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101 lines
2.9 KiB
C++
101 lines
2.9 KiB
C++
// $Id: computeMarginalAlg.cpp 1735 2007-02-26 13:46:37Z itaymay $
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#include "definitions.h"
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#include "treeIt.h"
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#include "computeMarginalAlg.h"
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#include <iostream>
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#include <cassert>
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using namespace std;
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void computeMarginalAlg::fillComputeMarginal(const tree& et,
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const sequenceContainer& sc,
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const stochasticProcess& sp,
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const int pos,
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const computePijHom& pi,
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suffStatGlobalHomPos& ssc,
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const suffStatGlobalHomPos& cup,
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const suffStatGlobalHomPos& cdown,
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doubleRep & posProb){
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// filling the exact probs.
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tree::nodeP mynode = NULL;
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ssc.allocatePlace(et.getNodesNum(),pi.alphabetSize());
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treeIterTopDownConst tIt(et);
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for (mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
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assert (mynode != NULL);
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int letter;
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if (mynode->isLeaf()) {
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for(letter=0; letter<pi.alphabetSize();letter++) {
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doubleRep val=convert(cup.get(mynode->id(),letter))?1.0:0.0;
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ssc.set(mynode->id(),letter,val);
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}
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continue;
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}
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doubleRep sumProb =0;
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for(letter=0; letter<pi.alphabetSize();letter++) {
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doubleRep prob=0.0;
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if (mynode->father()==NULL) prob=1.0; // special case of the root.
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else {
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for(int letter_in_f=0; letter_in_f<pi.alphabetSize();letter_in_f++) {
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prob +=cdown.get(mynode->id(),letter_in_f)*
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pi.getPij(mynode->id(),letter,letter_in_f);
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}
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}
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prob = prob*sp.freq(letter)*
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cup.get(mynode->id(),letter);
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ssc.set(mynode->id(),letter,prob);
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sumProb += prob;
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}
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for(letter=0; letter<pi.alphabetSize();letter++) {
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doubleRep getV = ssc.get(mynode->id(),letter);
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ssc.set(mynode->id(),letter,getV/sumProb);
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}
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// CHECKING:
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/* LOG(5,<<" checking marginal of node: "<<mynode->name()<<endl);
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MDOUBLE SSum =0;
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for (int u=0; u < pi.alphabetSize(); ++u) {
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LOG(5,<<ssc.get(mynode->id(),u)<<" ");
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SSum +=ssc.get(mynode->id(),u);
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}
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LOG(5,<<"\nsum of marginals = "<<SSum<<endl);
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*/
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if (mynode->isRoot()) posProb = convert(sumProb);
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}
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}
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/*
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if (val>1) {
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LOG(5,<<"x val = " << val<<endl);
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LOG(5,<<" my node = " << mynode->name()<<endl);
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LOG(5,<<" let = " << let << endl);
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LOG(5,<<" up = " << cup.get(mynode->id(),let));
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LOG(5,<< "pos prob = " << posProb<<endl);
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LOG(5,<<" root of tree = " << et.getRoot()->name()<<endl);
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errorMsg::reportError(" error in compute marginal >1 ");
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}
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if (val>1) {
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LOG(5,<<" val = " << val<<endl);
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LOG(5,<<" pos = " << pos<<endl);
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LOG(5,<<" my node = " << mynode->name()<<endl);
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LOG(5,<<" let = " << let << endl);
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LOG(5,<<" up = " << cup.get(mynode->id(),let)<<endl);
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LOG(5,<<" down[sameLetter] = " << cdown.get(mynode->id(),let)<<endl);
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LOG(5,<<" pij[sameLetter] = " << pi.getPij(mynode->id(),let,let)<<endl);
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LOG(5,<< "pos prob = " << posProb<<endl);
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LOG(5,<<" root of tree = " << et.getRoot()->name()<<endl);
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LOG(5,<<"sp.freq(letter) = "<<sp.freq(let)<<endl);
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errorMsg::reportError(" error in compute marginal >1 ");
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}
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*/
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