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// $Id: computeDownAlg.cpp 4585 2008-08-05 15:02:58Z cohenofi $
#include "definitions.h"
#include "computeDownAlg.h"
#include "treeIt.h"
void computeDownAlg::fillComputeDown(const tree& et,
const sequenceContainer& sc,
const int pos,
const computePijHom& pi,
suffStatGlobalHomPos& ssc,
const suffStatGlobalHomPos& cup){
ssc.allocatePlace(et.getNodesNum(), pi.alphabetSize());
treeIterTopDownConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
int letter,letterInFather,bro,letterInSon;
if (mynode->father()==NULL) {// if root
for(letter=0; letter<pi.alphabetSize();letter++) {
ssc.set(mynode->id(),letter,1.0);
}
mynode = tIt.next(); //continue
}
tree::nodeP fatherNode=mynode->father();
const int n_bro=fatherNode->getNumberOfSons();
for(letter=0; letter<pi.alphabetSize();letter++) {//alpha
doubleRep totalProb=1.0;
doubleRep fatherTerm=0;
if (fatherNode->father()!=NULL) {
for(letterInFather=0; letterInFather<pi.alphabetSize();letterInFather++)
fatherTerm += pi.getPij(fatherNode->id(),letter,letterInFather)*
ssc.get(fatherNode->id(),letterInFather);
}
else {
fatherTerm=1.0;
}
doubleRep brotherTerm=1.0;
for(bro = 0; bro < n_bro; bro++) {
tree::nodeP brother = fatherNode->getSon(bro);
if (brother != mynode) {
doubleRep tmp_bro=0.0;
for(letterInSon=0; letterInSon<pi.alphabetSize();letterInSon++) {
tmp_bro+=pi.getPij(fatherNode->getSon(bro)->id(),letter,letterInSon)*
cup.get(brother->id(),letterInSon);
}
brotherTerm *=tmp_bro;
}
}
totalProb = fatherTerm * brotherTerm;
ssc.set(mynode->id(),letter,totalProb);
}
}
}
//use Pij(t) from the stochastic process instead of precomputed probabilities (via the computePijHom class)
void computeDownAlg::fillComputeDown(const tree& et,
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc,
const suffStatGlobalHomPos& cup){
ssc.allocatePlace(et.getNodesNum(), sp.alphabetSize());
treeIterTopDownConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
int letter, letterInFather, bro, letterInSon;
if (mynode->isRoot()) {// if root: set all values to 1.0
for(letter = 0; letter < sp.alphabetSize(); letter++) {
ssc.set(mynode->id(), letter, 1.0);
}
mynode = tIt.next(); //continue
}
tree::nodeP fatherNode = mynode->father();
const int n_bro = fatherNode->getNumberOfSons();
for(letter = 0; letter < sp.alphabetSize(); letter++) {
doubleRep totalProb=1.0;
doubleRep fatherTerm=0;
if (fatherNode->isRoot())
{
fatherTerm = 1.0;
}
else
{
for(letterInFather = 0; letterInFather < sp.alphabetSize(); letterInFather++)
{
MDOUBLE dist = fatherNode->dis2father() * sp.getGlobalRate();
fatherTerm += sp.Pij_t(letter, letterInFather, dist)
* ssc.get(fatherNode->id(), letterInFather);
}
}
doubleRep brotherTerm = 1.0;
for(bro = 0; bro < n_bro; bro++) {
tree::nodeP brother = fatherNode->getSon(bro);
if (brother != mynode) {
doubleRep tmp_bro=0.0;
for(letterInSon = 0; letterInSon < sp.alphabetSize(); letterInSon++)
{
MDOUBLE dist = brother->dis2father() * sp.getGlobalRate();
tmp_bro += sp.Pij_t(letter, letterInSon, dist)
* cup.get(brother->id(), letterInSon);
}
brotherTerm *= tmp_bro;
}
}
totalProb = fatherTerm * brotherTerm;
ssc.set(mynode->id(), letter, totalProb);
}
}
}
//compute probabilities with a site-specific rate
void computeDownAlg::fillComputeDownSpecificRate(const tree& et,
const sequenceContainer& sc,
const int pos,
const stochasticProcess& sp,
suffStatGlobalHomPos& ssc,
const suffStatGlobalHomPos& cup,
const MDOUBLE gRate){
ssc.allocatePlace(et.getNodesNum(), sp.alphabetSize());
treeIterTopDownConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
int letter, letterInFather, bro, letterInSon;
if (mynode->isRoot()) {// if root: set all values to 1.0
for(letter = 0; letter < sp.alphabetSize(); letter++) {
ssc.set(mynode->id(), letter, 1.0);
}
mynode = tIt.next(); //continue
}
tree::nodeP fatherNode = mynode->father();
const int n_bro = fatherNode->getNumberOfSons();
for(letter = 0; letter < sp.alphabetSize(); letter++) {
doubleRep totalProb=1.0;
doubleRep fatherTerm=0;
if (fatherNode->isRoot())
{
fatherTerm = 1.0;
}
else
{
for(letterInFather = 0; letterInFather < sp.alphabetSize(); letterInFather++)
{
MDOUBLE dist = fatherNode->dis2father() * gRate * sp.getGlobalRate();
fatherTerm += sp.Pij_t(letter, letterInFather, dist)
* ssc.get(fatherNode->id(), letterInFather);
}
}
doubleRep brotherTerm = 1.0;
for(bro = 0; bro < n_bro; bro++) {
tree::nodeP brother = fatherNode->getSon(bro);
if (brother != mynode) {
doubleRep tmp_bro=0.0;
for(letterInSon = 0; letterInSon < sp.alphabetSize(); letterInSon++)
{
MDOUBLE dist = brother->dis2father() * gRate * sp.getGlobalRate();
tmp_bro += sp.Pij_t(letter, letterInSon, dist)
* cup.get(brother->id(), letterInSon);
}
brotherTerm *= tmp_bro;
}
}
totalProb = fatherTerm * brotherTerm;
ssc.set(mynode->id(), letter, totalProb);
}
}
}
// The filled sscGivenRoot is using the "Gam" class (over all rate categories) for placing letter@root hidden state
void computeDownAlg::fillComputeDownNonReversible(const tree& et,
const sequenceContainer& sc,
const int pos,
const computePijHom& pi,
suffStatGlobalGamPos& sscGivenRoot,
const suffStatGlobalHomPos& cup)
{
sscGivenRoot.allocatePlace(pi.alphabetSize(),et.getNodesNum(), pi.alphabetSize());
treeIterTopDownConst tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
int letter,letterInFather,bro,letterInSon;
if (mynode->father()==NULL) {//root
for (int letterAtRoot=0; letterAtRoot<pi.alphabetSize();letterAtRoot++){
for(letter=0; letter<pi.alphabetSize();letter++) {
MDOUBLE ind = (letterAtRoot==letter?1.0:0.0);
sscGivenRoot.set(letterAtRoot,mynode->id(),letter,ind);
}
}
mynode = tIt.next(); //continue
}
tree::nodeP fatherNode=mynode->father();
const int n_bro=fatherNode->getNumberOfSons();
for(int letterAtRoot=0; letterAtRoot<pi.alphabetSize();letterAtRoot++) {//root state
for(letter=0; letter<pi.alphabetSize();letter++) {//letter for current down calc (at father of node)
doubleRep totalProb=1.0;
doubleRep fatherTerm=0;
//down of father
if (fatherNode->father()!=NULL) { // not son of root
for(letterInFather=0; letterInFather<pi.alphabetSize();letterInFather++)//father of father
fatherTerm += pi.getPij(fatherNode->id(),letterInFather,letter)*
sscGivenRoot.get(letterAtRoot,fatherNode->id(),letterInFather);
}
else {//son of root
fatherTerm=(letterAtRoot==letter?1.0:0.0);
}
doubleRep brotherTerm=1.0;
for(bro = 0; bro < n_bro; bro++) {
tree::nodeP brother = fatherNode->getSon(bro);
if (brother != mynode) {
doubleRep tmp_bro=0.0;
for(letterInSon=0; letterInSon<pi.alphabetSize();letterInSon++) {
tmp_bro+=pi.getPij(fatherNode->getSon(bro)->id(),letter,letterInSon)*
cup.get(brother->id(),letterInSon);
}
brotherTerm *=tmp_bro;
}
}
totalProb = fatherTerm * brotherTerm;
sscGivenRoot.set(letterAtRoot,mynode->id(),letter,totalProb);
}
}
}
}
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