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36 lines
1.1 KiB
C++
36 lines
1.1 KiB
C++
// $Id: likelihoodComputation2Codon.h 4699 2008-08-14 14:19:46Z privmane $
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#ifndef ___LIKELIHOOD_COMPUTATION_2_CODON
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#define ___LIKELIHOOD_COMPUTATION_2_CODON
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#include "definitions.h"
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#include "computePijComponent.h"
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#include "sequenceContainer.h"
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#include "suffStatComponent.h"
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namespace likelihoodComputation2Codon {
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MDOUBLE getTreeLikelihoodAllPosAlphTheSame(const tree& et,
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const sequenceContainer& sc,
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const vector<stochasticProcess>& spVec,
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const distribution * distr);
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MDOUBLE getProbOfPosUpIsFilledSelectionGam(const int pos,const tree& et, //used for gamma model
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const sequenceContainer& sc,
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const stochasticProcess& sp,
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const suffStatGlobalGamPos& cup,
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const distribution * distr);
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MDOUBLE getTreeLikelihoodFromUp2(const tree& et,
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const sequenceContainer& sc,
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const stochasticProcess& sp,
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const suffStatGlobalGam& cup,
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Vdouble& posLike, // fill this vector with each position likelihood but without the weights.
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const distribution * distr,
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const Vdouble * weights=0);
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};
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#endif
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