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// $Id: allTreesSeparateModel.h 962 2006-11-07 15:13:34Z privmane $
#ifndef ___ALL_TREES_SEPARATE_MODEL
#define ___ALL_TREES_SEPARATE_MODEL
#include "definitions.h"
#include "tree.h"
#include "sequenceContainer.h"
#include "stochasticProcess.h"
#include <vector>
using namespace std;
void get3seqTreeAndIdLeftVec(const sequenceContainer* sc,
tree& starT,
vector<int>& idList);
tree getAnewTreeFrom( const tree& et,
tree::nodeP & mynode,
vector<int> & idLeft,
const string& nameToAdd);
class allTreesSeparateModel {
public:
explicit allTreesSeparateModel();
MDOUBLE getBestScore() {return _bestScore;}
tree getBestTree() {return _bestTree;}
void recursiveFind(tree et,
const vector<stochasticProcess>& sp,
const vector<sequenceContainer>& sc,
vector<int> idLeft,
const vector<Vdouble* > * weights=NULL,
const int maxIterations=1000,
const MDOUBLE epsilon=0.05);
void recursiveFind( const vector<sequenceContainer>* sc,
const vector<stochasticProcess>* sp,
const vector<Vdouble* > * weights= NULL,
const int maxIterations=1000,
const MDOUBLE epsilon=0.05); // one tree.
vector<tree> getTreeVecBest() {return _treeVecBest;}
private:
tree _bestTree;
MDOUBLE _bestScore;
vector<tree> _treeVecTmp; // same tree topologies, diff branch lengths
vector<tree> _treeVecBest;// same tree topologies, diff branch lengths
MDOUBLE evalTree( tree& et,
const vector<stochasticProcess>& sp,
const vector<sequenceContainer>& sc,
const int maxIterations,
const MDOUBLE epsilon,
const vector<Vdouble* > * weights = NULL);
};
#endif
// const stochasticProcess* _sp;
//const sequenceContainer* _sc;
//const Vdouble * _weights;
//vector<tree> getBestTreesSep() {return _bestSepTrees;}
//vector<tree> _bestSepTrees;
//vector<tree> _tmpSepTrees;
//vector<tree> recursiveFindSep(const vector<sequenceContainer>* sc,
// const vector<stochasticProcess>* sp,
// const vector<Vdouble *> * weights,
// const int maxIterations=1000,
// const MDOUBLE epsilon=0.05); // sep model
//const vector<sequenceContainer>* _scVec;
//vector<stochasticProcess>* _spVec; // not const, so in proportional for example it can be changed.
//const vector<Vdouble *> * _weightsVec;
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