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Viewing changes to src/Bpp/Phyl/Model/JCprot.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/JCprot.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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JCprot::JCprot(const ProteicAlphabet* alpha) :
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  AbstractReversibleSubstitutionModel(alpha, "JC69."), exp_(), p_(size_, size_),
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  freqSet_(0)
 
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  AbstractParameterAliasable("JC69."),
 
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  AbstractSubstitutionModel(alpha, "JC69."),
 
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  AbstractReversibleSubstitutionModel(alpha, "JC69."),
 
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  exp_(), p_(size_, size_), freqSet_(0)
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{
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  freqSet_ = new FixedProteinFrequenciesSet(alpha, freq_);
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  updateMatrices();
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}
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JCprot::JCprot(const ProteicAlphabet* alpha, ProteinFrequenciesSet* freqSet, bool initFreqs) :
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  AbstractReversibleSubstitutionModel(alpha, "JC69+F."), exp_(), p_(size_, size_),
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  freqSet_(freqSet)
 
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  AbstractParameterAliasable("JC69+F."),
 
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  AbstractSubstitutionModel(alpha, "JC69+F."),
 
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  AbstractReversibleSubstitutionModel(alpha, "JC69+F."),
 
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  exp_(), p_(size_, size_), freqSet_(freqSet)
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{
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  if (initFreqs) freqSet_->setFrequencies(freq_);
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  else freq_ = freqSet_->getFrequencies();