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71 lines
2.2 KiB
C++
71 lines
2.2 KiB
C++
// $Id: semphySearchBestTree.h 6002 2009-03-20 19:39:03Z privmane $
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#ifndef ___SEMPHY_SEARCH_BEST_TREE
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#define ___SEMPHY_SEARCH_BEST_TREE
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#include "alphabet.h"
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#include "sequenceContainer.h"
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#include "tree.h"
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#include "stochasticProcess.h"
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#include <iostream>
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using namespace std;
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class semphySearchBestTree {
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public:
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explicit semphySearchBestTree(sequenceContainer& sc,
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tree& startTree,
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const tree* ctPtr,
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stochasticProcess& sp,
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ostream& out,
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const int numOfRandomStart = 1,
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const bool optimizeAlpha = false,
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const double epsilonLikelihoodImprovement4alphaOptimiz = 0.001,
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const double epsilonLikelihoodImprovement4BBL = 0.001,
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const int maxIterationsBBL = 10,
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const Vdouble * weights = NULL);
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virtual ~semphySearchBestTree(){}
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private:
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MDOUBLE semphyBasicSearchBestTree(
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sequenceContainer& sc,
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tree& et,
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const tree* ctPtr,
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stochasticProcess& sp,
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const bool optimizeAlpha = false,
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const double epsilonLikelihoodImprovement4alphaOptimiz = 0.001,
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const double epsilonLikelihoodImprovement4BBL = 0.001,
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const int maxIterationsBBL = 10,
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const Vdouble * weights = NULL);
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MDOUBLE semphyBasicSearchBestTree(
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sequenceContainer& sc,
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tree& startTree,
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const tree* ctPtr,
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stochasticProcess& sp,
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ostream& out,
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const bool optimizeAlpha = false,
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const double epsilonLikelihoodImprovement4alphaOptimiz = 0.001,
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const double epsilonLikelihoodImprovement4BBL = 0.001,
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const int maxIterationsBBL = 10,
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const Vdouble * weights = NULL);
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MDOUBLE semphyBasicSearchBestTreeManyRandomStarts(
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sequenceContainer& sc,
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tree& et,
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const tree* ctPtr,
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stochasticProcess& sp,
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ostream& out,
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const int nRanStart,
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const bool optimizeAlpha = false,
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const double epsilonLikelihoodImprovement4alphaOptimiz = 0.001,
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const double epsilonLikelihoodImprovement4BBL = 0.001,
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const int maxIterationsBBL = 10,
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const Vdouble * weights = NULL);
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};
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#endif
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