Examples with BeagleOperationReport dr.evomodel.treelikelihood.BeagleOperationReport used on opensource projects

Example 1 with BeagleOperationReport

use of dr.evomodel.treelikelihood.BeagleOperationReport in project beast-mcmc by beast-dev.

the class BeagleOperationParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    SitePatterns patternList = (SitePatterns) xo.getChild(PatternList.class);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    BranchRateModel rateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    GammaSiteRateModel substitutionModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
    PrintWriter branch = null, operation = null;
    if (xo.hasAttribute(BRANCH_FILE_NAME)) {
        branch = XMLParser.getFilePrintWriter(xo, OPERATION_REPORT, BRANCH_FILE_NAME);
    }
    if (xo.hasAttribute(OPERATION_FILE_NAME)) {
        operation = XMLParser.getFilePrintWriter(xo, OPERATION_REPORT, OPERATION_FILE_NAME);
    }
    return new BeagleOperationReport(treeModel, patternList, rateModel, substitutionModel, alignment, branch, operation);
}