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140 lines
3.8 KiB
C++
140 lines
3.8 KiB
C++
// $Id: NNiProp.cpp 962 2006-11-07 15:13:34Z privmane $
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#include "definitions.h"
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#include "treeIt.h"
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#include "treeUtil.h"
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#include "NNiProp.h"
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#include "bblEM.h"
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#include "bblEMProportional.h"
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#include "logFile.h"
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#include <algorithm>
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#include <iostream>
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#include <iomanip>
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using namespace std;
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NNiProp::NNiProp(vector<sequenceContainer>& sc,
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vector<stochasticProcess>& sp,
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const vector<Vdouble *> * weights,
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vector<char>* nodeNotToSwap):_nodeNotToSwap(nodeNotToSwap),
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_sc(sc),_sp(sp),_weights(weights) {
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_bestScore = VERYSMALL;
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_treeEvaluated =-1;
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_out = NULL;
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}
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void NNiProp::setOfstream(ostream* out) {
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_out = out;
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}
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tree NNiProp::NNIstep(tree et) {
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et.create_names_to_internal_nodes();
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_bestScore = evalTree(et);
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_bestTree = et;
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treeIterTopDown tIt(et);
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for (tree::nodeP mynode = tIt.first(); mynode != tIt.end(); mynode = tIt.next()) {
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if (mynode->isLeaf() || mynode->isRoot()) continue; // swaping only internal nodes
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if (_nodeNotToSwap) {
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if ((*_nodeNotToSwap)[mynode->id()]) {
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continue;
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}
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}
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tree newT1 = NNIswap1(et,mynode);
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tree newT2 = NNIswap2(et,mynode);
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MDOUBLE treeScore1 = evalTree(newT1);
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if (treeScore1 > _bestScore) {
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_bestTree = newT1;
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_bestScore = treeScore1;
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LOG(5,<<"new Best Tree: "<<_bestScore<<endl);
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if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
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_bestTree.output(*_out);
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}
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MDOUBLE treeScore2 = evalTree(newT2);
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if (treeScore2 > _bestScore) {
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_bestTree = newT2;
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_bestScore = treeScore2;
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LOG(5,<<"new Best Tree: "<<_bestScore<<endl);
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if (_out) (*_out)<<"new Best Tree: "<<_bestScore<<endl;
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_bestTree.output(*_out);
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}
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}
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return _bestTree;
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}
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tree NNiProp::NNIswap1(tree et,tree::nodeP mynode) {
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tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
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#ifdef VERBOS
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LOG(5,<<"b4 swap1"<<endl);
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LOGDO(5,et.output(myLog::LogFile()));
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#endif
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tree::nodeP fatherNode = mynodeInNewTree->father();
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tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
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// it might be me
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if (nodeToSwap1 == mynodeInNewTree) nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
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tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(0);
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et.removeNodeFromSonListOfItsFather(nodeToSwap1);
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et.removeNodeFromSonListOfItsFather(nodeToSwap2);
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nodeToSwap2->setFather(fatherNode);
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fatherNode->setSon(nodeToSwap2);
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nodeToSwap1->setFather(mynodeInNewTree);
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mynodeInNewTree->setSon(nodeToSwap1);
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#ifdef VERBOS
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LOG(5,<<"after swap1"<<endl);
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LOGDO(5,et.output(myLog::LogFile()));
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#endif
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return et;
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}
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tree NNiProp::NNIswap2(tree et,tree::nodeP mynode) {
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#ifdef VERBOS
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LOG(5,<<"b4 swap2"<<endl);
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LOGDO(5,et.output(myLog::LogFile()));
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#endif
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tree::nodeP mynodeInNewTree = et.findNodeByName(mynode->name());
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tree::nodeP fatherNode = mynodeInNewTree->father();
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tree::nodeP nodeToSwap1 = mynodeInNewTree->father()->getSon(0);
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// it might be me
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if (nodeToSwap1 == mynodeInNewTree) nodeToSwap1 = mynodeInNewTree->father()->getSon(1);
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tree::nodeP nodeToSwap2 = mynodeInNewTree->getSon(1);
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et.removeNodeFromSonListOfItsFather(nodeToSwap1);
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et.removeNodeFromSonListOfItsFather(nodeToSwap2);
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nodeToSwap2->setFather(fatherNode);
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fatherNode->setSon(nodeToSwap2);
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nodeToSwap1->setFather(mynodeInNewTree);
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mynodeInNewTree->setSon(nodeToSwap1);
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#ifdef VERBOS
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LOG(5,<<"after swap2"<<endl);
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LOGDO(5,et.output(myLog::LogFile()));
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#endif
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return et;
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}
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MDOUBLE NNiProp::evalTree(tree& et) {
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#ifdef VERBOS
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LOG(5,<<"b4 bbl in alltrees"<<endl);
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LOGDO(5,et.output(myLog::LogFile()));
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#endif
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bblEMProportional bblEMprop1(et,_sc,_sp,_weights);
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MDOUBLE res = bblEMprop1.getTreeLikelihood();
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// MDOUBLE res = 12;
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_treeEvaluated++;
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// cerr.precision(5);
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_out->precision(5);
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if (_treeEvaluated) LOG(5,<<"tree: "<<_treeEvaluated<< "score = "<<res<<endl);
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if ((_out)&&(_treeEvaluated)) (*_out)<<"tree: "<<_treeEvaluated<< "score = "<<res<<endl;
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return res;
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}
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