Examples with MicrosatelliteSimulator dr.app.seqgen.MicrosatelliteSimulator used on opensource projects

Example 1 with MicrosatelliteSimulator

use of dr.app.seqgen.MicrosatelliteSimulator in project beast-mcmc by beast-dev.

the class MicrosatelliteSimulatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Microsatellite msatDataType = (Microsatellite) xo.getChild(Microsatellite.class);
    Taxa taxa = (Taxa) xo.getChild(Taxa.class);
    Tree tree = (Tree) xo.getChild(Tree.class);
    MicrosatelliteModel msatModel = (MicrosatelliteModel) xo.getChild(MicrosatelliteModel.class);
    BranchRateModel brModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    if (brModel == null) {
        brModel = new DefaultBranchRateModel();
    }
    MicrosatelliteSimulator msatSim = new MicrosatelliteSimulator(msatDataType, taxa, tree, new GammaSiteModel(msatModel), brModel);
    Patterns patterns = msatSim.simulateMsatPattern();
    String msatPatId = xo.getAttribute("id", "simMsatPat");
    patterns.setId(msatPatId);
    MicrosatellitePatternParser.printDetails(patterns);
    MicrosatellitePatternParser.printMicrosatContent(patterns);
    return patterns;
}