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// $Id: NNiProp.cpp 962 2006-11-07 15:13:34Z privmane $
#include "definitions.h"
#include "treeIt.h"
#include "treeUtil.h"
#include "NNiProp.h"
#include "bblEM.h"
#include "bblEMProportional.h"
#include "logFile.h"
#include <algorithm>
#include <iostream>
#include <iomanip>
using namespace std;
NNiProp::NNiProp(vector<sequenceContainer>& sc,
vector<stochasticProcess>& sp,
const vector<Vdouble *> * weights,
vector<char>* nodeNotToSwap):_nodeNotToSwap(nodeNotToSwap),
_sc(sc),_sp(sp),_weights(weights) {
_bestScore = VERYSMALL;
_treeEvaluated =-1;
_out = NULL;
}
void NNiProp::setOfstream(ostream* out) {
_out = out;
}
tree NNiProp::NNIstep(tree et) {
et.create_names_to_internal_nodes();
_bestScore = evalTree(et);
_bestTree = et;
treeIterTopDown tIt(et);
for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
if (mynode->isLeaf() || mynode->isRoot()) continue; // swaping only internal nodes
if (_nodeNotToSwap) {
if ((*_nodeNotToSwap)[mynode->id()]) {
continue;
}
}
tree newT1 = NNIswap1(et,mynode);
tree newT2 = NNIswap2(et,mynode);
MDOUBLE treeScore1 = evalTree(newT1);
if (treeScore1 > _bestScore) {
_bestTree = newT1;
_bestScore = treeScore1;
LOG(5,<<"new Best Tree: "<<_bestScore<<endl);
if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
_bestTree.output(*_out);
}
MDOUBLE treeScore2 = evalTree(newT2);
if (treeScore2 > _bestScore) {
_bestTree = newT2;
_bestScore = treeScore2;
LOG(5,<<"new Best Tree: "<<_bestScore<<endl);
if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
_bestTree.output(*_out);
}
}
return _bestTree;
}
tree NNiProp::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 NNiProp::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 NNiProp::evalTree(tree& et) {
#ifdef VERBOS
LOG(5,<<"b4 bbl in alltrees"<<endl);
LOGDO(5,et.output(myLog::LogFile()));
#endif
bblEMProportional bblEMprop1(et,_sc,_sp,_weights);
MDOUBLE res = bblEMprop1.getTreeLikelihood();
// MDOUBLE res = 12;
_treeEvaluated++;
// cerr.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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