int part)
{
NodeVector nodes1,nodes2;
int i;
getBranches(nodes1, nodes2);
double *checkVAL = new double[branchNum];
memset(checkVAL,0,at(part)->branchNum*sizeof(double));
for (i = 0; i < nodes1.size(); i++){
if(((SuperNeighbor*)nodes1[i]->findNeighbor(nodes2[i]))->link_neighbors[part])
checkVAL[((SuperNeighbor*)nodes1[i]->findNeighbor(nodes2[i]))->link_neighbors[part]->id] +=
nodes1[i]->findNeighbor(nodes2[i])->length * part_info[part].part_rate;
}
NodeVector nodes1_sub, nodes2_sub;
at(part)->getBranches(nodes1_sub, nodes2_sub);
for(int j = 0; j<nodes1_sub.size();j++){
nodes1_sub[j]->findNeighbor(nodes2_sub[j])->length = checkVAL[nodes1_sub[j]->findNeighbor(nodes2_sub[j])->id];
nodes2_sub[j]->findNeighbor(nodes1_sub[j])->length = checkVAL[nodes1_sub[j]->findNeighbor(nodes2_sub[j])->id];
}
delete [] checkVAL;
}
void PhyloSuperTreePlen::printMapInfo() {
NodeVector nodes1, nodes2;
getBranches(nodes1, nodes2);
int part = 0;
drawTree(cout, WT_BR_SCALE | WT_INT_NODE | WT_TAXON_ID | WT_NEWLINE | WT_BR_LEN);
for (iterator it = begin(); it != end(); it++, part++) {
cout << "Subtree for partition " << part << endl;
(*it)->drawTree(cout, WT_BR_SCALE | WT_INT_NODE | WT_TAXON_ID | WT_NEWLINE | WT_BR_LEN);
for (int i = 0; i < nodes1.size(); i++) {
PhyloNeighbor *nei1 = ((SuperNeighbor*)nodes1[i]->findNeighbor(nodes2[i]))->link_neighbors[part];
PhyloNeighbor *nei2 = ((SuperNeighbor*)nodes2[i]->findNeighbor(nodes1[i]))->link_neighbors[part];
cout << nodes1[i]->findNeighbor(nodes2[i])->id << ":";
if (nodes1[i]->isLeaf()) cout << nodes1[i]->name; else cout << nodes1[i]->id;
cout << ",";
if (nodes2[i]->isLeaf()) cout << nodes2[i]->name; else cout << nodes2[i]->id;
cout <<"("<<nodes1[i]->findNeighbor(nodes2[i])->length<<")"<< " -> ";
if (nei2) {
cout << nei2->id << ":";
if (nei2->node->isLeaf())
cout << nei2->node->name;
else cout << nei2->node->id;
}
else cout << -1;
cout << ",";
if (nei1){
if (nei1->node->isLeaf())
cout << nei1->node->name;
else cout << nei1->node->id;
cout <<"("<<nei1->length<<")";
}
else cout << -1;
cout << endl;
}
}
}
void PhyloSuperTreePlen::initPartitionInfo() {
//PhyloSuperTree::initPartitionInfo();
for (int part = 0; part < size(); part++){
if(part_info[part].part_rate == 0.0) { part_info[part].part_rate = 1.0; }
part_info[part].cur_score = 0.0;
}
}
void PhyloSuperTreePlen::printNNIcasesNUM(){
cout<<"For each \"NNI case\" on subtree the number of times it appeared during NNI evaluation:"<<endl;
cout<<"Case 1: NO_EPS = "<<allNNIcases_computed[0]<<endl;
cout<<"Case 2: ONE_EPS = "<<allNNIcases_computed[1]<<endl;
cout<<"Case 3: TWO_EPS = "<<allNNIcases_computed[2]<<endl;
cout<<"Case 4: THREE_EPS = "<<allNNIcases_computed[3]<<endl;
cout<<"Case 5: MANY_EPS = "<<allNNIcases_computed[4]<<endl;
}
void PhyloSuperTreePlen::computeBranchLengths()
{
}
int PhyloSuperTreePlen::fixNegativeBranch(bool force, Node *node, Node *dad) {
mapTrees();
int fixed = 0;
for (iterator it = begin(); it != end(); it++) {
(*it)->initializeAllPartialPars();
(*it)->clearAllPartialLH();
fixed += (*it)->fixNegativeBranch(force);
(*it)->clearAllPartialLH();
}
// FOR OLGA: because this check is not performed, branch lengths of user tree will change even with -fixbr command line
if (fixed) {
PhyloSuperTree::computeBranchLengths();
// it is necessary to map the branch lengths from supertree into gene trees!
mapTrees();
}
return fixed;
}
void PhyloSuperTreePlen::changeNNIBrans(NNIMove nnimove) {
PhyloTree::changeNNIBrans(nnimove);
//mapBranchLen();
}
/**
initialize partial_lh vector of all PhyloNeighbors, allocating central_partial_lh
*/
void PhyloSuperTreePlen::initializeAllPartialLh() {
iterator it;
int part, partid;
int ntrees = size();
block_size.resize(ntrees);
scale_block_size.resize(ntrees);
vector<uint64_t> mem_size, lh_cat_size, buffer_size;
mem_size.resize(ntrees);
lh_cat_size.resize(ntrees);
buffer_size.resize(ntrees);
uint64_t
total_mem_size = 0,
total_block_size = 0,
total_scale_block_size = 0,
total_lh_cat_size = 0,
total_buffer_size = 0;
if (part_order.empty())
computePartitionOrder();
for (partid = 0; partid < ntrees; partid++) {
part = part_order[partid];
it = begin() + part;
// extra #numStates for ascertainment bias correction
mem_size[part] = get_safe_upper_limit((*it)->getAlnNPattern()) + get_safe_upper_limit((*it)->aln->num_states);
size_t mem_cat_size = mem_size[part] * (*it)->getRate()->getNRate() *
(((*it)->model_factory->fused_mix_rate)? 1 : (*it)->getModel()->getNMixtures());
block_size[part] = mem_cat_size * (*it)->aln->num_states;
scale_block_size[part] = mem_cat_size;
lh_cat_size[part] = mem_size[part] * (*it)->getRate()->getNDiscreteRate() *
(((*it)->model_factory->fused_mix_rate)? 1 : (*it)->getModel()->getNMixtures());
total_mem_size += mem_size[part];
total_block_size += block_size[part];
total_scale_block_size += scale_block_size[part];
total_lh_cat_size += lh_cat_size[part];
total_buffer_size += (buffer_size[part] = (*it)->getBufferPartialLhSize());
}
if (!_pattern_lh)
_pattern_lh = aligned_alloc<double>(total_mem_size);
at(part_order[0])->_pattern_lh = _pattern_lh;
if (!_pattern_lh_cat)
_pattern_lh_cat = aligned_alloc<double>(total_lh_cat_size);
at(part_order[0])->_pattern_lh_cat = _pattern_lh_cat;
if (!theta_all)
theta_all = aligned_alloc<double>(total_block_size);
if (!buffer_scale_all)
buffer_scale_all = aligned_alloc<double>(total_mem_size);
if (!buffer_partial_lh)
buffer_partial_lh = aligned_alloc<double>(total_buffer_size);
at(part_order[0])->theta_all = theta_all;
at(part_order[0])->buffer_scale_all = buffer_scale_all;
at(part_order[0])->buffer_partial_lh = buffer_partial_lh;
if (!ptn_freq) {
ptn_freq = aligned_alloc<double>(total_mem_size);
ptn_freq_computed = false;
}
at(part_order[0])->ptn_freq = ptn_freq;
at(part_order[0])->ptn_freq_computed = false;
if (!ptn_invar)
ptn_invar = aligned_alloc<double>(total_mem_size);
at(part_order[0])->ptn_invar = ptn_invar;
// size_t IT_NUM = (params->nni5) ? 6 : 2;
size_t IT_NUM = 2;
if (!nni_partial_lh) {
nni_partial_lh = aligned_alloc<double>(IT_NUM*total_block_size);
}
at(part_order[0])->nni_partial_lh = nni_partial_lh;
if (!nni_scale_num) {
nni_scale_num = aligned_alloc<UBYTE>(IT_NUM*total_scale_block_size);
}
at(part_order[0])->nni_scale_num = nni_scale_num;
for (partid = 1; partid < ntrees; partid++) {
part = part_order[partid-1];
it = begin() + part_order[partid];
iterator prev_it = begin()+part_order[partid-1];
(*it)->_pattern_lh = (*prev_it)->_pattern_lh + mem_size[part];
(*it)->_pattern_lh_cat = (*prev_it)->_pattern_lh_cat + lh_cat_size[part];
(*it)->theta_all = (*prev_it)->theta_all + block_size[part];
(*it)->buffer_scale_all = (*prev_it)->buffer_scale_all + mem_size[part];
(*it)->buffer_partial_lh = (*prev_it)->buffer_partial_lh + buffer_size[part];
(*it)->ptn_freq = (*prev_it)->ptn_freq + mem_size[part];
(*it)->ptn_freq_computed = false;
(*it)->ptn_invar = (*prev_it)->ptn_invar + mem_size[part];
(*it)->nni_partial_lh = (*prev_it)->nni_partial_lh + IT_NUM*block_size[part];
(*it)->nni_scale_num = (*prev_it)->nni_scale_num + IT_NUM*scale_block_size[part];
}
// compute total memory for all partitions
uint64_t total_partial_lh_entries = 0, total_scale_num_entries = 0, total_partial_pars_entries = 0;
partial_lh_entries.resize(ntrees);
scale_num_entries.resize(ntrees);
partial_pars_entries.resize(ntrees);
for (it = begin(), part = 0; it != end(); it++, part++) {
(*it)->getMemoryRequired(partial_lh_entries[part], scale_num_entries[part], partial_pars_entries[part]);
total_partial_lh_entries += partial_lh_entries[part];
total_scale_num_entries += scale_num_entries[part];
total_partial_pars_entries += partial_pars_entries[part];
}
// allocate central memory for all partitions
if (!central_partial_lh) {
try {
central_partial_lh = aligned_alloc<double>(total_partial_lh_entries);
central_scale_num = aligned_alloc<UBYTE>(total_scale_num_entries);
} catch (std::bad_alloc &ba) {
outError("Not enough memory for partial likelihood vectors (bad_alloc)");
}
}
// if (!central_partial_pars) {
// try {
// central_partial_pars = aligned_alloc<UINT>(total_partial_pars_entries);
// } catch (std::bad_alloc &ba) {
// outError("Not enough memory for partial parsimony vectors (bad_alloc)");
// }
// }
// assign individual chunk just to prevent reallocation of memory, they will not be used
for (it = begin(); it != end(); it++) {
(*it)->central_partial_lh = central_partial_lh;
(*it)->central_scale_num = central_scale_num;
// (*it)->central_partial_pars = central_partial_pars;
}
double *lh_addr = central_partial_lh;
UBYTE *scale_addr = central_scale_num;
UINT *pars_addr = central_partial_pars;
clearAllPartialLH(true);
initializeAllPartialLh(lh_addr, scale_addr, pars_addr);
ASSERT((lh_addr - central_partial_lh) < total_partial_lh_entries*sizeof(double) && lh_addr > central_partial_lh);
tip_partial_lh = NULL;
for (it = begin(), part = 0; it != end(); it++, part++) {
(*it)->tip_partial_lh = lh_addr;
uint64_t tip_partial_lh_size = (*it)->aln->num_states * ((*it)->aln->STATE_UNKNOWN+1) * (*it)->model->getNMixtures();
tip_partial_lh_size = ((tip_partial_lh_size+3)/4)*4;
lh_addr += tip_partial_lh_size;
}
// 2016-09-29: redirect partial_lh when root does not occur in partition tree
SuperNeighbor *root_nei = (SuperNeighbor*)root->neighbors[0];
for (it = begin(), part = 0; it != end(); it++, part++) {
if (root_nei->link_neighbors[part])
continue;
NodeVector nodes;
(*it)->getInternalNodes(nodes);
for (NodeVector::iterator nit = nodes.begin(); nit != nodes.end(); nit++) {
bool has_partial_lh = false;
FOR_NEIGHBOR_IT(*nit, NULL, neiit)
if ( ((PhyloNeighbor*)(*neiit)->node->findNeighbor(*nit))->partial_lh) {
has_partial_lh = true;
break;
}
if (has_partial_lh)
continue;
// add partial_lh
PhyloNeighbor *back_nei = (PhyloNeighbor*)(*nit)->neighbors[0]->node->findNeighbor(*nit);
back_nei->partial_lh = lh_addr;
back_nei->scale_num = scale_addr;
lh_addr = lh_addr + block_size[part];
scale_addr = scale_addr + scale_block_size[part];
}
}
}
void PhyloSuperTreePlen::initializeAllPartialLh(double* &lh_addr, UBYTE* &scale_addr, UINT* &pars_addr, PhyloNode *node, PhyloNode *dad) {
if (!node)
node = (PhyloNode*) root;
if (dad) {
// assign a region in central_partial_lh to both Neihgbors (dad->node, and node->dad)
SuperNeighbor *nei = (SuperNeighbor*) node->findNeighbor(dad);
SuperNeighbor *nei_back = (SuperNeighbor*) dad->findNeighbor(node);
for (int partid = 0; partid < size(); partid++) {
int part = part_order[partid];
PhyloNeighbor *nei_part = nei->link_neighbors[part];
if (!nei_part) continue;
PhyloNeighbor *nei_part_back = nei_back->link_neighbors[part];
if (params->lh_mem_save == LM_PER_NODE) {
if (!nei_part_back->node->isLeaf()) {
if (!nei_part_back->partial_lh) {
nei_part_back->partial_lh = lh_addr;
nei_part_back->scale_num = scale_addr;
lh_addr = lh_addr + block_size[part];
scale_addr = scale_addr + scale_block_size[part];
}
} else {
nei_part_back->partial_lh = NULL;
nei_part_back->scale_num = NULL;
}
// nei_part->partial_lh = NULL;
// nei_part->scale_num = NULL;
} else {
if (nei_part->node->isLeaf()) {
nei_part->partial_lh = NULL; // do not allocate memory for tip, use tip_partial_lh instead
nei_part->scale_num = NULL;
} else if (!nei_part->partial_lh) {
nei_part->partial_lh = lh_addr;
nei_part->scale_num = scale_addr;
lh_addr = lh_addr + block_size[part];
scale_addr = scale_addr + scale_block_size[part];
}
// nei_part->partial_pars = pars_addr;
// pars_addr += partial_pars_entries[part];
nei_part = nei_back->link_neighbors[part];
if (nei_part->node->isLeaf()) {
nei_part->partial_lh = NULL; // do not allocate memory for tip, use tip_partial_lh instead
nei_part->scale_num = NULL;
} else if (!nei_part->partial_lh) {
nei_part->partial_lh = lh_addr;
nei_part->scale_num = scale_addr;
lh_addr = lh_addr + block_size[part];
scale_addr = scale_addr + scale_block_size[part];
}
// nei_part->partial_pars = pars_addr;
// pars_addr += partial_pars_entries[part];
}
}
}
FOR_NEIGHBOR_IT(node, dad, it) initializeAllPartialLh(lh_addr, scale_addr, pars_addr, (PhyloNode*) (*it)->node, node);
}
void PhyloSuperTreePlen::initializeAllPartialLh(int &index, int &indexlh, PhyloNode *node, PhyloNode *dad) {
// this function should not be used, assertion raised if accidentally called
ASSERT(0);
}
void PhyloSuperTreePlen::reorientPartialLh(PhyloNeighbor* dad_branch, Node *dad) {
SuperNeighbor *sdad_branch = (SuperNeighbor*) dad_branch;
SuperNeighbor *snode_branch = (SuperNeighbor*) dad_branch->node->findNeighbor(dad);
for (int part = 0; part < size(); part++)
if (sdad_branch->link_neighbors[part]) {
at(part)->reorientPartialLh(sdad_branch->link_neighbors[part], snode_branch->link_neighbors[part]->node);
}
}
string PhyloSuperTreePlen::getTreeString() {
return PhyloTree::getTreeString();
}
void PhyloSuperTreePlen::readTreeString(const string &tree_string) {
PhyloTree::readTreeString(tree_string);
}
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