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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 "ancestralReconstructStates.h"
#include <cmath>
using namespace std;
/********************************************************************************************
ancestralReconstructStates
*********************************************************************************************/
ancestralReconstructStates::ancestralReconstructStates(const tree &tr, const sequenceContainer &sc, stochasticProcess *sp):
_tr(tr), _sc(sc){
if(!sp){
errorMsg::reportError("error in the constructor ancestralReconstructStates sp argument is NULL");
}
else{
_sp = sp;
}
_statesV.resize(_sc.seqLen());
for (int pos = 0; pos <_sc.seqLen(); ++pos){
initializeStatesVector(pos);
}
}
void ancestralReconstructStates::initializeStatesVector(int pos){
_statesV[pos].resize(_tr.getNodesNum(),-1000);
checkThatNamesInTreeAreSameAsNamesInSequenceContainer(_tr,_sc);
seqContainerTreeMap scTreeMap(_sc,_tr);
vector <tree::nodeP> leaves;
_tr.getAllLeaves(leaves,_tr.getRoot());
for (unsigned int i=0; i< leaves.size();i++){
int myleafId = (leaves[i])->id();
int mySeqId = scTreeMap.seqIdOfNodeI(myleafId);
_statesV[pos][myleafId] = _sc[mySeqId][pos];
}
}
/********************************************************************************************
upL[node][letter] = max(letter_here){P(letter->letter_here)*upL[son1][letter_here]*upL[son2][letter_here]} for letter at father node.
backtrack[node][letter] = argmax of above
*********************************************************************************************/
void ancestralReconstructStates::traverseUpML(VVVdouble &upL, VVVint &backtrack){ // input as empty vector to be filled
LOGnOUT(4,<<"traverseUpML..."<<endl);
upL.resize(_sc.seqLen());
backtrack.resize(_sc.seqLen());
for (int pos = 0; pos <_sc.seqLen(); ++pos){
traverseUpML(upL[pos], backtrack[pos], pos);
}
}
/********************************************************************************************
*********************************************************************************************/
void ancestralReconstructStates::traverseUpML(VVdouble &upL, VVint &backtrack, int pos){ // input as empty vector to be filled
computePijGam pi;
pi.fillPij(_tr,*_sp);
upL.resize(_tr.getNodesNum());
for (unsigned int i = 0; i < upL.size(); i++)
upL[i].resize(_sp->alphabetSize());
backtrack.resize(_tr.getNodesNum());
for (unsigned int i = 0; i < backtrack.size(); i++)
backtrack[i].resize(_sp->alphabetSize());
treeIterDownTopConst tIt(_tr);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
int father_state = 0;
if (mynode->isLeaf()) {
for (father_state=0; father_state<_sp->alphabetSize();father_state++){ // looping over states at father
int myState = _statesV[pos][mynode->id()];
if(myState == _sc.getAlphabet()->unknown()){
myState = father_state; // same as relations=1, for missing data
}
for (int i=0; i < _sp->categories();++i) {
upL[mynode->id()][father_state] += pi.getPij(i,mynode->id(),father_state,myState)*_sp->ratesProb(i);
}
backtrack[mynode->id()][father_state]=myState;
}
}
else if (!(mynode->isRoot())) {
for (father_state=0; father_state<_sp->alphabetSize();father_state++){ // looping over states at father
MDOUBLE myMax = -1;
int myArgMax=-1;
for (int my_state=0;my_state<_sp->alphabetSize();my_state++){ // loop to find max over current node
//MDOUBLE val=_sp->Pij_t(father_state,my_state,mynode->dis2father());
MDOUBLE val=0;
for (int i=0; i < _sp->categories();++i) {
val += pi.getPij(i,mynode->id(),father_state,my_state)*_sp->ratesProb(i);
}
for (int son=0;son<mynode->getNumberOfSons();son++)
val*=upL[mynode->getSon(son)->id()][my_state];
if (val>myMax){
myMax=val;
myArgMax=my_state;
}
}
if ((myMax<0) || (myArgMax<0))
errorMsg::reportError("Error in traverseUpML: cannot find maximum");
upL[mynode->id()][father_state]=myMax;
backtrack[mynode->id()][father_state]=myArgMax;
}
}
else {// root
for (int root_state=0; root_state<_sp->alphabetSize();root_state++){
MDOUBLE val=_sp->freq(root_state);
for (int son=0;son<mynode->getNumberOfSons();son++)
val*=upL[mynode->getSon(son)->id()][root_state];
upL[mynode->id()][root_state]=val;
}
}
}
}
/********************************************************************************************
return likelihood of max joint reconstruction
*********************************************************************************************/
Vdouble ancestralReconstructStates::traverseDownML(VVVdouble &upL, VVVint &backtrack,VVVint &transitionTypeCount) { // input as already filled vector
LOGnOUT(4,<<"traverseDownML..."<<endl);
Vdouble LofJointV;
LofJointV.resize(_sc.seqLen());
transitionTypeCount.resize(_sc.seqLen());
for (int pos = 0; pos <_sc.seqLen(); ++pos){
LofJointV[pos] = traverseDownML(upL[pos], backtrack[pos],transitionTypeCount[pos], pos);
}
return LofJointV;
}
/********************************************************************************************
fill _statesV, transitionTypeCount
*********************************************************************************************/
MDOUBLE ancestralReconstructStates::traverseDownML(VVdouble &upL, VVint &backtrack,VVint &transitionTypeCount, int pos) { // input as already filled vector
if (backtrack.size() == 0)
errorMsg::reportError("error in ancestralReconstruct::traverseDownML, input vector backtrack must be filled (call traverseUpML() first)");
MDOUBLE LofJoint;
int stateOfRoot;
findMaxInVector(upL[(_tr.getRoot())->id()], LofJoint, stateOfRoot);
_statesV[pos][(_tr.getRoot())->id()] = stateOfRoot;
transitionTypeCount.resize(_sp->alphabetSize());
for (unsigned int i = 0; i < transitionTypeCount.size(); i++)
transitionTypeCount[i].resize(_sp->alphabetSize(),0);
treeIterTopDownConst tIt(_tr);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
if (mynode->isRoot()) continue;
int myId = mynode->id();
int stateAtFather = _statesV[pos][mynode->father()->id()];
int myState = _statesV[pos][mynode->id()];
if(myState == _sc.getAlphabet()->unknown()){
myState = stateAtFather; // same as relations=1, for missing data
}
if (mynode->isLeaf()) {
transitionTypeCount[stateAtFather][myState]++;
if ((_statesV[pos][mynode->id()]!=stateAtFather))
LOG(7,<<"switch from "<<mynode->father()->name()<<"("<<stateAtFather<<") to "<<mynode->name()<<"("<<_statesV[pos][mynode->id()]<<")"<<endl);
continue;
}
if(_statesV[pos][mynode->id()] == -2)
cout<<_statesV[pos][mynode->id()]<<" unKnown at pos="<<pos<<" node="<<mynode->id()<<endl;
_statesV[pos][mynode->id()]=backtrack[myId][stateAtFather];
transitionTypeCount[stateAtFather][_statesV[pos][mynode->id()]]++;
}
return log(LofJoint);
}
/********************************************************************************************
compute Prob(letter at Node N is x|Data): the posterior probabilities at ancestral states
Use the pre-calculated joint posterior probability P(N=x, father(N)=y|D) and just sum over these probs:
Prob(N=x|Data) = sum{fatherState}[P(N=x, father(N)=y|D)]}
stores results in member VVVdouble[pos][node][state] _ancestralProbs
use VVVVdouble _probChanges_PosNodeXY == jointPost[pos][nodeID][fatherLetter][letter]- after computePosteriorOfChangeGivenTerminals
*********************************************************************************************/
void ancestralReconstructStates::computeAncestralPosterior(const VVVVdouble& jointPost)
{
LOGnOUT(4,<<"computeAncestralPosterior (take into acount joint probabilty)..."<<endl);
int numNodes = _tr.getNodesNum();
int alphabetSize = _sp->alphabetSize();
//int alphabetSizeForProbsSize = alphabetSize;
//bool isThereMissingData = _sc.getAlphabetDistribution(true)[2]>0;
//if(isThereMissingData)
// alphabetSizeForProbsSize++; // resize for one more
_ancestralProbs.resize(_sc.seqLen());
for (int pos = 0; pos <_sc.seqLen(); ++pos){
resizeMatrix(_ancestralProbs[pos], numNodes, alphabetSize);
treeIterTopDownConst tIt(_tr);
int letter;
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
if (mynode->isRoot()) {
//for(letter = 0; letter<alphabetSize; ++letter) // itay's version - the computed vals are all 0
// _ancestralProbs[pos][mynode->id()][letter] = jointPost[pos][mynode->id()][0][letter];
for(letter = 0; letter < alphabetSize; ++letter) {
MDOUBLE sum = 0.0;
for(int sonLetter = 0; sonLetter < alphabetSize; ++sonLetter) {
sum += jointPost[pos][mynode->getSon(0)->id()][letter][sonLetter]; // sum over the son joint prob (instead of father)
}
_ancestralProbs[pos][mynode->id()][letter] = sum;
}
continue;
}
for(letter = 0; letter < alphabetSize; ++letter) {
MDOUBLE sum = 0.0;
for(int fatherLetter = 0; fatherLetter < alphabetSize; ++fatherLetter) {
sum += jointPost[pos][mynode->id()][fatherLetter][letter];
}
_ancestralProbs[pos][mynode->id()][letter] = sum;
}
}
}
}
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