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91 lines
4.0 KiB
C++
91 lines
4.0 KiB
C++
#include "definitions.h"
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#include "computeDownAlg.h"
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#include "computeUpAlg.h"
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#include "matrixUtils.h"
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#include "treeIt.h"
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#include "likelihoodComputation.h"
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#include "computePosteriorExpectationOfSubstitutions_nonReversibleSp.h"
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using namespace std;
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/********************************************************************************************
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Posterior of observing a certain state substitution along a branch:
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P(Node=x,Father=y|D) = P(D,Node=x,Father=y)/P(D)
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usage: posteriorPerNodePer2States[mynode->id()][fatherState][sonState]
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*********************************************************************************************/
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void computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosteriorOfChangeGivenTerminals(VVVdouble &posteriorPerNodePer2States, int pos){
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int numNodes = _tr.getNodesNum();
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int alphabetSize = _sp->alphabetSize();
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posteriorPerNodePer2States.resize(numNodes);
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for (int n=0;n<posteriorPerNodePer2States.size();++n)
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resizeMatrix(posteriorPerNodePer2States[n],alphabetSize,alphabetSize);
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suffStatGlobalHomPos sscUp;
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suffStatGlobalGamPos sscDownNonRev; // The "Gam" is used for the letter at father - sscGivenRoot
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sscUp.allocatePlace(numNodes,alphabetSize);
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computePijHom pi;
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pi.fillPij(_tr,*_sp);
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computeUpAlg comp_Up;
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computeDownAlg comp_Down;
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comp_Up.fillComputeUp(_tr,_sc,pos,pi,sscUp);
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comp_Down.fillComputeDownNonReversible(_tr,_sc,pos,pi,sscDownNonRev,sscUp);
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treeIterTopDownConst tIt(_tr);
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MDOUBLE ll = convert(likelihoodComputation::getLofPos(pos,_tr,_sc,pi,*_sp));
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for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
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for (int sonState = 0; sonState<alphabetSize; ++sonState){
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for (int fatherState = 0; fatherState<alphabetSize; ++fatherState){
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posteriorPerNodePer2States[mynode->id()][fatherState][sonState]= computePosterioGivenTerminalsPerBranch(mynode->id(),sonState,fatherState,sscUp,sscDownNonRev, pi,ll,mynode->name());
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}
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}
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}
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}
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/********************************************************************************************
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Posterior of observing a certain state substitution along a branch:
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P(Node=sonState,Father=fatherState|D) = P(D,Node=sonState,Father=fatherState)/P(D)
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usage: posteriorPerNodePer2States[mynode->id()][fatherState][sonState]
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*********************************************************************************************/
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MDOUBLE computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch
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(int nodeId,int sonState, int fatherState,suffStatGlobalHomPos &sscUp,
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suffStatGlobalGamPos &sscDown,computePijHom &pi, MDOUBLE &LLData, const string nodeName)
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{
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MDOUBLE res=0.0;
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MDOUBLE resDXY, Down, Up, pij;
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for (int stateAtRoot = 0; stateAtRoot<_sp->alphabetSize(); ++stateAtRoot){
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Down = convert(sscDown.get(stateAtRoot,nodeId,fatherState));
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Up = convert(sscUp.get(nodeId,sonState));
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pij = pi.getPij(nodeId,fatherState,sonState);
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res+=(_sp->freq(stateAtRoot)*
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Down*
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Up*
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pij);
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}
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resDXY = res;
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res/=LLData;
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// if(gainLossOptions::_printDEBUGinfo)
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// LOG(3,<<nodeName<<" son "<<sonState<<" Down "<<Down<<" father "<<fatherState<<" Up "<<Up<<" pij "<<pij<<" resDXY "<<resDXY<<" LLData "<<LLData<<" prob "<<res<<endl);
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if (res > 1 + 1e-4){
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LOGnOUT(3,<<nodeId<<" son "<<sonState<<" Down "<<Down<<" father "<<fatherState<<" Up "<<Up<<" pij "<<pij<<" resDXY "<<resDXY<<" LLData "<<LLData<<" prob "<<res<<endl);
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res = 1;
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}
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if (res<-1e-4){
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LOGnOUT(3,<<nodeId<<" son "<<sonState<<" Down "<<Down<<" father "<<fatherState<<" Up "<<Up<<" pij "<<pij<<" resDXY "<<resDXY<<" LLData "<<LLData<<" prob "<<res<<endl);
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res = 0;
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}
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if ((res > 1 + 0.000001) || (res<-0.000001)){
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string err = "Error in computePosteriorExpectationOfSubstitutions_nonReversibleSp::computePosterioGivenTerminalsPerBranch, non probability value ";
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err+=double2string(res);
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err+=" at node ";
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err+=int2string(nodeId);
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err+= " sonState ";
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err+= int2string(sonState);
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err+= " fatherState ";
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err+= int2string(fatherState);
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errorMsg::reportError(err);
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}
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return res;
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} |