Examples with YangCodonModel dr.oldevomodel.substmodel.YangCodonModel used on opensource projects

Example 1 with YangCodonModel

use of dr.oldevomodel.substmodel.YangCodonModel in project beast-mcmc by beast-dev.

the class YangCodonModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Codons codons = Codons.UNIVERSAL;
    if (xo.hasAttribute(GeneticCode.GENETIC_CODE)) {
        String codeStr = xo.getStringAttribute(GeneticCode.GENETIC_CODE);
        if (codeStr.equals(GeneticCode.UNIVERSAL.getName())) {
            codons = Codons.UNIVERSAL;
        } else if (codeStr.equals(GeneticCode.VERTEBRATE_MT.getName())) {
            codons = Codons.VERTEBRATE_MT;
        } else if (codeStr.equals(GeneticCode.YEAST.getName())) {
            codons = Codons.YEAST;
        } else if (codeStr.equals(GeneticCode.MOLD_PROTOZOAN_MT.getName())) {
            codons = Codons.MOLD_PROTOZOAN_MT;
        } else if (codeStr.equals(GeneticCode.INVERTEBRATE_MT.getName())) {
            codons = Codons.INVERTEBRATE_MT;
        } else if (codeStr.equals(GeneticCode.CILIATE.getName())) {
            codons = Codons.CILIATE;
        } else if (codeStr.equals(GeneticCode.ECHINODERM_MT.getName())) {
            codons = Codons.ECHINODERM_MT;
        } else if (codeStr.equals(GeneticCode.EUPLOTID_NUC.getName())) {
            codons = Codons.EUPLOTID_NUC;
        } else if (codeStr.equals(GeneticCode.BACTERIAL.getName())) {
            codons = Codons.BACTERIAL;
        } else if (codeStr.equals(GeneticCode.ALT_YEAST.getName())) {
            codons = Codons.ALT_YEAST;
        } else if (codeStr.equals(GeneticCode.ASCIDIAN_MT.getName())) {
            codons = Codons.ASCIDIAN_MT;
        } else if (codeStr.equals(GeneticCode.FLATWORM_MT.getName())) {
            codons = Codons.FLATWORM_MT;
        } else if (codeStr.equals(GeneticCode.BLEPHARISMA_NUC.getName())) {
            codons = Codons.BLEPHARISMA_NUC;
        } else if (codeStr.equals(GeneticCode.NO_STOPS.getName())) {
            codons = Codons.NO_STOPS;
        }
    }
    Parameter omegaParam = (Parameter) xo.getElementFirstChild(OMEGA);
    Parameter kappaParam = (Parameter) xo.getElementFirstChild(KAPPA);
    FrequencyModel freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
    return new YangCodonModel(codons, omegaParam, kappaParam, freqModel);
}