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/*
Copyright (C) 2011 Tal Pupko TalP@tauex.tau.ac.il.
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 3 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, see <http://www.gnu.org/licenses/>.
*/
#include "simulateChangesAlongTree.h"
#include "talRandom.h"
#include "matrixUtils.h"
#include "gainLoss.h"
#include <algorithm>
simulateChangesAlongTree::simulateChangesAlongTree(const tree& inTree, const stochasticProcess& sp, alphabet* pAlph)
: _tree(inTree), _sp(sp), _pAlph(pAlph)
{
}
simulateChangesAlongTree::~simulateChangesAlongTree()
{
}
void simulateChangesAlongTree::init()
{
//init the vector of waiting times.
_waitingTimeParams.clear();
_waitingTimeParams.resize(_pAlph->size());
int i, j;
for (i = 0; i < _pAlph->size(); ++i)
{
_waitingTimeParams[i] = -_sp.dPij_dt(i, i, 0.0);
}
//init _jumpProbs.
//_jumpProbs[i][j] = Q[i][j] / -Q[i][i]
_jumpProbs.clear();
_jumpProbs.resize(_pAlph->size());
for (i = 0; i < _pAlph->size(); ++i)
{
MDOUBLE sum = 0.0;
_jumpProbs[i].resize(_pAlph->size());
for (j = 0; j < _pAlph->size(); ++j)
{
if (i == j)
_jumpProbs[i][j] = 0.0;
else
{
_jumpProbs[i][j] = _sp.dPij_dt(i, j, 0.0) / _waitingTimeParams[i];
}
sum += _jumpProbs[i][j];
}
if (! DEQUAL(sum, 1.0)){
string err = "error in simulateJumps::init(): sum probabilities is not 1 and equal to ";
err+=double2string(sum);
errorMsg::reportError(err);
}
}
int nodesNum = _tree.getNodesNum();
_changesOccurred.clear();
_changesOccurred.resize(nodesNum);
for (int i=0; i<nodesNum; ++i)
resizeMatrix(_changesOccurred[i], _pAlph->size(), _pAlph->size());
_nodesContent.clear();
_nodesContent.resize(nodesNum, 0);
}
sequenceContainer simulateChangesAlongTree::simulatePosition(){
init();
Vdouble freqs(_pAlph->size(),0.0);
for (int i = 0; i< freqs.size(); ++i)
freqs[i]=_sp.freq(i);
int rootState = giveRandomState(_pAlph->size(), freqs);
//int rootState = giveRandomState(_pAlph, freqs);
_nodesContent[_tree.getRoot()->id()] = rootState;
simulateOnce(_tree.getRoot(),0,rootState,0);
simulateOnce(_tree.getRoot(),0,rootState,1);
if (_tree.getRoot()->getNumberOfSons() > 2)
simulateOnce(_tree.getRoot(),0,rootState,2);
return _sc;
}
void simulateChangesAlongTree::simulateOnce(tree::nodeP curNode,
MDOUBLE disFromNode,
int previousContent, int whichSon){
tree::nodeP sonNode = curNode->getSon(whichSon);
MDOUBLE avgWaitingTime = 1.0 / _waitingTimeParams[previousContent];
MDOUBLE timeTillChange = talRandom::rand_exp(avgWaitingTime);
disFromNode += timeTillChange;
//int nextContent = giveRandomState(_pAlph, previousContent, _jumpProbs);
int nextContent = giveRandomState(_pAlph->size(), previousContent, _jumpProbs);
while (disFromNode < sonNode->dis2father()) {
_changesOccurred[sonNode->id()][previousContent][nextContent]++;
previousContent=nextContent;
MDOUBLE avgWaitingTime = 1.0 / _waitingTimeParams[previousContent];
MDOUBLE timeTillChange = talRandom::rand_exp(avgWaitingTime);
disFromNode += timeTillChange;
//nextContent = giveRandomState(_pAlph, nextContent, _jumpProbs);
nextContent = giveRandomState(_pAlph->size(), nextContent, _jumpProbs);
}
while (disFromNode >= sonNode->dis2father()) {
_nodesContent[sonNode->id()] = previousContent;
if (sonNode->isLeaf()) {
//string name = "leaf_" + int2string(sonNode->id()) + "_" + sonNode->name();
string name = sonNode->name();
sequence seq(int2string(previousContent),name, "", sonNode->id(), _pAlph);
_sc.add(seq);
return;
}
simulateOnce(sonNode, 0, previousContent, 1);
disFromNode-=sonNode->dis2father();
curNode = sonNode;
sonNode = curNode->getSon(0);
}
_changesOccurred[sonNode->id()][previousContent][nextContent]++;
simulateOnce(curNode, disFromNode, nextContent, 0);
}
VVint simulateChangesAlongTree::getChangesForBranch(int nodeID){
if (nodeID>_changesOccurred.size())
errorMsg::reportError("error in simulateChangesAlongTree::getChangesForBranch, nodeID doesn't exist");
return _changesOccurred[nodeID];
}
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