Examples with GhostTreeModel dr.evomodel.bigfasttree.ghosttree.GhostTreeModel used on opensource projects

Example 1 with GhostTreeModel

use of dr.evomodel.bigfasttree.ghosttree.GhostTreeModel in project beast-mcmc by beast-dev.

the class CladeAwareSubtreePruneRegraft method getRelevantClade.

private CladeRef getRelevantClade(NodeRef nodeRef) {
    if (isGhostTree) {
        // TODO test this branch
        GhostTreeModel ghostTreeModel = ((GhostTreeModel) tree);
        CorporealTreeModel corporealTreeModel = ghostTreeModel.getCorporealTreeModel();
        if (((GhostTreeModel) tree).hasCorporealCounterPart(nodeRef)) {
            NodeRef corporealNode = ghostTreeModel.getCorporealCounterPart(nodeRef);
            if (corporealTreeModel.isRoot(corporealNode)) {
                return cladeModel.getClade(corporealNode);
            } else {
                return cladeModel.getClade(corporealTreeModel.getParent(corporealNode));
            }
        } else if (ghostTreeModel.getNextCorporealDescendent(nodeRef) != null) {
            NodeRef corporealNode = ghostTreeModel.getNextCorporealDescendent(nodeRef);
            if (corporealTreeModel.isRoot(corporealNode)) {
                return cladeModel.getClade(corporealNode);
            } else {
                return cladeModel.getClade(corporealTreeModel.getParent(corporealNode));
            }
        } else {
            if (tree.isRoot(nodeRef)) {
                return cladeModel.getClade(corporealTreeModel.getRoot());
            }
            return getRelevantClade(tree.getParent(nodeRef));
        }
    } else {
        return cladeModel.getClade(tree.getParent(nodeRef));
    }
}

Example 2 with GhostTreeModel

use of dr.evomodel.bigfasttree.ghosttree.GhostTreeModel in project beast-mcmc by beast-dev.

the class CladeAwareSubtreePruneRegraft method getDistances.

private void getDistances(double height, NodeRef node, CladeRef clade, List<Double> nodeDistances, List<Double> effectiveNodeHeights, List<NodeRef> nodes) {
    double effectiveHeight = Math.max(tree.getNodeHeight(node), height);
    if (tree.getParent(node) == null) {
        totalDistanceTraversed += 0;
    } else {
        double effectiveBranchLength = tree.getNodeHeight(tree.getParent(node)) - effectiveHeight;
        totalDistanceTraversed += effectiveBranchLength;
    }
    nodeDistances.add(totalDistanceTraversed);
    nodes.add(node);
    effectiveNodeHeights.add(effectiveHeight);
    boolean goOn;
    if (isGhostTree) {
        if (((GhostTreeModel) tree).hasCorporealCounterPart(node)) {
            NodeRef corpNode = ((GhostTreeModel) tree).getCorporealCounterPart(node);
            goOn = cladeModel.getClade(corpNode) == clade && tree.getNodeHeight(node) > height;
        } else {
            // if just a ghost node keep going
            goOn = true;
        }
    } else {
        goOn = cladeModel.getClade(node) == clade && tree.getNodeHeight(node) > height;
    }
    if (goOn) {
        for (int i = 0; i < tree.getChildCount(node); i++) {
            NodeRef child = tree.getChild(node, i);
            getDistances(height, child, clade, nodeDistances, effectiveNodeHeights, nodes);
        }
    }
}

Example 3 with GhostTreeModel

use of dr.evomodel.bigfasttree.ghosttree.GhostTreeModel in project beast-mcmc by beast-dev.

the class GhostTreeModelParser method parseXMLObject.

/**
 * @return a tree object based on the XML element it was passed.
 */
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Tree tree = (Tree) xo.getChild(Tree.class);
    TaxonList ghostTaxa = (TaxonList) xo.getElementFirstChild(GHOST_TAXA);
    GhostTreeModel treeModel = new GhostTreeModel(xo.getId(), tree, ghostTaxa);
    Logger.getLogger("dr.evomodel").info("\nCreating the tree model, '" + xo.getId() + "'" + "\n\nwith " + ghostTaxa.getTaxonCount() + " ghost lineages.");
    Logger.getLogger("dr.evomodel").info("  taxon count = " + treeModel.getExternalNodeCount());
    Logger.getLogger("dr.evomodel").info("  tree height = " + treeModel.getNodeHeight(treeModel.getRoot()));
    return treeModel;
}

Example 4 with GhostTreeModel

use of dr.evomodel.bigfasttree.ghosttree.GhostTreeModel in project beast-mcmc by beast-dev.

the class GhostTreeModelTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    Taxa ghostTaxa = new Taxa("ghost");
    ghostTaxa.addTaxon(new Taxon("g1"));
    ghostTaxa.addTaxon(new Taxon("g2"));
    Taxa corporealTaxa = new Taxa("corporeal");
    corporealTaxa.addTaxon(new Taxon("0"));
    corporealTaxa.addTaxon(new Taxon("1"));
    corporealTaxa.addTaxon(new Taxon("2"));
    Taxa allTaxa = new Taxa(ghostTaxa);
    allTaxa.addTaxa(corporealTaxa);
    NewickImporter importer = new NewickImporter("(((g1:0.5,0:1):0.5,1:1):1,(g2:1,2:1):0.5)");
    Tree superTree = importer.importTree(allTaxa);
    ghostTree = new GhostTreeModel(superTree, ghostTaxa);
    corporealTree = ghostTree.getCorporealTreeModel();
}