/** * Parses an element from an DOM document into a DemographicModel. Recognises ConstantPopulation and * ExponentialGrowth. */ public class EmpiricalAminoAcidModelParser extends AbstractXMLObjectParser { public static final String EMPIRICAL_AMINO_ACID_MODEL = "aminoAcidModel"; public static final String FREQUENCIES = "frequencies"; public static final String TYPE = "type"; public String getParserName() { return EMPIRICAL_AMINO_ACID_MODEL; } public Object parseXMLObject(XMLObject xo) throws XMLParseException { FrequencyModel freqModel = null; if (xo.hasAttribute(FREQUENCIES)) { XMLObject cxo = xo.getChild(FREQUENCIES); freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class); } EmpiricalRateMatrix rateMatrix = null; String type = xo.getStringAttribute(TYPE); if (type.equals(AminoAcidModelType.BLOSUM_62.getXMLName())) { rateMatrix = Blosum62.INSTANCE; } else if (type.equals(AminoAcidModelType.DAYHOFF.getXMLName())) { rateMatrix = Dayhoff.INSTANCE; } else if (type.equals(AminoAcidModelType.JTT.getXMLName())) { rateMatrix = dr.evomodel.substmodel.JTT.INSTANCE; } else if (type.equals(AminoAcidModelType.MT_REV_24.getXMLName())) { rateMatrix = MTREV.INSTANCE; } else if (type.equals(AminoAcidModelType.CP_REV_45.getXMLName())) { rateMatrix = CPREV.INSTANCE; } else if (type.equals(AminoAcidModelType.WAG.getXMLName())) { rateMatrix = dr.evomodel.substmodel.WAG.INSTANCE; } else if (type.equals(AminoAcidModelType.FLU.getXMLName())) { rateMatrix = dr.evomodel.substmodel.FLU.INSTANCE; } return new EmpiricalAminoAcidModel(rateMatrix, freqModel); } // ************************************************************************ // AbstractXMLObjectParser implementation // ************************************************************************ public XMLSyntaxRule[] getSyntaxRules() { return rules; } private XMLSyntaxRule[] rules = new XMLSyntaxRule[] { new StringAttributeRule( TYPE, "The type of empirical amino-acid rate matrix", AminoAcidModelType.xmlNames(), false), new ElementRule( FREQUENCIES, FrequencyModel.class, "If the frequencies are omitted than the empirical frequencies associated with the selected model are used.", true) }; public String getParserDescription() { return "An empirical amino acid substitution model."; } public Class getReturnType() { return EmpiricalAminoAcidModel.class; } }