Examples with NexusImporter dr.evolution.io.NexusImporter used on opensource projects

Example 21 with NexusImporter

use of dr.evolution.io.NexusImporter in project beast-mcmc by beast-dev.

the class GetAncestralSequenceFromSplitTrait method analyze.

/**
     * Recursively analyzes log files.
     *
     * @param treeAnnotatorInputFile       the file to analyze (if this is a directory then the files within it are analyzed)
     * @throws dr.inference.trace.TraceException
     *          if the trace file is in the wrong format or corrupted
     */
private void analyze(File treeAnnotatorInputFile) throws TraceException {
    try {
        FileReader fileReader = new FileReader(treeAnnotatorInputFile);
        TreeImporter importer = new NexusImporter(fileReader);
        FlexibleTree tree = (FlexibleTree) importer.importNextTree();
        for (int i = 0; i < tree.getNodeCount(); i++) {
            Hashtable<Integer, State> states = new Hashtable<Integer, State>();
            for (Iterator<String> j = tree.getNodeAttributeNames(tree.getNode(i)); j.hasNext(); ) {
                String name = j.next();
                if (name.indexOf("states_") >= 0) {
                    Integer d = Integer.parseInt(name.replaceFirst("states_", "").replaceFirst("\\..+", ""));
                    //= new State(name.);
                    State s;
                    if (states.containsKey(d)) {
                        s = states.get(d);
                    } else {
                        s = new State(d);
                    }
                    if (name.matches("states_" + d + ".prob")) {
                        Object o = tree.getNodeAttribute(tree.getNode(i), name);
                        double probability = (Double) o;
                        s.setProbability(probability);
                    } else if (name.matches("states_" + d)) {
                        Object o = tree.getNodeAttribute(tree.getNode(i), name);
                        String value = (String) o;
                        s.setState(value.replaceAll("\"", ""));
                    } else if (name.matches("states_" + d + ".set.prob")) {
                        /* Not necessary but lets parse it anyways */
                        Object[] o = (Object[]) tree.getNodeAttribute(tree.getNode(i), name);
                        double[] probabilities = new double[o.length];
                        for (int k = 0; k < o.length; k++) {
                            probabilities[k] = (Double) o[k];
                        }
                        s.setProbabilities(probabilities);
                    } else if (name.matches("states_" + d + ".set")) {
                        /* Not necessary but lets parse it anyways */
                        Object[] o = (Object[]) tree.getNodeAttribute(tree.getNode(i), name);
                        String[] set = new String[o.length];
                        for (int k = 0; k < o.length; k++) {
                            set[k] = ((String) o[k]).replaceAll("\"", "");
                        }
                        s.setSet(set);
                    }
                    //                        }
                    states.put(d, s);
                }
            }
            State[] statesArray = states.values().toArray(new State[states.size()]);
            Arrays.sort(statesArray);
            /* Set the default length to the number of characters that it would need */
            StringBuffer sb = new StringBuffer(statesArray.length * statesArray[0].getState().length());
            for (State s : statesArray) {
                sb.append(s.getState());
            }
            tree.setNodeAttribute(tree.getNode(i), "seq", sb.toString());
        }
        /* Export the new tree with the new sequences */
        TreeExporter exporter = new NexusExporter(System.out);
        exporter.exportTree(tree);
        System.out.println("Begin trees;");
        System.out.println("\ttree max_tree = " + tree.toString());
        System.out.println("End;");
    } catch (IOException e) {
        System.err.println("Error Parsing Input log: " + e.getMessage());
    } catch (Importer.ImportException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
    }
}

Example 22 with NexusImporter

use of dr.evolution.io.NexusImporter in project beast-mcmc by beast-dev.

the class Utils method importTreeFromFile.

// END: importTaxaFromFile
public static Tree importTreeFromFile(File file) throws IOException, ImportException {
    Tree tree = null;
    BufferedReader reader = new BufferedReader(new FileReader(file));
    String line = reader.readLine();
    if (line.toUpperCase().startsWith("#NEXUS")) {
        NexusImporter importer = new NexusImporter(reader);
        tree = importer.importTree(null);
    } else {
        NewickImporter importer = new NewickImporter(reader);
        tree = importer.importTree(null);
    }
    reader.close();
    return tree;
}

Example 23 with NexusImporter

use of dr.evolution.io.NexusImporter in project beast-mcmc by beast-dev.

the class TreeStatFrame method processTreeFile.

protected void processTreeFile(File inFile, File outFile) throws IOException, Importer.ImportException {
    processTreeFileAction.setEnabled(false);
    BufferedReader r = new BufferedReader(new FileReader(inFile));
    String line = r.readLine();
    r.close();
    final ProgressMonitorInputStream in = new ProgressMonitorInputStream(this, "Reading " + inFile.getName(), new FileInputStream(inFile));
    in.getProgressMonitor().setMillisToDecideToPopup(0);
    in.getProgressMonitor().setMillisToPopup(0);
    final Reader reader = new InputStreamReader(new BufferedInputStream(in));
    //        final Reader reader = new FileReader(inFile);
    final TreeImporter importer;
    if (line.toUpperCase().startsWith("#NEXUS")) {
        importer = new NexusImporter(reader);
    } else {
        reader.close();
        importer = new NewickImporter(reader);
    }
    final Tree firstTree = importer.importNextTree();
    boolean isUltrametric = TreeUtils.isUltrametric(firstTree);
    boolean isBinary = TreeUtils.isBinary(firstTree);
    boolean stop = false;
    // check that the trees conform with the requirements of the selected statistics
    for (int i = 0; i < treeStatData.statistics.size(); i++) {
        TreeSummaryStatistic tss = (TreeSummaryStatistic) treeStatData.statistics.get(i);
        String label = tss.getSummaryStatisticName();
        if (!isUltrametric && !tss.allowsNonultrametricTrees()) {
            if (JOptionPane.showConfirmDialog(this, "Warning: These trees may not be ultrametric and this is\na requirement of the " + label + " statistic. Do you wish to continue?", "Warning", JOptionPane.YES_NO_OPTION) != JOptionPane.YES_OPTION) {
                stop = true;
                break;
            }
            // don't ask the question again...
            isUltrametric = true;
        }
        if (!isBinary && !tss.allowsPolytomies()) {
            if (JOptionPane.showConfirmDialog(this, "Warning: These trees may not be strictly bifurcating and this is\na requirement of the " + label + " statistic. Do you wish to continue?", "Warning", JOptionPane.YES_NO_OPTION) != JOptionPane.YES_OPTION) {
                stop = true;
                break;
            }
            // don't ask the question again...
            isBinary = true;
        }
    }
    if (stop) {
        processTreeFileAction.setEnabled(true);
        return;
    }
    final PrintWriter writer = new PrintWriter(new FileWriter(outFile));
    //        Thread readThread = new Thread() {
    //            public void run() {
    Tree tree = firstTree;
    writer.print("state");
    for (int i = 0; i < treeStatData.statistics.size(); i++) {
        TreeSummaryStatistic tss = (TreeSummaryStatistic) treeStatData.statistics.get(i);
        int dim = tss.getStatisticDimensions(tree);
        for (int j = 0; j < dim; j++) {
            writer.print("\t" + tss.getStatisticLabel(tree, j));
        }
    }
    writer.println();
    state = 0;
    do {
        writer.print(state);
        for (int i = 0; i < treeStatData.statistics.size(); i++) {
            TreeSummaryStatistic tss = (TreeSummaryStatistic) treeStatData.statistics.get(i);
            double[] stats = tss.getSummaryStatistic(tree);
            for (int j = 0; j < stats.length; j++) {
                writer.print("\t" + stats[j]);
            }
        }
        writer.println();
        state += 1;
        final int currentState = state;
        in.getProgressMonitor().setNote("Processing Tree " + currentState + "...");
        //                    EventQueue.invokeLater(
        //                            new Runnable() {
        //                                public void run() {
        //                                    progressLabel.setText("Processing Tree " + currentState + "...");
        //                                }
        //                            });
        //                    try {
        tree = importer.importNextTree();
    //                    } catch (final IOException e) {
    //                        EventQueue.invokeLater(
    //                                new Runnable() {
    //                                    public void run() {
    //                                        JOptionPane.showMessageDialog(TreeStatFrame.this, "File I/O Error: " + e.getMessage(),
    //                                                "File I/O Error",
    //                                                JOptionPane.ERROR_MESSAGE);
    //                                    }
    //                                });
    //                    } catch (final Importer.ImportException e) {
    //                        EventQueue.invokeLater(
    //                                new Runnable() {
    //                                    public void run() {
    //                                        JOptionPane.showMessageDialog(TreeStatFrame.this, "Error importing tree: " + e.getMessage(),
    //                                                "Tree Import Error",
    //                                                JOptionPane.ERROR_MESSAGE);
    //                                    }
    //                                });
    //                    }
    } while (tree != null);
    //            }
    //        };
    //
    //        readThread.start();
    //        while (readThread.isAlive()) {
    //            Thread.yield();
    //        }
    reader.close();
    writer.close();
    progressLabel.setText("" + state + " trees processed.");
    processTreeFileAction.setEnabled(true);
}

Example 24 with NexusImporter

use of dr.evolution.io.NexusImporter in project beast-mcmc by beast-dev.

the class TreeStatFrame method importFromFile.

protected void importFromFile(File file) throws IOException, Importer.ImportException {
    BufferedReader reader = new BufferedReader(new FileReader(file));
    String line = reader.readLine();
    Tree tree = null;
    if (line.toUpperCase().startsWith("#NEXUS")) {
        NexusImporter importer = new NexusImporter(reader);
        tree = importer.importTree(null);
    } else {
        reader.close();
        reader = new BufferedReader(new FileReader(file));
        NewickImporter importer = new NewickImporter(reader);
        tree = importer.importTree(null);
    }
    treeStatData.allTaxa = TreeUtils.getLeafSet(tree);
    statusLabel.setText(Integer.toString(treeStatData.allTaxa.size()) + " taxa loaded.");
    reader.close();
    fireDataChanged();
}

Example 25 with NexusImporter

use of dr.evolution.io.NexusImporter in project beast-mcmc by beast-dev.

the class TreeShape method main.

public static void main(String[] args) throws Exception {
    NexusImporter importer = new NexusImporter(new FileReader(args[0]));
    Tree[] trees = importer.importTrees(null);
    System.out.println("File = " + args[0]);
    double[] treeness = new double[trees.length];
    for (int i = 0; i < treeness.length; i++) {
        treeness[i] = getTreeness(trees[i]);
    }
    System.out.println("Mean treeness = " + dr.stats.DiscreteStatistics.mean(treeness));
    System.out.println("Lower (95%) treeness = " + dr.stats.DiscreteStatistics.quantile(0.025, treeness));
    System.out.println("Upper (95%) treeness = " + dr.stats.DiscreteStatistics.quantile(0.975, treeness));
}