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131 lines
3.7 KiB
C++
131 lines
3.7 KiB
C++
// $Id: bestParamUSSRV.h 1975 2007-04-22 13:47:28Z privmane $
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#ifndef BEST_PARAM_USSRV
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#define BEST_PARAM_USSRV
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#include "definitions.h"
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#include "sequenceContainer.h"
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#include "stochasticProcess.h"
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#include "gammaDistribution.h"
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#include "tree.h"
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#include "replacementModelSSRV.h"
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#include "stochasticProcessSSRV.h"
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#include "C_evalParamUSSRV.h"
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#include "bestAlpha.h"
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#include "numRec.h"
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#include "bblEM.h"
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#include "logFile.h"
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#include "bestAlphaAndNu.h"
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#include "bblEM2USSRV.h"
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#include "someUtil.h"
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#include <ctime>
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// ***************
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// * USSRV *
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// ***************
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class bestParamUSSRV
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{
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public:
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explicit bestParamUSSRV(bool AlphaOptimization, bool NuOptimization,
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bool FOptimization, bool bblOptimization):
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_AlphaOptimizationFlag(AlphaOptimization),
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_NuOptimizationFlag(NuOptimization),
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_FOptimizationFlag(FOptimization),
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_bblOptimizationFlag(bblOptimization) {}
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MDOUBLE operator() (tree& et,
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const sequenceContainer& sc,
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const sequenceContainer& baseSc,
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ussrvModel& model,
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const Vdouble * weights=NULL,
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const MDOUBLE AlphaUpperBound = 15,
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const MDOUBLE NuUpperBound = 15,
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const MDOUBLE FUpperBound = 1,
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const MDOUBLE epsilonParamOptimization = 0.01,
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const MDOUBLE epsilonLikelihoodImprovment = 0.01,
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const int maxIterations = 50,
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const int maxOfParametersAndBblIterations = 40);
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MDOUBLE getBestAlpha() {return _bestAlpha;}
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MDOUBLE getBestNu() {return _bestNu;}
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MDOUBLE getBestF() {return _bestF;}
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MDOUBLE getBestL() {return _bestL;}
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private:
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MDOUBLE _bestAlpha;
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MDOUBLE _bestNu;
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MDOUBLE _bestF;
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MDOUBLE _bestL;
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// flags
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bool _AlphaOptimizationFlag;
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bool _NuOptimizationFlag;
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bool _FOptimizationFlag;
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bool _bblOptimizationFlag;
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};
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// ***************
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// * SSRV *
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// ***************
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class bestParamSSRV
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{
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public:
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explicit bestParamSSRV(bool AlphaOptimization, bool NuOptimization, bool tamura92Optimization,
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bool bblOptimization):
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_AlphaOptimizationFlag(AlphaOptimization),
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_NuOptimizationFlag(NuOptimization),
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_tamura92OptimizationFlag(tamura92Optimization),
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_bblOptimizationFlag(bblOptimization) {}
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MDOUBLE operator() (tree& et,
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const sequenceContainer& sc,
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stochasticProcessSSRV& ssrvSp,
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const Vdouble * weights=NULL,
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const MDOUBLE AlphaUpperBound = 15,
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const MDOUBLE NuUpperBound = 15,
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const MDOUBLE TrTvUpperBound = 10,
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const MDOUBLE epsilonParamOptimization = 0.01,
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const MDOUBLE epsilonLikelihoodImprovment = 0.01,
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const MDOUBLE epsilonBbl = 0.05,
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const int maxIterations = 50,
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const int maxOfParametersAndBblIterations = 40);
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// Variant that can work on a const tree - only if we're not doing BBL
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// WARNING: Running this with bblOptimization==true will give a fatal error
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MDOUBLE operator() (const tree& et,
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const sequenceContainer& sc,
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stochasticProcessSSRV& ssrvSp,
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const Vdouble * weights=NULL,
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const MDOUBLE AlphaUpperBound = 15,
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const MDOUBLE NuUpperBound = 15,
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const MDOUBLE TrTvUpperBound = 10,
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const MDOUBLE epsilonParamOptimization = 0.01,
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const MDOUBLE epsilonLikelihoodImprovment = 0.01,
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const MDOUBLE epsilonBbl = 0.05,
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const int maxIterations = 50,
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const int maxOfParametersAndBblIterations = 40);
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MDOUBLE getBestAlpha() {return _bestAlpha;}
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MDOUBLE getBestNu() {return _bestNu;}
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MDOUBLE getBestTrTv() {return _bestTrTv;}
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MDOUBLE getBestTheta() {return _bestTheta;}
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MDOUBLE getBestL() {return _bestL;}
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private:
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MDOUBLE _bestAlpha;
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MDOUBLE _bestNu;
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MDOUBLE _bestTrTv;
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MDOUBLE _bestTheta;
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MDOUBLE _bestL;
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// flags
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bool _AlphaOptimizationFlag;
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bool _NuOptimizationFlag;
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bool _tamura92OptimizationFlag;
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bool _bblOptimizationFlag;
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};
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#endif // BEST_PARAM_USSRV
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