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// $Id: NNiSep.cpp 962 2006-11-07 15:13:34Z privmane $
#include "definitions.h"
#include "treeIt.h"
#include "treeUtil.h"
#include "NNiSep.h"
#include "bblEM.h"
#include "logFile.h"
#include "bblEMSeperate.h"
#include <algorithm>
#include <iostream>
#include <iomanip>
using namespace std;
NNiSep::NNiSep(vector<sequenceContainer>& sc,
vector<stochasticProcess>& sp,
const vector<Vdouble *> * weights,
vector<char>* nodeNotToSwap): _nodeNotToSwap(nodeNotToSwap),
_sc(sc),_sp(sp),_weights(weights) {
_bestTrees.resize(sc.size());
_bestScore=VERYSMALL;
_treeEvaluated =-1;
}
void NNiSep::setOfstream(ostream* out) {
_out = out;
}
vector<tree> NNiSep::NNIstep(vector<tree> et) {
const int nGene = et.size();
int z;
for (z=0; z < nGene; ++z) {
et[z].create_names_to_internal_nodes();
}
_bestTrees = et;
_bestScore = evalTrees(_bestTrees);
treeIterTopDown tIt(et[0]);
vector<tree::nodeP> mynode(nGene);
mynode[0] = tIt.first();
for (z=1; z < nGene; ++z ) {
mynode[z] = et[z].findNodeByName(mynode[0]->name());
}
while (mynode[0] != tIt.end()) {
bool haveToBeChecked = true;
if ((mynode[0]->isLeaf() || mynode[0]->isRoot())) haveToBeChecked = false;
if (_nodeNotToSwap) {
if ((*_nodeNotToSwap)[mynode[0]->id()]) {
haveToBeChecked = false;
}
}
if (haveToBeChecked) { // swaping only internal nodes that are not "fixed"
for (z=1; z < nGene; ++z ) {
mynode[z] = et[z].findNodeByName(mynode[0]->name());
}
vector<tree> newT1;
vector<tree> newT2;
for (z=0; z < nGene; ++z ) {
newT1.push_back(NNIswap1(et[z],mynode[z]));
newT2.push_back(NNIswap2(et[z],mynode[z]));
}
MDOUBLE treeScore1 = evalTrees(newT1);
if (treeScore1 > _bestScore) {
_bestTrees = newT1;
_bestScore = treeScore1;
LOG(5,<<"new Best Trees: "<<_bestScore<<endl);
if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
if (_out) (*_out)<<"tree topology (of gene 1 in case of many genes): "<<endl;
_bestTrees[0].output(*_out);
}
MDOUBLE treeScore2 = evalTrees(newT2);
if (treeScore2 > _bestScore) {
_bestTrees = newT2;
_bestScore = treeScore2;
LOG(5,<<"new Best Trees: "<<_bestScore<<endl);
if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
if (_out) (*_out)<<"tree topology (of gene 1 in case of many genes): "<<endl;
_bestTrees[0].output(*_out);
}
}
//nextloop:
mynode[0] = tIt.next();
}
return _bestTrees;
}
tree NNiSep::NNIswap1(tree et,tree::nodeP mynode) {
tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
#ifdef VERBOS
LOG(5,<<"b4 swap1"<<endl);
LOGDO(5,et.output(myLog::LogFile()));
#endif
tree::nodeP fatherNode = mynodeInNewTree->father();
tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
// it might be me
if (nodeToSwap1 == mynodeInNewTree) nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(0);
et.removeNodeFromSonListOfItsFather(nodeToSwap1);
et.removeNodeFromSonListOfItsFather(nodeToSwap2);
nodeToSwap2->setFather(fatherNode);
fatherNode->setSon(nodeToSwap2);
nodeToSwap1->setFather(mynodeInNewTree);
mynodeInNewTree->setSon(nodeToSwap1);
#ifdef VERBOS
LOG(5,<<"after swap1"<<endl);
LOGDO(5,et.output(myLog::LogFile()));
#endif
return et;
}
tree NNiSep::NNIswap2(tree et,tree::nodeP mynode) {
#ifdef VERBOS
LOG(5,<<"b4 swap2"<<endl);
LOGDO(5,et.output(myLog::LogFile()));
#endif
tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
tree::nodeP fatherNode = mynodeInNewTree->father();
tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
// it might be me
if (nodeToSwap1 == mynodeInNewTree) nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(1);
et.removeNodeFromSonListOfItsFather(nodeToSwap1);
et.removeNodeFromSonListOfItsFather(nodeToSwap2);
nodeToSwap2->setFather(fatherNode);
fatherNode->setSon(nodeToSwap2);
nodeToSwap1->setFather(mynodeInNewTree);
mynodeInNewTree->setSon(nodeToSwap1);
#ifdef VERBOS
LOG(5,<<"after swap2"<<endl);
LOGDO(5,et.output(myLog::LogFile()));
#endif
return et;
}
MDOUBLE NNiSep::evalTrees(vector<tree>& et) {
#ifdef VERBOS
LOG(5,<<"b4 bbl in alltrees"<<endl);
for (vector<tree>::const_iterator i=et.begin();i!=et.end();++i)
LOGDO(5,i->output(myLog::LogFile()));
#endif
bblEMSeperate bblemsep1(et,_sc,_sp,_weights);
MDOUBLE res = bblemsep1.getTreeLikelihood();
_treeEvaluated++;
LOG(5,.precision(5));
_out->precision(5);
if (_treeEvaluated) LOG(5,<<"tree: "<<_treeEvaluated<< "score = "<<res<<endl);
if ((_out)&&(_treeEvaluated)) (*_out)<<"tree: "<<_treeEvaluated<< "score = "<<res<<endl;
return res;
}
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