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

Example 41 with NewickImporter

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

the class CoalGenFrame method importFromFile.

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

Example 42 with NewickImporter

use of dr.evolution.io.NewickImporter 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 43 with NewickImporter

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

the class SeqGen method main.

public static void main(String[] argv) {
    String treeFileName = argv[0];
    String outputFileStem = argv[1];
    int length = 500;
    double[] frequencies = new double[] { 0.25, 0.25, 0.25, 0.25 };
    double kappa = 10.0;
    double alpha = 0.5;
    double substitutionRate = argv.length < 3 ? 1.0E-3 : Double.parseDouble(argv[2]);
    int categoryCount = argv.length < 4 ? 8 : Integer.parseInt(argv[3]);
    //1.56E-6;
    double damageRate = argv.length < 5 ? 0 : Double.parseDouble(argv[4]);
    System.out.println("substitutionRate = " + substitutionRate + "; categoryCount = " + categoryCount + "; damageRate = " + damageRate);
    FrequencyModel freqModel = new FrequencyModel(dr.evolution.datatype.Nucleotides.INSTANCE, frequencies);
    HKY hkyModel = new HKY(kappa, freqModel);
    SiteModel siteModel = null;
    if (categoryCount > 1) {
        siteModel = new GammaSiteModel(hkyModel, alpha, categoryCount);
    } else {
        // no rate heterogeneity
        siteModel = new GammaSiteModel(hkyModel);
    }
    List<Tree> trees = new ArrayList<Tree>();
    FileReader reader = null;
    try {
        reader = new FileReader(treeFileName);
        //            TreeImporter importer = new NexusImporter(reader);
        TreeImporter importer = new NewickImporter(reader);
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            trees.add(tree);
            System.out.println("tree height = " + tree.getNodeHeight(tree.getRoot()) + "; leave nodes = " + tree.getExternalNodeCount());
        }
    } catch (FileNotFoundException e) {
        e.printStackTrace();
        return;
    } catch (Importer.ImportException e) {
        e.printStackTrace();
        return;
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
    SeqGen seqGen = new SeqGen(length, substitutionRate, freqModel, hkyModel, siteModel, damageRate);
    int i = 1;
    for (Tree tree : trees) {
        Alignment alignment = seqGen.simulate(tree);
        FileWriter writer = null;
        try {
            //                writer = new FileWriter(outputFileStem + (i < 10 ? "00" : (i < 100 ? "0" : "")) + i + ".nex");
            //                NexusExporter exporter = new NexusExporter(writer);
            //
            //                exporter.exportAlignment(alignment);
            //
            //                writer.close();
            String outputFileName = outputFileStem + "-" + substitutionRate + ".fasta";
            writer = new FileWriter(outputFileName);
            BufferedWriter bf = new BufferedWriter(writer);
            FastaExporter exporter = new FastaExporter(bf);
            exporter.exportSequences(alignment.getSequenceList());
            bf.close();
            System.out.println("Write " + i + "th sequence file : " + outputFileName);
            i++;
        } catch (IOException e) {
            e.printStackTrace();
            return;
        }
    }
}

Example 44 with NewickImporter

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

the class SequenceSimulator method main.

// getDefaultSiteModel
public static void main(String[] args) {
    try {
        int nReplications = 10;
        // create tree
        NewickImporter importer = new NewickImporter("((A:1.0,B:1.0)AB:1.0,(C:1.0,D:1.0)CD:1.0)ABCD;");
        Tree tree = importer.importTree(null);
        // create site model
        SiteModel siteModel = getDefaultSiteModel();
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // feed to sequence simulator and generate leaves
        SequenceSimulator treeSimulator = new SequenceSimulator(tree, siteModel, branchRateModel, nReplications);
        Sequence ancestralSequence = new Sequence();
        ancestralSequence.appendSequenceString("TCAGGTCAAG");
        treeSimulator.setAncestralSequence(ancestralSequence);
        System.out.println(treeSimulator.simulate().toString());
    } catch (Exception e) {
        e.printStackTrace();
    }
//END: try-catch block
}

Example 45 with NewickImporter

use of dr.evolution.io.NewickImporter 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);
}