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