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// $Id: allTrees.cpp 962 2006-11-07 15:13:34Z privmane $
#include "definitions.h"
#include "allTrees.h"
#include "treeUtil.h"
#include "treeIt.h"
#include "bblEM.h"
#include <algorithm>
#include <iostream>
#include "someUtil.h"
using namespace std;
#ifndef VERBOS
#define VERBOS
#endif
allTrees::allTrees(bool keepAllTrees) : _keepAllTrees(keepAllTrees) {
_bestScore = VERYSMALL;
}
void get3seqTreeAndIdLeftVec(const sequenceContainer* sc,
tree& starT,
vector<int>& idList){
sequenceContainer::constTaxaIterator tIt;
sequenceContainer::constTaxaIterator tItEnd;
tIt.begin(*sc);
tItEnd.end(*sc);
while(tIt != tItEnd) {
idList.push_back(tIt->id());
++tIt;
}
if (sc->numberOfSeqs()<3) errorMsg::reportError(" searching a tree for number of sequences < 3 ");
starT.createRootNode();
starT.createNode(starT.getRoot(),1);
starT.createNode(starT.getRoot(),2);
starT.createNode(starT.getRoot(),3);
const string nameOfSeq1 = (*sc)[idList[idList.size()-1]].name();
const string nameOfSeq2 = (*sc)[idList[idList.size()-2]].name();
const string nameOfSeq3 = (*sc)[idList[idList.size()-3]].name();
idList.pop_back();
idList.pop_back();
idList.pop_back();
starT.getRoot()->getSon(0)->setName(nameOfSeq1);
starT.getRoot()->getSon(1)->setName(nameOfSeq2);
starT.getRoot()->getSon(2)->setName(nameOfSeq3);
starT.createFlatLengthMatrix();
}
void allTrees::recursiveFind( const sequenceContainer* sc,
const stochasticProcess* sp,
const Vdouble * weights,
const int maxIterations,
const MDOUBLE epsilon){
tree starT;
vector<int> ids;
get3seqTreeAndIdLeftVec(sc,starT,ids);
recursiveFind(starT,*sp,*sc,ids,weights,maxIterations,epsilon);
}
tree getAnewTreeFrom(const tree& et, tree::nodeP & mynode,
vector<int> & idLeft, const string& nameToAdd) {
tree newT = et;
tree::nodeP mynodeInNewTree = newT.findNodeByName(mynode->name());
// int NameToAdd = idLeft[idLeft.size()-1];
idLeft.pop_back();
tree::nodeP fatherNode = mynodeInNewTree->father();
tree::nodeP newInternalNode = newT.createNode(fatherNode, newT.getNodesNum());
mynodeInNewTree->setFather(newInternalNode);
newInternalNode->setSon(mynodeInNewTree);
fatherNode->removeSon(mynodeInNewTree);
tree::nodeP newOTU= newT.createNode(newInternalNode, newT.getNodesNum());;
//string nameX = (*sc)[NameToAdd].name();
newOTU->setName(nameToAdd);
newOTU->setDisToFather(tree::FLAT_LENGTH_VALUE);
newInternalNode->setDisToFather(tree::FLAT_LENGTH_VALUE);
newT.create_names_to_internal_nodes();
return newT;
}
void allTrees::recursiveFind(tree et,
const stochasticProcess& sp,
const sequenceContainer& sc,
vector<int> idLeft,
const Vdouble * weights,
const int maxIterations,
const MDOUBLE epsilon) {
if (idLeft.empty()) {
//static int k=1; k++;
MDOUBLE treeScore = evalTree(et,sp,sc,maxIterations,epsilon,weights);
if (_keepAllTrees) {
_allPossibleTrees.push_back(et);
_allPossibleScores.push_back(treeScore);
}
LOG(5,<<".");
//LOG(5,<<"tree: "<<k<<" l= "<<treeScore<<endl);
if (treeScore > _bestScore) {
//LOG(5,<<"new Best score!"<<endl);
_bestTree = et;
_bestScore = treeScore;
}
} else {
treeIterTopDown tIt(et);
tree::nodeP mynode = tIt.first();
mynode = tIt.next(); // skipping the root
for (; mynode != tIt.end(); mynode = tIt.next()) {
int NameToAdd = idLeft[idLeft.size()-1];
tree newT = getAnewTreeFrom(et,mynode,idLeft,sc[NameToAdd].name());
recursiveFind(newT,sp,sc,idLeft,weights,maxIterations,epsilon);
idLeft.push_back(NameToAdd);
}
}
}
MDOUBLE allTrees::evalTree( tree& et,
const stochasticProcess& sp,
const sequenceContainer& sc,
const int maxIterations,
const MDOUBLE epsilon,
const Vdouble * weights) {
bblEM bblEM1(et,sc,sp,weights,maxIterations,epsilon);
MDOUBLE res =bblEM1.getTreeLikelihood();
return res;
}
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