Examples with MetagenomeData dr.evolution.MetagenomeData used on opensource projects

Example 1 with MetagenomeData

use of dr.evolution.MetagenomeData in project beast-mcmc by beast-dev.

the class MetagenomeDataParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TaxonList taxa = null;
    taxa = (TaxonList) xo.getChild(TaxonList.class);
    if (taxa == null)
        taxa = (Tree) xo.getChild(Tree.class);
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    LinkageConstraints lc = (LinkageConstraints) xo.getChild(LinkageConstraints.class);
    boolean fixedReferenceTree = false;
    if (xo.hasAttribute("fixedReferenceTree")) {
        fixedReferenceTree = xo.getBooleanAttribute("fixedReferenceTree");
    }
    MetagenomeData md = new MetagenomeData(taxa, alignment, lc, fixedReferenceTree);
    return md;
}

Example 2 with MetagenomeData

use of dr.evolution.MetagenomeData in project beast-mcmc by beast-dev.

the class HiddenLinkageModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String linkageGroupCount = xo.getAttribute(LINKAGE_GROUP_COUNT, xo.getId());
    MetagenomeData data = (MetagenomeData) xo.getChild(MetagenomeData.class);
    int tc = Integer.parseInt(linkageGroupCount);
    return new HiddenLinkageModel(tc, data);
}