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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 "tinatree.h"
TinaTree::TinaTree()
: PhyloTree()
{
}
TinaTree::TinaTree(Alignment *alignment) : PhyloTree(alignment) {
}
TinaTree::~TinaTree()
{
}
int TinaTree::computeParsimonyScore(int ptn, int &states, PhyloNode *node, PhyloNode *dad) {
int score = 0;
states = 0;
if (!node) node = (PhyloNode*) root;
if (node->degree() > 3)
outError("Does not work with multifurcating tree");
if (verbose_mode == VB_DEBUG)
cout << ptn << " " << node->id << " " << node->name << endl;
if (node->isLeaf()) {
char state;
if (node->name == ROOT_NAME) {
state = aln->STATE_UNKNOWN;
} else {
ASSERT(node->id < aln->getNSeq());
state = (*aln)[ptn][node->id];
}
if (state == aln->STATE_UNKNOWN) {
states = (1 << aln->num_states) - 1;
} else if (state < aln->num_states)
states = (1 << state);
else {
// ambiguous character, for DNA, RNA
states = state - 3;
}
}
if (!node->isLeaf() || node == root) {
int union_states = 0;
int intersect_states = (1 << aln->num_states) - 1;
if (states != 0) {
union_states = states;
intersect_states = states;
}
FOR_NEIGHBOR_IT(node, dad, it) {
int states_child;
int score_child = computeParsimonyScore(ptn, states_child, (PhyloNode*) ((*it)->node), node);
union_states |= states_child;
intersect_states &= states_child;
score += score_child;
}
if (intersect_states)
states = intersect_states;
else {
states = union_states;
score++;
}
}
return score;
}
int TinaTree::computeParsimonyScore() {
ASSERT(root && root->isLeaf());
int score = 0;
for (int ptn = 0; ptn < aln->size(); ptn++)
if (!aln->at(ptn).isConst()) {
int states;
int ptn_score = computeParsimonyScore(ptn, states);
score += ptn_score * (*aln)[ptn].frequency;
if (verbose_mode >= VB_MAX) {
for (int seq=0; seq < aln->getNSeq(); seq++)
cout << aln->convertStateBackStr(aln->at(ptn)[seq]);
cout << " " << ptn_score << endl;
}
}
if (verbose_mode >= VB_MAX)
cout << endl;
return score;
}
void TinaTree::initializeAllPartialLh() {
int index, indexlh;
initializeAllPartialLh(index, indexlh);
ASSERT(index == (nodeNum - 1)*2);
}
void TinaTree::initializeAllPartialLh(int &index, int &indexlh, PhyloNode *node, PhyloNode *dad) {
int pars_block_size = getBitsBlockSize();
if (!node) {
node = (PhyloNode*) root;
// allocate the big central partial likelihoods memory
if (!central_partial_pars) {
if (verbose_mode >= VB_MAX)
cout << "Allocating " << (leafNum - 1)*4 * pars_block_size * sizeof (UINT) << " bytes for partial parsimony vectors" << endl;
central_partial_pars = new UINT[(leafNum-1)*4*pars_block_size];
if (!central_partial_pars)
outError("Not enough memory for partial parsimony vectors");
}
index = 0;
}
if (dad) {
// assign a region in central_partial_lh to both Neihgbors (dad->node, and node->dad)
PhyloNeighbor *nei = (PhyloNeighbor*) node->findNeighbor(dad);
//assert(!nei->partial_lh);
nei->partial_pars = central_partial_pars + (index * pars_block_size);
nei = (PhyloNeighbor*) dad->findNeighbor(node);
//assert(!nei->partial_lh);
nei->partial_pars = central_partial_pars + ((index + 1) * pars_block_size);
index += 2;
ASSERT(index < nodeNum * 2 - 1);
}
FOR_NEIGHBOR_IT(node, dad, it)
initializeAllPartialLh(index, indexlh, (PhyloNode*) (*it)->node, node);
}
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