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Viewing changes to src/Bpp/Phyl/Model/HKY85.cpp

  • Committer: Package Import Robot
  • Author(s): Julien Dutheil
  • Date: 2013-02-09 16:00:00 UTC
  • mfrom: (1.1.1)
  • Revision ID: package-import@ubuntu.com-20130209160000-5v65ba68z8032nzj
Tags: 2.0.3-1
* Reorganized model hierarchy
* New pairwise models
* Several bugs fixed

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src/Bpp/Phyl/Model/HKY85.cpp
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//
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/*
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Copyright or © or Copr. CNRS, (November 16, 2004)
 
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Copyright or © or Copr. Bio++ Development Team, (November 16, 2004)
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This software is a computer program whose purpose is to provide classes
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for phylogenetic data analysis.
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*/
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#include "HKY85.h"
 
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#include "FrequenciesSet.h"
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#include <Bpp/Numeric/Matrix/MatrixTools.h>
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        double piC,
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        double piG,
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        double piT):
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        AbstractReversibleSubstitutionModel(alpha, "HKY85."),
 
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  AbstractParameterAliasable("HKY85."),
 
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  AbstractSubstitutionModel(alpha, "HKY85."),
 
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  AbstractReversibleSubstitutionModel(alpha, "HKY85."),
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  kappa_(kappa), k1_(), k2_(), r_(),
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  piA_(piA), piC_(piC), piG_(piG), piT_(piT), piY_(), piR_(),
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  theta_(piG + piC), theta1_(piA / (1. - theta_)), theta2_(piG / theta_),
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{
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        Parameter kappaP("HKY85.kappa", kappa, &Parameter::R_PLUS_STAR);
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        addParameter_(kappaP);
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        Parameter thetaP("HKY85.theta" , theta_, new IncludingInterval(0.001, 0.999), true);
 
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        Parameter thetaP("HKY85.theta" , theta_, &FrequenciesSet::FREQUENCE_CONSTRAINT);
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        addParameter_(thetaP);
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        Parameter theta1P("HKY85.theta1", theta1_, new IncludingInterval(0.001, 0.999), true);
 
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        Parameter theta1P("HKY85.theta1", theta1_, &FrequenciesSet::FREQUENCE_CONSTRAINT);
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        addParameter_(theta1P);
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        Parameter theta2P("HKY85.theta2", theta2_, new IncludingInterval(0.001, 0.999), true);
 
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        Parameter theta2P("HKY85.theta2", theta2_, &FrequenciesSet::FREQUENCE_CONSTRAINT);
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        addParameter_(theta2P);
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        updateMatrices();
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}