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

Example 41 with Tree

use of dr.evolution.tree.Tree 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);
}

Example 42 with Tree

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

the class TraceCorrelationAssert method createPrimateTreeModel.

//************************** data ****************************
protected TreeModel createPrimateTreeModel() {
    SimpleNode[] nodes = new SimpleNode[10];
    for (int n = 0; n < 10; n++) {
        nodes[n] = new SimpleNode();
    }
    //        nodes[0].setHeight(0);
    // human
    nodes[0].setTaxon(taxa[0]);
    // chimp
    nodes[1].setTaxon(taxa[1]);
    // bonobo
    nodes[2].setTaxon(taxa[2]);
    nodes[3].setHeight(0.010772);
    nodes[3].addChild(nodes[1]);
    nodes[3].addChild(nodes[2]);
    nodes[4].setHeight(0.024003);
    nodes[4].addChild(nodes[0]);
    nodes[4].addChild(nodes[3]);
    // gorilla
    nodes[5].setTaxon(taxa[3]);
    nodes[6].setHeight(0.036038);
    nodes[6].addChild(nodes[4]);
    nodes[6].addChild(nodes[5]);
    // orangutan
    nodes[7].setTaxon(taxa[4]);
    nodes[8].setHeight(0.069125);
    nodes[8].addChild(nodes[6]);
    nodes[8].addChild(nodes[7]);
    // siamang
    nodes[9].setTaxon(taxa[5]);
    SimpleNode root = new SimpleNode();
    root.setHeight(0.099582);
    root.addChild(nodes[8]);
    root.addChild(nodes[9]);
    Tree tree = new SimpleTree(root);
    tree.setUnits(Units.Type.YEARS);
    //treeModel
    return new TreeModel(tree);
}

Example 43 with Tree

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

the class OldTreesPanel method createTree.

private void createTree() {
    if (generateTreeDialog == null) {
        generateTreeDialog = new GenerateTreeDialog(frame);
    }
    int result = generateTreeDialog.showDialog(options);
    if (result != JOptionPane.CANCEL_OPTION) {
        GenerateTreeDialog.MethodTypes methodType = generateTreeDialog.getMethodType();
        PartitionData partition = generateTreeDialog.getDataPartition();
        Patterns patterns = new Patterns(partition.getAlignment());
        DistanceMatrix distances = new F84DistanceMatrix(patterns);
        Tree tree;
        TemporalRooting temporalRooting;
        switch(methodType) {
            case NJ:
                tree = new NeighborJoiningTree(distances);
                temporalRooting = new TemporalRooting(tree);
                tree = temporalRooting.findRoot(tree, TemporalRooting.RootingFunction.CORRELATION);
                break;
            case UPGMA:
                tree = new UPGMATree(distances);
                temporalRooting = new TemporalRooting(tree);
                break;
            default:
                throw new IllegalArgumentException("unknown method type");
        }
        tree.setId(generateTreeDialog.getName());
        options.userTrees.add(tree);
        treesTableModel.fireTableDataChanged();
        int row = options.userTrees.size() - 1;
        treesTable.getSelectionModel().setSelectionInterval(row, row);
    }
    fireTreePriorsChanged();
}

Example 44 with Tree

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

the class PartitionTreeModelPanel method setupPanel.

public void setupPanel() {
    removeAll();
    if (options.isEBSPSharingSamePrior() || options.useStarBEAST) {
        addComponentWithLabel("Ploidy type:", ploidyTypeCombo);
    }
    if (partitionTreeModel.getDataType().getType() != DataType.MICRO_SAT) {
        addSpanningComponent(randomTreeRadio);
        addSpanningComponent(upgmaTreeRadio);
        addSpanningComponent(userTreeRadio);
        addComponents(userTreeLabel, userTreeCombo);
        userTreeCombo.removeAllItems();
        if (options.userTrees.size() < 1) {
            userTreeCombo.addItem(NO_TREE);
        } else {
            Object selectedItem = userTreeCombo.getSelectedItem();
            for (Tree tree : options.userTrees) {
                userTreeCombo.addItem(tree.getId());
            }
            if (selectedItem != null) {
                userTreeCombo.setSelectedItem(selectedItem);
            } else {
                userTreeCombo.setSelectedIndex(0);
            }
        }
        //            addComponent(treeDisplayButton);  // todo JTreeDisplay not work properly
        addComponents(treeFormatLabel, treeFormatCombo);
        addComponent(userTreeInfo);
    }
    //		generateTreeAction.setEnabled(options != null && options.dataPartitions.size() > 0);
    setOptions();
    validate();
    repaint();
}

Example 45 with Tree

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

the class PatristicDistanceMatrix method main.

public static void main(String[] args) throws IOException, Importer.ImportException {
    File file = new File(args[0]);
    File outFile = new File(args[1]);
    PrintWriter writer = new PrintWriter(new FileWriter(outFile));
    NexusImporter importer = new NexusImporter(new FileReader(file));
    Tree[] trees = importer.importTrees(null);
    System.out.println("Found " + trees.length + " trees.");
    for (Tree tree : trees) {
        PatristicDistanceMatrix matrix = new PatristicDistanceMatrix(tree);
        writer.println(matrix.toString());
    }
    writer.flush();
    writer.close();
}