mirror of
http://43.156.76.180:8026/YuuMJ/EukPhylo.git
synced 2025-12-28 07:00:25 +08:00
207 lines
7.3 KiB
C++
207 lines
7.3 KiB
C++
// $Id: computeCounts.cpp 9899 2011-10-11 19:56:48Z rubi $
|
|
|
|
#include "computeCounts.h"
|
|
void computeCounts::computeCountsNodeFatherNodeSonHomPos(const sequenceContainer& sc,
|
|
const computePijHom& pi,
|
|
const stochasticProcess& sp,
|
|
const suffStatGlobalHomPos& cup,
|
|
const suffStatGlobalHomPos& cdown,
|
|
const MDOUBLE weight,
|
|
const doubleRep posProb,
|
|
const tree::nodeP nodeSon,
|
|
countTableComponentHom& _ctc,
|
|
const MDOUBLE rateCategorProb
|
|
)
|
|
{
|
|
assert(posProb>0.0);
|
|
if (weight == 0) return;
|
|
int alph1,alph2;
|
|
for (alph1 =0; alph1< pi.alphabetSize(); ++alph1) {
|
|
for (alph2 =0; alph2< pi.alphabetSize(); ++alph2) {
|
|
|
|
doubleRep tmp = cup.get(nodeSon->id(),alph1) *
|
|
cdown.get(nodeSon->id(),alph2) *
|
|
pi.getPij(nodeSon->id(),alph1,alph2)*
|
|
sp.freq(alph1)
|
|
* rateCategorProb
|
|
/
|
|
posProb;
|
|
_ctc.addToCounts(alph1,alph2,convert(tmp)*weight);
|
|
}
|
|
}
|
|
}
|
|
|
|
//old
|
|
void computeCounts::computeCountsNodeFatherNodeSonHomPosProportionalEB(const sequenceContainer& sc,
|
|
const computePijHom& pi,
|
|
const stochasticProcess& sp,
|
|
const suffStatGlobalHomPos& cup,
|
|
const suffStatGlobalHomPos& cdown,
|
|
const MDOUBLE weight,
|
|
const doubleRep posProb,
|
|
const tree::nodeP nodeSon,
|
|
countTableComponentHom& _ctc,
|
|
const MDOUBLE globalLocalRateCategorProb)
|
|
{
|
|
assert(posProb>0.0);
|
|
if (weight == 0) return;
|
|
int alph1,alph2;
|
|
for (alph1 =0; alph1< pi.alphabetSize(); ++alph1) {
|
|
for (alph2 =0; alph2< pi.alphabetSize(); ++alph2) {
|
|
//here we multiply: P(a,b|globalRate_x,localRate_y,D)*P(globalRate_x,localRate_y|D)
|
|
//which is: (up*down)*[(P(D|globalRate_x,localRate_y)*GlobalLocalRateCategoriesProb)/posProb]
|
|
doubleRep tmp = (cup.get(nodeSon->id(),alph1) *
|
|
cdown.get(nodeSon->id(),alph2)) *
|
|
(pi.getPij(nodeSon->id(),alph1,alph2) *
|
|
sp.freq(alph1) *
|
|
globalLocalRateCategorProb
|
|
/
|
|
posProb);
|
|
_ctc.addToCounts(alph1,alph2,convert(tmp)*weight);
|
|
}
|
|
}
|
|
}
|
|
|
|
//new
|
|
void computeCounts::computeCountsNodeFatherNodeSonHomPosProportionalEB(const sequenceContainer& sc,
|
|
const computePijHom& pi,
|
|
const stochasticProcess& sp,
|
|
const suffStatGlobalHomPos& cup,
|
|
const suffStatGlobalHomPos& cdown,
|
|
const MDOUBLE weight,
|
|
const VdoubleRep posProbVec,
|
|
const tree::nodeP nodeSon,
|
|
countTableComponentHom& _ctc)
|
|
{
|
|
if (weight == 0) return;
|
|
int alph1,alph2;
|
|
doubleRep posProb(0.0);
|
|
for(int globalRateCat = 0;globalRateCat < posProbVec.size();++globalRateCat){
|
|
posProb += posProbVec[globalRateCat];
|
|
}
|
|
for (alph1 =0; alph1< pi.alphabetSize(); ++alph1) {
|
|
for (alph2 =0; alph2< pi.alphabetSize(); ++alph2) {
|
|
//here we multiply: P(a,b|globalRate_x,localRate_y,D)*P(globalRate_x,localRate_y|D)
|
|
//which is: (up*down)*[(P(D|globalRate_x,localRate_y)*GlobalLocalRateCategoriesProb)/posProb]
|
|
doubleRep tmp = (cup.get(nodeSon->id(),alph1) *
|
|
cdown.get(nodeSon->id(),alph2)) *
|
|
(pi.getPij(nodeSon->id(),alph1,alph2) *
|
|
sp.freq(alph1)
|
|
/
|
|
posProb);
|
|
_ctc.addToCounts(alph1,alph2,convert(tmp)*weight);
|
|
}
|
|
}
|
|
}
|
|
|
|
void computeCounts::computeCountsNodeFatherNodeSonHomPos(const sequenceContainer& sc,
|
|
const computePijHom& pi,
|
|
const stochasticProcess& sp,
|
|
const suffStatGlobalHomPos& cup,
|
|
const suffStatGlobalHomPos& cdown, //_cdown[categor][letterAtRoot]
|
|
const MDOUBLE weight,
|
|
const doubleRep posProb,
|
|
const tree::nodeP nodeSon,
|
|
countTableComponentHom& _ctc, //_computeCountsV[mynode->id()][letterAtRoot][categor]
|
|
const MDOUBLE rateCategorProb,
|
|
const int letterInRoot
|
|
)
|
|
{
|
|
assert(posProb>0.0);
|
|
if (weight == 0) return;
|
|
int alph1,alph2;
|
|
for (alph1 =0; alph1< pi.alphabetSize(); ++alph1) {
|
|
for (alph2 =0; alph2< pi.alphabetSize(); ++alph2) {
|
|
doubleRep tmp = cup.get(nodeSon->id(),alph1) *
|
|
cdown.get(nodeSon->id(),alph2) * // down was already given with specific root
|
|
pi.getPij(nodeSon->id(),alph1,alph2)*
|
|
sp.freq(alph1) // fixed root? or already computed byt the downAlg?
|
|
* rateCategorProb
|
|
//* sp.freq(letterInRoot) // to account for the additional letterAtRoot loop - move it to after getCounts
|
|
/posProb;
|
|
_ctc.addToCounts(alph1,alph2,convert(tmp)*weight);
|
|
}
|
|
}
|
|
}
|
|
|
|
|
|
|
|
void computeCounts::fillCountTableComponentGam(countTableComponentGam& ctcGam,
|
|
const stochasticProcess& sp,
|
|
const sequenceContainer& sc,
|
|
const computePijGam& pij0,
|
|
const suffStatGlobalGam& cup,
|
|
const suffStatGlobalGam& cdown,
|
|
const Vdouble * weights,
|
|
tree::nodeP nodeSon,
|
|
const VdoubleRep& posProbVec) {
|
|
ctcGam.countTableComponentAllocatePlace(sp.alphabetSize(),sp.categories());
|
|
for (int rateCat =0; rateCat< sp.categories(); ++ rateCat) {
|
|
fillCountTableComponentGamSpecRateCategor(rateCat,ctcGam[rateCat],sp,
|
|
sc,pij0[rateCat],
|
|
cup,cdown,weights,posProbVec,nodeSon);
|
|
}
|
|
}
|
|
|
|
void computeCounts::fillCountTableComponentGamSpecRateCategor(const int rateCategor,
|
|
countTableComponentHom& ctcHom,
|
|
const stochasticProcess& sp,
|
|
const sequenceContainer& sc,
|
|
const computePijHom& pi,
|
|
const suffStatGlobalGam& cup,
|
|
const suffStatGlobalGam& cdown,
|
|
const Vdouble * weights,
|
|
const VdoubleRep& posProbVec, //prob of the position with gamma
|
|
tree::nodeP nodeSon) {
|
|
computeCounts cc;
|
|
for (int pos = 0; pos < sc.seqLen(); ++pos) {
|
|
MDOUBLE weig = (weights ? (*weights)[pos] : 1.0);
|
|
cc.computeCountsNodeFatherNodeSonHomPos(sc,pi,sp,cup[pos][rateCategor],
|
|
cdown[pos][rateCategor],
|
|
weig,posProbVec[pos],nodeSon,
|
|
ctcHom,sp.ratesProb(rateCategor));
|
|
}
|
|
}
|
|
/*
|
|
void computeCounts::computeCountsNodeXNodeYHomPos(
|
|
const tree::nodeP nodeX,
|
|
const tree::nodeP nodeY) {
|
|
|
|
const tree::nodeP nodeFather = nodeSon->father();
|
|
_ctc.zero();
|
|
if (_weight!=NULL) { // this is one of the MAIN LOOPS. no "if"s deep inside it!
|
|
for (int pos=0; pos< _pi.seqLen(); ++pos) {
|
|
if ((*_weight)[pos] == 0) continue;
|
|
for (int alph1 =0; alph1< _pi.alphabetSize(); ++alph1) {
|
|
for (int alph2 =0; alph2< _pi.alphabetSize(); ++alph2) {
|
|
for (int rate =0; rate< _pi.categories(); ++rate) {
|
|
MDOUBLE tmp = _cup.get(nodeSon->id(),pos,rate,alph1) *
|
|
_cdown.get(nodeSon->id(),pos,rate,alph2) *
|
|
_pi.pij(pos)->getPij(nodeSon->id(),alph1,alph2,rate)*
|
|
_pi.stocProcessFromPos(pos)->freq(alph1)/
|
|
_cprobAtEachPos.getProb(pos);
|
|
_ctc.addToCounts(alph1,alph2,rate,tmp*(*_weight)[pos]);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
else {
|
|
for (int pos=0; pos< _pi.seqLen(); ++pos) {
|
|
for (int alph1 =0; alph1< _pi.alphabetSize(); ++alph1) {
|
|
for (int alph2 =0; alph2< _pi.alphabetSize(); ++alph2) {
|
|
for (int rate =0; rate< _pi.categories(); ++rate) {
|
|
MDOUBLE tmp = _cup.get(nodeSon->id(),pos,rate,alph1) *
|
|
_cdown.get(nodeSon->id(),pos,rate,alph2) *
|
|
_pi.pij(pos)->getPij(nodeSon->id(),alph1,alph2,rate)*
|
|
_pi.stocProcessFromPos(pos)->freq(alph1)/
|
|
_cprobAtEachPos.getProb(pos);
|
|
_ctc.addToCounts(alph1,alph2,rate,tmp);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
}
|
|
*/
|
|
|