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// $Id: computeUpAlgFactors.cpp 8034 2010-06-03 20:26:39Z itaymay $
#include "definitions.h"
#include "computeUpAlg.h"
#include "seqContainerTreeMap.h"
#include "logFile.h"
#include <iostream>
#include <cassert>
#include <cmath>
#include <cstdlib>
using namespace std;
void computeNodeFactorAndSetSsc(MDOUBLE & minFactor,suffStatGlobalHomPos& ssc, int nodeId, const int alphSize){
// given a number = probability (val), it is changed to a new number which is 10 to the power of factor + val.
// for example if val = 0.001, it is changed to 0.1 and factor 2.
minFactor=100000;
for (int i=0; i < alphSize; ++i) {
MDOUBLE tmpfactor=0;
doubleRep val = ssc.get(nodeId,i);
if (val >0) {
while (val < 0.1) {
val *=10;
tmpfactor++;
}
}
else tmpfactor=minFactor;
if (tmpfactor<minFactor) minFactor=tmpfactor;
}
for (int j=0; j < alphSize; ++j) {
doubleRep tmp = ssc.get(nodeId,j);
tmp = tmp * pow(static_cast<MDOUBLE>(10.0),minFactor);
ssc.set(nodeId,j,tmp);
}
}
void computeUpAlg::fillComputeUpWithFactors(const tree& et,
const sequenceContainer& sc,
const int pos,
const computePijHom& pi,
suffStatGlobalHomPos& ssc,
vector<MDOUBLE>& factors) {
factors.resize(et.getNodesNum(),0.0);
seqContainerTreeMap sctm(sc,et);
ssc.allocatePlace(et.getNodesNum(),pi.alphabetSize());
treeIterDownTopConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
int letter;
if (mynode->getNumberOfSons() == 0) {// leaf
for(letter=0; letter<pi.alphabetSize();letter++) {
const int seqID = sctm.seqIdOfNodeI(mynode->id());
doubleRep val = sc.getAlphabet()->relations(sc[seqID][pos],letter);
ssc.set(mynode->id(),letter,val);
}
computeNodeFactorAndSetSsc(factors[mynode->id()],ssc,mynode->id(),pi.alphabetSize());
}
else {
for(letter=0; letter<pi.alphabetSize();letter++) {
doubleRep total_prob=1.0;
for(int i=0; i < mynode->getNumberOfSons(); ++i){
doubleRep prob=0.0;
for(int letInSon=0; letInSon<pi.alphabetSize();letInSon++) {
prob += ssc.get(mynode->getSon(i)->id(),letInSon)*
pi.getPij(mynode->getSon(i)->id(),letter,letInSon);
}
total_prob*=prob;
}
ssc.set(mynode->id(),letter,total_prob);
}
computeNodeFactorAndSetSsc(factors[mynode->id()],ssc,mynode->id(),pi.alphabetSize());
for(int k=0; k < mynode->getNumberOfSons();++k) {
factors[mynode->id()]+=factors[mynode->getSon(k)->id()];
}
}
}
}
void computeUpAlg::fillComputeUpWithFactors(const tree& et,
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc,
vector<MDOUBLE>& factors) {
factors.resize(et.getNodesNum(),0.0);
seqContainerTreeMap sctm(sc,et);
ssc.allocatePlace(et.getNodesNum(),sp.alphabetSize());
treeIterDownTopConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
int letter;
if (mynode->getNumberOfSons() == 0) {// leaf
for(letter=0; letter<sp.alphabetSize();letter++) {
const int seqID = sctm.seqIdOfNodeI(mynode->id());
doubleRep val = sc.getAlphabet()->relations(sc[seqID][pos],letter);
ssc.set(mynode->id(),letter,val);
}
computeNodeFactorAndSetSsc(factors[mynode->id()],ssc,mynode->id(),sp.alphabetSize());
}
else {
for(letter=0; letter<sp.alphabetSize();letter++) {
doubleRep total_prob=1.0;
for(int i=0; i < mynode->getNumberOfSons();++i){
doubleRep prob=0.0;
for(int letInSon=0; letInSon<sp.alphabetSize();letInSon++) {
prob += ssc.get(mynode->getSon(i)->id(),letInSon)*
sp.Pij_t(letter,letInSon,mynode->getSon(i)->dis2father()*sp.getGlobalRate());// taking care of the glubal is new.
}
assert(prob>=0);
total_prob*=prob;
}
ssc.set(mynode->id(),letter,total_prob);
}
computeNodeFactorAndSetSsc(factors[mynode->id()],ssc,mynode->id(),sp.alphabetSize());
for(int k=0; k < mynode->getNumberOfSons();++k) {
factors[mynode->id()]+=factors[mynode->getSon(k)->id()];
}
}
}
}
void computeUpAlg::fillComputeUpSpecificGlobalRateFactors(const tree& et,
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc,
const MDOUBLE gRate,
vector<MDOUBLE>& factors) {
factors.resize(et.getNodesNum(),0.0);
seqContainerTreeMap sctm(sc,et);
ssc.allocatePlace(et.getNodesNum(),sp.alphabetSize());
treeIterDownTopConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
#ifdef VERBOS
LOG(5,<<endl<<endl<<"doing node: "<<mynode->name()<<endl);
#endif
int letter;
if (mynode->getNumberOfSons() == 0) {// leaf
for(letter=0; letter<sp.alphabetSize();letter++) {
const int seqID = sctm.seqIdOfNodeI(mynode->id());
doubleRep val = sc.getAlphabet()->relations(sc[seqID][pos],letter);
ssc.set(mynode->id(),letter,val);
}
computeNodeFactorAndSetSsc(factors[mynode->id()],ssc,mynode->id(),sp.alphabetSize());
}
else {
int letterWithTotalProbEqZero =0;
for(letter=0; letter<sp.alphabetSize();letter++) {
doubleRep total_prob=1.0;
for(int i=0; i < mynode->getNumberOfSons();++i){
doubleRep prob=0.0;
for(int letInSon=0; letInSon<sp.alphabetSize();letInSon++) {
assert(ssc.get(mynode->getSon(i)->id(),letInSon)>=0);
assert(sp.Pij_t(letter,letInSon,mynode->getSon(i)->dis2father()*gRate)>=0);
prob += ssc.get(mynode->getSon(i)->id(),letInSon)*
sp.Pij_t(letter,letInSon,mynode->getSon(i)->dis2father()*gRate);
}
assert(prob>=0);
total_prob*=prob;
}
if (total_prob ==0) ++letterWithTotalProbEqZero;
ssc.set(mynode->id(),letter,total_prob);
} // end of else
computeNodeFactorAndSetSsc(factors[mynode->id()],ssc,mynode->id(),sp.alphabetSize());
for(int k=0; k < mynode->getNumberOfSons();++k) {
factors[mynode->id()]+=factors[mynode->getSon(k)->id()];
}
if (letterWithTotalProbEqZero == sp.alphabetSize() && (mynode->getNumberOfSons() > 0)) {
LOG(5,<<" total prob =0");
for (int z=0; z <mynode->getNumberOfSons(); ++z) {
LOG(5,<<"son "<<z<<" is "<<mynode->getSon(z)->name()<<endl);
LOG(5,<<"dis2father is "<<mynode->getSon(z)->dis2father()<<endl);
for(int letInSon=0; letInSon<sp.alphabetSize();letInSon++) {
LOG(5,<<"let = "<<letInSon<<endl);
LOG(5,<<"ssc.get(mynode->sons[z]->id(),letInSon) = "<<convert(ssc.get(mynode->getSon(z)->id(),letInSon))<<endl);
// LOG(5,<<"sp.Pij_t(letter,letInSon,mynode->getSon(i)->dis2father()*gRate) = "<<sp.Pij_t(letter,letInSon,mynode->sons[i]->dis2father()*gRate)<<endl);
// LOG(5,<<"mynode->getSon(i)->dis2father() = "<<mynode->getSon(i)->dis2father()<<endl);
}
}
exit(3);
}
}
}
}
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