Examples with RootedTree jebl.evolution.trees.RootedTree used on opensource projects

Example 6 with RootedTree

use of jebl.evolution.trees.RootedTree in project beast-mcmc by beast-dev.

the class TreeSpaceFrame method importDataFile.

public void importDataFile(File file) throws IOException, ImportException {
    Reader reader = new FileReader(file);
    BufferedReader bufferedReader = new BufferedReader(reader);
    String line = bufferedReader.readLine();
    while (line != null && line.length() == 0) {
        line = bufferedReader.readLine();
    }
    if ((line != null && line.toUpperCase().contains("#NEXUS"))) {
        int treeCount = 0;
        do {
            line = bufferedReader.readLine();
        } while (line != null && !line.contains("("));
        while (line != null) {
            if (line.contains("(")) {
                treeCount++;
                if (treeCount > 1) {
                    break;
                }
            }
            line = bufferedReader.readLine();
        }
        // is a NEXUS file
        RootedTree tree = importFirstTree(file);
        if (tree != null) {
            if (treeCount > 1) {
                InputFile inputFile = new InputFile(file, tree, -1);
                document.addTreeFile(inputFile);
                treePlotter.setTrees(loadTrees(inputFile));
                inputFile.setTreeCount(treeCount);
                document.fireDataChanged();
            } else {
                InputFile inputFile = new InputFile(file, tree);
                document.addTreeFile(inputFile);
                treePlotter.setTrees(loadTrees(inputFile));
                inputFile.setTreeCount(treeCount);
                document.fireDataChanged();
            }
        }
    } else {
        JOptionPane.showMessageDialog(this, "Error parsing imported file. This may not be a NEXUS file", "Error reading file", JOptionPane.ERROR_MESSAGE);
    }
}

Example 7 with RootedTree

use of jebl.evolution.trees.RootedTree in project beast-mcmc by beast-dev.

the class TreeSpaceFrame method importFirstTree.

// nexus
private RootedTree importFirstTree(File file) throws IOException, ImportException {
    RootedTree tree = null;
    FileReader reader = new FileReader(file);
    NexusImporter importer = new NexusImporter(reader);
    tree = (RootedTree) importer.importNextTree();
    return tree;
}

Example 8 with RootedTree

use of jebl.evolution.trees.RootedTree in project beast-mcmc by beast-dev.

the class CoalGenApp method simulate.

public static void simulate(String inputFileName, String treesFileName, String outputFileName) throws IOException, TraceException, Importer.ImportException {
    File logFile = new File(inputFileName);
    System.out.println("Loading trace file: " + inputFileName);
    LogFileTraces traces = new LogFileTraces(inputFileName, logFile);
    traces.loadTraces();
    traces.setBurnIn(0);
    System.out.println(traces.getStateCount() + " states loaded");
    System.out.println();
    System.out.println("Opening trees file: " + treesFileName);
    //        BufferedReader reader = new BufferedReader(new FileReader(treesFileName));
    System.out.println("Simulating...");
    System.out.println("0              25             50             75            100");
    System.out.println("|--------------|--------------|--------------|--------------|");
    int stepSize = traces.getStateCount() / 60;
    if (stepSize < 1)
        stepSize = 1;
    PrintWriter writer = new PrintWriter(new FileWriter(outputFileName));
    FileReader fileReader = new FileReader(treesFileName);
    TreeImporter importer = new NexusImporter(fileReader);
    EmpiricalDemographicFunction demo = null;
    IntervalGenerator intervals = null;
    TreeSimulator sim = null;
    CoalGenData data = new CoalGenData();
    data.traces = traces;
    // const stepwise bsp
    data.setDemographicModel(7);
    data.setupSkyline();
    double[] popSizes = new double[data.popSizeCount];
    double[] groupSizes = new double[data.groupSizeCount];
    NewickExporter exporter = new NewickExporter(writer);
    int count = 0;
    try {
        while (importer.hasTree()) {
            RootedTree inTree = (RootedTree) importer.importNextTree();
            if (sim == null) {
                setSamplingTimes(inTree);
                sim = new TreeSimulator(inTree.getTaxa(), "date");
            }
            data.getNextSkyline(popSizes, groupSizes);
            double[] times = getTimes(inTree, groupSizes);
            demo = new EmpiricalDemographicFunction(popSizes, times, true);
            intervals = new CoalescentIntervalGenerator(demo);
            RootedTree outTree = sim.simulate(intervals);
            exporter.exportTree(outTree);
            writer.println();
            writer.flush();
            if (count > 0 && count % stepSize == 0) {
                System.out.print("*");
                System.out.flush();
            }
            count++;
        }
    } catch (ImportException e) {
        e.printStackTrace();
    }
    fileReader.close();
    writer.close();
}

Example 9 with RootedTree

use of jebl.evolution.trees.RootedTree in project beast-mcmc by beast-dev.

the class TreeKMLGenerator method main.

public static void main(String[] args) {
    String inputTreeFile = args[0];
    RootedTree tree = null;
    try {
        TreeImporter importer = new NexusImporter(new FileReader(inputTreeFile));
        tree = (RootedTree) importer.importNextTree();
    } catch (ImportException e) {
        e.printStackTrace();
        return;
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
    TreeKMLGenerator generator = new TreeKMLGenerator(tree);
    Settings settings = new Settings(AnalysisType.CONTINUOUS);
    //        settings.getAltitudeTreeSettings().setTreeType(TreeType.ARC_TREE);
    //        settings.getAltitudeTreeSettings().getBranchStyle().setColorProperty("height");
    settings.getGroundTreeSettings().setTreeType(TreeType.SURFACE_TREE);
    settings.getGroundTreeSettings().getBranchStyle().setColorProperty("height");
    settings.setPlotAltitude(0);
    settings.setMostRecentDate(2003);
    //settings.setAgeCutOff(1995);
    settings.setTimeDivisionCount(0);
    settings.setTraitName("antigenic");
    settings.setLatitudeName("antigenic1");
    settings.setLongitudeName("antigenic2");
    try {
        BufferedWriter out = new BufferedWriter(new FileWriter(args[0] + ".kml"));
        Document doc = new Document(generator.generate(args[0], settings));
        try {
            XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat());
            outputter.output(doc, out);
        } catch (IOException e) {
            System.err.println(e);
        }
        out.close();
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
}

Example 10 with RootedTree

use of jebl.evolution.trees.RootedTree in project beast-mcmc by beast-dev.

the class TreeGeoJSONGenerator method main.

public static void main(String[] args) {
    String inputTreeFile = args[0];
    RootedTree tree = null;
    try {
        TreeImporter importer = new NexusImporter(new FileReader(inputTreeFile));
        tree = (RootedTree) importer.importNextTree();
    } catch (ImportException e) {
        e.printStackTrace();
        return;
    } catch (IOException e) {
        e.printStackTrace();
        return;
    }
    TreeGeoJSONGenerator generator = new TreeGeoJSONGenerator(tree, null);
    try {
        generator.generate("", new PrintWriter(new File("output.geojson")));
    } catch (FileNotFoundException e) {
        //To change body of catch statement use File | Settings | File Templates.
        e.printStackTrace();
    }
}