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

Example 11 with FlexibleTree

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

the class NewickImporter method importNextTree.

/**
     * import the next tree.
     * return the tree or null if no more trees are available
     */
public Tree importNextTree() throws IOException, ImportException {
    FlexibleTree tree = null;
    try {
        skipUntil("(");
        unreadCharacter('(');
        FlexibleNode root = readInternalNode(lastTree);
        tree = new FlexibleTree(root, false, true);
    } catch (EOFException e) {
    //
    }
    lastTree = tree;
    return tree;
}

Example 12 with FlexibleTree

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

the class NewickImporter method importTree.

/**
     * importTree.
     */
public Tree importTree(TaxonList taxonList) throws IOException, ImportException {
    setCommentDelimiters('[', ']', '\0', '\0', '&');
    try {
        skipUntil("(");
        unreadCharacter('(');
        final FlexibleNode root = readInternalNode(taxonList);
        if (getLastMetaComment() != null) {
            root.setAttribute(COMMENT, getLastMetaComment());
        }
        return new FlexibleTree(root, false, true);
    } catch (EOFException e) {
        throw new ImportException("incomplete tree");
    }
}

Example 13 with FlexibleTree

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

the class PathogenFrame method readFromFile.

protected boolean readFromFile(File file) throws IOException {
    Reader reader = new FileReader(file);
    BufferedReader bufferedReader = new BufferedReader(reader);
    String line = bufferedReader.readLine();
    while (line != null && line.length() == 0) {
        line = bufferedReader.readLine();
    }
    boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS"));
    reader = new FileReader(file);
    Tree tree = null;
    try {
        if (isNexus) {
            NexusImporter importer = new NexusImporter(reader);
            tree = importer.importTree(taxa);
        } else {
            NewickImporter importer = new NewickImporter(reader);
            tree = importer.importTree(taxa);
        }
    } catch (Importer.ImportException ime) {
        JOptionPane.showMessageDialog(this, "Error parsing imported file: " + ime, "Error reading file", JOptionPane.ERROR_MESSAGE);
        ime.printStackTrace();
        return false;
    } catch (IOException ioex) {
        JOptionPane.showMessageDialog(this, "File I/O Error: " + ioex, "File I/O Error", JOptionPane.ERROR_MESSAGE);
        ioex.printStackTrace();
        return false;
    } catch (Exception ex) {
        JOptionPane.showMessageDialog(this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
        ex.printStackTrace();
        return false;
    }
    if (tree == null) {
        JOptionPane.showMessageDialog(this, "The file is not in a suitable format or contains no trees.", "Error reading file", JOptionPane.ERROR_MESSAGE);
        return false;
    }
    FlexibleTree binaryTree = new FlexibleTree(tree, true);
    binaryTree.resolveTree();
    trees.add(binaryTree);
    if (taxa == null) {
        taxa = binaryTree;
    }
    getExportTreeAction().setEnabled(true);
    getExportDataAction().setEnabled(true);
    return true;
}

Example 14 with FlexibleTree

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

the class PathogenFrame method writeTimeTreeFile.

protected void writeTimeTreeFile(PrintStream ps) throws IOException {
    FlexibleTree tree = new FlexibleTree(pathogenPanel.getTreeAsViewed());
    Regression r = pathogenPanel.getTemporalRooting().getRootToTipRegression(pathogenPanel.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 15 with FlexibleTree

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

the class MapperFrame method readFromFile.

protected boolean readFromFile(File file) throws IOException {
    Reader reader = new FileReader(file);
    BufferedReader bufferedReader = new BufferedReader(reader);
    String line = bufferedReader.readLine();
    while (line != null && line.length() == 0) {
        line = bufferedReader.readLine();
    }
    boolean isNexus = (line != null && line.toUpperCase().contains("#NEXUS"));
    reader = new FileReader(file);
    Tree tree = null;
    try {
    //            if (isNexus) {
    //                NexusImporter importer = new NexusImporter(reader);
    //                tree = importer.importTree(taxa);
    //            } else {
    //                NewickImporter importer = new NewickImporter(reader);
    //                tree = importer.importTree(taxa);
    //            }
    //        } catch (Importer.ImportException ime) {
    //            JOptionPane.showMessageDialog(this, "Error parsing imported file: " + ime,
    //                    "Error reading file",
    //                    JOptionPane.ERROR_MESSAGE);
    //            ime.printStackTrace();
    //            return false;
    //        } catch (IOException ioex) {
    //            JOptionPane.showMessageDialog(this, "File I/O Error: " + ioex,
    //                    "File I/O Error",
    //                    JOptionPane.ERROR_MESSAGE);
    //            ioex.printStackTrace();
    //            return false;
    } catch (Exception ex) {
        JOptionPane.showMessageDialog(this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
        ex.printStackTrace();
        return false;
    }
    if (tree == null) {
        JOptionPane.showMessageDialog(this, "The file is not in a suitable format or contains no trees.", "Error reading file", JOptionPane.ERROR_MESSAGE);
        return false;
    }
    FlexibleTree binaryTree = new FlexibleTree(tree, true);
    binaryTree.resolveTree();
    trees.add(binaryTree);
    //        if (taxa == null) {
    //            taxa = binaryTree;
    //        }
    getExportDataAction().setEnabled(true);
    return true;
}