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