NtdBMAParser.java

package dr.evomodelxml.substmodel;

import dr.xml.*;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.NtdBMA;
import dr.inference.model.Variable;

/**
 * @author Chieh-Hsi Wu
 * Parser for nucleotide subsitution
 */
public class NtdBMAParser extends AbstractXMLObjectParser {
    public static final String NTD_BMA = "ntdBMA";
    public static final String KAPPA = "kappa";
    public static final String TN = "tn";
    public static final String AT = "at";
    public static final String AC = "ac";
    public static final String GC = "gc";
    public static final String GT = "gt";
    public static final String MODEL_CHOOSE = "modelChoose";

    public static final String FREQUENCIES = "frequencies";

    public String getParserName() {
        return NTD_BMA;
    }

    public Object parseXMLObject(XMLObject xo) throws XMLParseException {



        Variable kappa = (Variable) xo.getElementFirstChild(KAPPA);
        Variable tn = (Variable) xo.getElementFirstChild(TN);
        Variable ac = (Variable) xo.getElementFirstChild(AC);
        Variable at = (Variable) xo.getElementFirstChild(AT);
        Variable gc = (Variable) xo.getElementFirstChild(GC);
        Variable gt  = (Variable) xo.getElementFirstChild(GT);
        Variable modelChoose  = (Variable) xo.getElementFirstChild(MODEL_CHOOSE);
        XMLObject cxo = xo.getChild(FREQUENCIES);
        FrequencyModel freqModel = (FrequencyModel) cxo.getChild(FrequencyModel.class);


        return new NtdBMA(kappa, tn, ac, at, gc, gt, modelChoose, freqModel);
    }

    public Class getReturnType() {
        return NtdBMA.class;
    }

    public XMLSyntaxRule[] getSyntaxRules() {
        return rules;
    }

    private final XMLSyntaxRule[] rules = {
            new ElementRule(FREQUENCIES,
                    new XMLSyntaxRule[]{new ElementRule(FrequencyModel.class)}),
            new ElementRule(KAPPA,
                    new XMLSyntaxRule[]{new ElementRule(Variable.class)}, true),
            new ElementRule(AC,
                    new XMLSyntaxRule[]{new ElementRule(Variable.class)}, true),
            new ElementRule(AT,
                    new XMLSyntaxRule[]{new ElementRule(Variable.class)}, true),
            new ElementRule(GC,
                    new XMLSyntaxRule[]{new ElementRule(Variable.class)}, true),
            new ElementRule(GT,
                    new XMLSyntaxRule[]{new ElementRule(Variable.class)}, true),
            new ElementRule(MODEL_CHOOSE,
                    new XMLSyntaxRule[]{new ElementRule(Variable.class)}, true),
    };
        public String getParserDescription() {
        return "A model that allows model averaging over nucleotide substitution models.";
    }
}