Examples with SimpleTree dr.evolution.tree.SimpleTree used on opensource projects

Example 11 with SimpleTree

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

the class GibbsIndependentCoalescentOperator method doOperation.

/**
	 * change the parameter and return the hastings ratio.
     */
public double doOperation() {
    CoalescentSimulator simulator = new CoalescentSimulator();
    List<TaxonList> taxonLists = new ArrayList<TaxonList>();
    double rootHeight = -1.0;
    double oldLikelihood = 0.0;
    double newLikelihood = 0.0;
    // should have one child that is node
    for (int i = 0; i < xo.getChildCount(); i++) {
        final Object child = xo.getChild(i);
        //careful: Trees are TaxonLists ... (AER); see OldCoalescentSimulatorParser
        if (child instanceof Tree) {
        //do nothing
        } else if (child instanceof TaxonList) {
            //taxonLists.add((TaxonList) child);
            taxonLists.add((Taxa) child);
            //taxa added
            break;
        }
    }
    try {
        Tree[] trees = new Tree[taxonLists.size()];
        // simulate each taxonList separately
        for (int i = 0; i < taxonLists.size(); i++) {
            trees[i] = simulator.simulateTree(taxonLists.get(i), demoModel);
        }
        oldLikelihood = coalescent.getLogLikelihood();
        SimpleTree simTree = simulator.simulateTree(trees, demoModel, rootHeight, trees.length != 1);
        //this would be the normal way to do it
        treeModel.beginTreeEdit();
        //now it's allowed to adjust the tree structure
        treeModel.adoptTreeStructure(simTree);
        //endTreeEdit() would then fire the events
        treeModel.endTreeEdit();
        newLikelihood = coalescent.getLogLikelihood();
    } catch (IllegalArgumentException iae) {
        try {
            throw new XMLParseException(iae.getMessage());
        } catch (XMLParseException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    //return oldLikelihood - newLikelihood;
    return 0;
}

Example 12 with SimpleTree

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

the class ConditionalCladeFrequency method report.

/**
     * Creates the report. The estimated posterior of the given tree is printed.
     *
     * @throws IOException if general I/O error occurs
     */
public void report(Reader r) throws IOException, Importer.ImportException {
    System.err.println("making report");
    ArrayList<Tree> referenceTrees = new ArrayList<Tree>();
    BufferedReader reader = new BufferedReader(r);
    String line = reader.readLine();
    if (line.toUpperCase().startsWith("#NEXUS")) {
        NexusImporter importer = new NexusImporter(reader);
        Tree[] trees = importer.importTrees(null);
        for (Tree tree : trees) {
            referenceTrees.add(tree);
            SimpleTree sTree = new SimpleTree(tree);
            System.out.println("Estimated marginal posterior by condiational clade frequencies:");
            System.out.println(getTreeProbability(sTree) + "\t\t" + sTree);
        }
    } else {
        throw new RuntimeException("Could not read reference tree. Only Nexus format is supported.");
    }
    System.out.flush();
}