Examples with TreeModel dr.evomodel.tree.TreeModel used on opensource projects

Example 46 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class TreeBitRandomWalkOperatorParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    String trait1 = null;
    String trait2 = null;
    if (xo.hasAttribute(INDICTATOR_TRAIT))
        trait1 = xo.getStringAttribute(INDICTATOR_TRAIT);
    if (xo.hasAttribute(TRAIT2))
        trait2 = xo.getStringAttribute(TRAIT2);
    int k = xo.getAttribute("k", 1);
    boolean swapTrait2 = xo.getAttribute(SWAP_TRAIT2, true);
    return new TreeBitRandomWalkOperator(treeModel, trait1, trait2, weight, k, swapTrait2);
}

Example 47 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class GibbsSubtreeSwapParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    final boolean pruned = xo.getAttribute("pruned", true);
    return new GibbsSubtreeSwap(treeModel, pruned, weight);
}

Example 48 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class ImportancePruneAndRegraftParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    int samples = xo.getIntegerAttribute("samples");
    return new ImportancePruneAndRegraft(treeModel, weight, samples);
}

Example 49 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class ImportanceSubtreeSwapParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    final double weight = xo.getDoubleAttribute(MCMCOperator.WEIGHT);
    final int samples = xo.getIntegerAttribute("samples");
    return new ImportanceSubtreeSwap(treeModel, weight, samples);
}

Example 50 with TreeModel

use of dr.evomodel.tree.TreeModel in project beast-mcmc by beast-dev.

the class TraceCorrelationAssert method createSpecifiedTree.

protected void createSpecifiedTree(String t) throws Exception {
    //        Tree.Utils.newick(tree)
    //create tree
    NewickImporter importer = new NewickImporter(t);
    Tree tree = importer.importTree(null);
    //treeModel
    treeModel = new TreeModel(tree);
}