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

Example 71 with Tree

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

the class TreeLengthFinder method report.

/**
     * Recursively analyzes trees files.
     *
     * @param name       the file to analyze (if this is a directory then the files within it are analyzed)
     * @param burnin     the burnin to use
     */
private void report(String name, int burnin) {
    double treeLength = 0.0;
    int count = 0;
    try {
        FileReader fileReader = new FileReader(new File(name));
        TreeImporter importer = new NexusImporter(fileReader);
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            if (count >= burnin) {
                treeLength += TreeLength.FACTORY.createStatistic().getSummaryStatistic(tree)[0];
            }
            count++;
        }
        treeLength /= (count - burnin);
        System.out.println(name + "\t" + burnin + "\t" + treeLength);
    } catch (Importer.ImportException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
    } catch (IOException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
    }
}

Example 72 with Tree

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

the class TreeSpaceFrame method processTrees1.

private int processTrees1(InputFile inputFile) throws IOException {
    PrintStream progressStream = System.out;
    int totalTrees = 10000;
    int totalTreesUsed = 0;
    progressStream.println("Reading trees (bar assumes 10,000 trees)...");
    progressStream.println("0              25             50             75            100");
    progressStream.println("|--------------|--------------|--------------|--------------|");
    int stepSize = totalTrees / 60;
    if (stepSize < 1)
        stepSize = 1;
    CladeSystem cladeSystem = document.getCladeSystem();
    FileReader fileReader = new FileReader(inputFile.getFile());
    TreeImporter importer = new dr.evolution.io.NexusImporter(fileReader);
    try {
        totalTrees = 0;
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            if (totalTrees >= inputFile.getBurnin()) {
                cladeSystem.add(tree, true);
                totalTreesUsed += 1;
            }
            if (totalTrees > 0 && totalTrees % stepSize == 0) {
                progressStream.print("*");
                progressStream.flush();
            }
            totalTrees++;
        }
    } catch (Importer.ImportException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
        return 0;
    }
    fileReader.close();
    progressStream.println();
    progressStream.println();
    if (totalTrees < 1) {
        System.err.println("No trees");
        return 0;
    }
    if (totalTreesUsed <= 1) {
        if (inputFile.getBurnin() > 0) {
            System.err.println("No trees to use: burnin too high");
            return 0;
        }
    }
    cladeSystem.normalizeClades(totalTreesUsed);
    progressStream.println("Total trees read: " + totalTrees);
    if (inputFile.getBurnin() > 0) {
        progressStream.println("Ignoring first " + inputFile.getBurnin() + " trees.");
    }
    int cladeCount = cladeSystem.getCladeMap().keySet().size();
    progressStream.println("Total unique clades: " + cladeCount);
    progressStream.println();
    progressStream.println("Processing trees for correlated clades:");
    fileReader = new FileReader(inputFile.getFile());
    importer = new dr.evolution.io.NexusImporter(fileReader);
    try {
        totalTrees = 0;
        while (importer.hasTree()) {
            Tree tree = importer.importNextTree();
            if (totalTrees >= inputFile.getBurnin()) {
                cladeSystem.addCooccurances(tree);
            }
            if (totalTrees > 0 && totalTrees % stepSize == 0) {
                progressStream.print("*");
                progressStream.flush();
            }
            totalTrees++;
        }
    } catch (Importer.ImportException e) {
        System.err.println("Error Parsing Input Tree: " + e.getMessage());
        return 0;
    }
    fileReader.close();
    progressStream.println();
    progressStream.println();
    double THRESHOLD = 0.05;
    PrintWriter writer = new PrintWriter("clade_co-occurance.txt");
    writer.println("source\tsize\ttarget\tco-occurence");
    java.util.List<CladeSystem.Clade> allClades = cladeSystem.getClades();
    for (CladeSystem.Clade clade1 : allClades) {
        String name1;
        int card1 = clade1.bits.cardinality();
        if (card1 == 1) {
            name1 = clade1.label;
        } else {
            name1 = "clade" + (clade1.index + 1);
        }
        if (clade1.parents != null) {
            for (CladeSystem.Clade clade2 : clade1.parents.keySet()) {
                String name2;
                int card2 = clade2.bits.cardinality();
                name2 = "clade" + (clade2.index + 1);
                double value = clade1.parents.get(clade2);
                value /= totalTreesUsed;
                if (value > THRESHOLD) {
                    if (card1 > card2) {
                        writer.println(name1 + "_" + card1 + "\t" + card1 + "\t" + name2 + "_" + card2 + "\t" + value);
                    } else {
                        writer.println(name2 + "_" + card2 + "\t" + card2 + "\t" + name1 + "_" + card1 + "\t" + value);
                    }
                }
            }
        }
    }
    writer.close();
    writer = new PrintWriter("clade_frequency.txt");
    writer.println("source\tsize\tfrequency");
    for (CladeSystem.Clade clade1 : allClades) {
        String name1;
        int card1 = clade1.bits.cardinality();
        if (card1 == 1) {
            name1 = clade1.label;
        } else {
            name1 = "clade" + (clade1.index + 1);
        }
        double value = clade1.count;
        value /= totalTreesUsed;
        if (value > THRESHOLD) {
            writer.println(name1 + "_" + card1 + "\t" + card1 + "\t" + value);
        }
    }
    writer.close();
    progressStream.println();
    cladePlotter.setCladeSystem(cladeSystem);
    return totalTreesUsed;
}

Example 73 with Tree

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

the class OrderNexusTranslationTable method main.

public static void main(String[] args) throws Importer.ImportException, IOException {
    NexusImporter importer = new NexusImporter(new FileReader(args[0]));
    Tree[] trees = importer.importTrees(null);
    System.out.println("Read " + trees.length + " trees from " + args[0]);
    String newFileName = args[0] + ".new";
    PrintStream ps = new PrintStream(new FileOutputStream(newFileName));
    NexusExporter exporter = new NexusExporter(ps);
    exporter.setTreePrefix("STATE_");
    NumberFormat format = NumberFormat.getNumberInstance();
    format.setMaximumFractionDigits(7);
    exporter.setNumberFormat(format);
    exporter.setSortedTranslationTable(true);
    exporter.exportTrees(trees, false);
    ps.flush();
    ps.close();
    System.out.println("Wrote " + trees.length + " trees to " + newFileName);
}

Example 74 with Tree

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

the class BeagleSeqSimTest method simulateCodon.

// END: simulateAminoAcid
static void simulateCodon() {
    try {
        boolean calculateLikelihood = true;
        System.out.println("Test case 6: simulate codons");
        MathUtils.setSeed(666);
        int sequenceLength = 10;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        TreeModel treeModel = new TreeModel(tree);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create Frequency Model
        Parameter freqs = new Parameter.Default(Utils.UNIFORM_CODON_FREQUENCIES);
        FrequencyModel freqModel = new FrequencyModel(Codons.UNIVERSAL, freqs);
        // create substitution model
        Parameter alpha = new Parameter.Default(1, 10);
        Parameter beta = new Parameter.Default(1, 5);
        //			Parameter kappa = new Parameter.Default(1, 1);
        MG94CodonModel mg94 = new MG94CodonModel(Codons.UNIVERSAL, alpha, beta, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(mg94);
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        Alignment alignment = simulator.simulate(simulateInPar, false);
        System.out.println(alignment.toString());
        if (calculateLikelihood) {
            // NewBeagleSequenceLikelihood nbtl = new
            // NewBeagleSequenceLikelihood(alignment, treeModel,
            // substitutionModel, (SiteModel) siteRateModel,
            // branchRateModel, null, false,
            // PartialsRescalingScheme.DEFAULT);
            ConvertAlignment convert = new ConvertAlignment(Nucleotides.INSTANCE, GeneticCode.UNIVERSAL, alignment);
            BeagleTreeLikelihood nbtl = new //
            BeagleTreeLikelihood(//
            convert, //
            treeModel, //
            substitutionModel, //
            siteRateModel, //
            branchRateModel, //
            null, //
            false, PartialsRescalingScheme.DEFAULT, true);
            System.out.println("likelihood = " + nbtl.getLogLikelihood());
        }
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch
}

Example 75 with Tree

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

the class BeagleSeqSimTest method simulateThreePartitions.

// END: simulateTwoPartitions
static void simulateThreePartitions(int i, int N) {
    try {
        MathUtils.setSeed(666);
        System.out.println("Test case 3: simulateThreePartitions");
        int sequenceLength = 100000;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        TreeModel treeModel = new TreeModel(tree);
        // create Frequency Model
        Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
        FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        // create substitution model
        Parameter kappa = new Parameter.Default(1, 10);
        HKY hky = new HKY(kappa, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(hky);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        3);
        // create partition
        Partition Partition = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        1, // to
        sequenceLength - 1, // every
        3);
        // create partition
        Partition partition3 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        2, // to
        sequenceLength - 1, // every
        3);
        partitionsList.add(partition1);
        partitionsList.add(Partition);
        partitionsList.add(partition3);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        if (i == (N - 1)) {
            System.out.println(simulator.simulate(simulateInPar, false).toString());
        } else {
            simulator.simulate(simulateInPar, false);
        }
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}