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Viewing changes to test/test_mapping_codon.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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Lines of Context:
test/test_mapping_codon.cpp
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  CodonAlphabet* alphabet = new StandardCodonAlphabet(&AlphabetTools::DNA_ALPHABET);
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  GeneticCode* gc = new StandardGeneticCode(&AlphabetTools::DNA_ALPHABET);
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  //ReversibleSubstitutionModel* model = new YN98(gc, FrequenciesSet::getFrequenciesSetForCodons(FrequenciesSet::F0, *alphabet));
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  ReversibleSubstitutionModel* model = new CodonNeutralReversibleSubstitutionModel(
 
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  SubstitutionModel* model = new CodonRateSubstitutionModel(
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        dynamic_cast<const CodonAlphabet*>(gc->getSourceAlphabet()),
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        new JCnuc(dynamic_cast<CodonAlphabet*>(alphabet)->getNucleicAlphabet()));
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  MatrixTools::printForR(model->getGenerator(), "g");