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

Example 26 with FlexibleTree

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

the class TempestFrame method writeTimeTreeFile.

protected void writeTimeTreeFile(PrintStream ps) throws IOException {
    FlexibleTree tree = new FlexibleTree(tempestPanel.getTreeAsViewed());
    Regression r = tempestPanel.getTemporalRooting().getRootToTipRegression(tempestPanel.getTreeAsViewed());
    for (int i = 0; i < tree.getInternalNodeCount(); i++) {
        NodeRef node = tree.getInternalNode(i);
        double height = tree.getNodeHeight(node);
        tree.setNodeHeight(node, height / r.getGradient());
    }
    TreeUtils.setHeightsFromDates(tree);
    NexusExporter nexusExporter = new NexusExporter(new PrintStream(ps));
    nexusExporter.exportTree(tree);
}

Example 27 with FlexibleTree

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

the class WithinCaseCoalescent method debugTreelet.

public void debugTreelet(Tree treelet, String fileName) {
    try {
        FlexibleTree treeCopy = new FlexibleTree(treelet);
        for (int j = 0; j < treeCopy.getNodeCount(); j++) {
            FlexibleNode node = (FlexibleNode) treeCopy.getNode(j);
            node.setAttribute("Number", node.getNumber());
        }
        NexusExporter testTreesOut = new NexusExporter(new PrintStream(fileName));
        testTreesOut.exportTree(treeCopy);
    } catch (IOException ignored) {
        System.out.println("IOException");
    }
}