/**
* 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;
}
}
