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69 lines
1.5 KiB
C++
69 lines
1.5 KiB
C++
// $Id: allTrees.h 1731 2007-02-26 13:45:23Z itaymay $
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#ifndef ___ALL_TREES
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#define ___ALL_TREES
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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 allTrees {
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public:
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explicit allTrees(bool keepAllTrees = false);
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MDOUBLE getBestScore() {return _bestScore;}
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tree getBestTree() {return _bestTree;}
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void getAllTreesAndLikelihoods(vector<tree>& resTree,VdoubleRep & scores) {
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resTree = _allPossibleTrees;
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scores = _allPossibleScores;
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}
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void recursiveFind( tree et,
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const stochasticProcess& sp,
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const sequenceContainer& sc,
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vector<int> idLeft,
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const 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 sequenceContainer* sc,
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const stochasticProcess* sp,
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const 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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private:
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tree _bestTree;
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MDOUBLE _bestScore;
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vector<tree> _allPossibleTrees;
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vector<doubleRep> _allPossibleScores;
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const bool _keepAllTrees;
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MDOUBLE evalTree(tree& et,
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const stochasticProcess& sp,
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const sequenceContainer& sc,
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const int maxIterations,
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const MDOUBLE epsilon,
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const Vdouble * weights = NULL);
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};
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#endif
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