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

Example 16 with Tree

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

the class BeagleSeqSimTest method simulateAminoAcid.

// END: simulateThreePartitions
static void simulateAminoAcid() {
    try {
        System.out.println("Test case 4: simulateAminoAcid");
        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(new double[] { 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05, 0.05 });
        FrequencyModel freqModel = new FrequencyModel(AminoAcids.INSTANCE, freqs);
        // create substitution model
        EmpiricalRateMatrix rateMatrix = Blosum62.INSTANCE;
        EmpiricalAminoAcidModel empiricalAminoAcidModel = new EmpiricalAminoAcidModel(rateMatrix, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(empiricalAminoAcidModel);
        // 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);
        System.out.println(simulator.simulate(simulateInPar, false).toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch
}

Example 17 with Tree

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

the class BeagleSeqSimTest method simulateRandomBranchAssignment.

// END: main
static void simulateRandomBranchAssignment() {
    try {
        System.out.println("Test case I dunno which: simulate random branch assignments");
        MathUtils.setSeed(666);
        int sequenceLength = 10;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        File treeFile = new File("/home/filip/Dropbox/BeagleSequenceSimulator/SimTree/SimTree.figtree");
        Tree tree = Utils.importTreeFromFile(treeFile);
        TreeModel treeModel = new TreeModel(tree);
        // create Frequency Model
        Parameter freqs = new Parameter.Default(Utils.UNIFORM_CODON_FREQUENCIES);
        FrequencyModel freqModel = new FrequencyModel(Codons.UNIVERSAL, freqs);
        // create base subst model
        Parameter omegaParameter = new Parameter.Default("omega", 1, 1.0);
        Parameter kappaParameter = new Parameter.Default("kappa", 1, 1.0);
        GY94CodonModel baseSubModel = new GY94CodonModel(Codons.UNIVERSAL, omegaParameter, kappaParameter, freqModel);
        RandomBranchModel substitutionModel = new RandomBranchModel(treeModel, baseSubModel, 0.25, false, -1);
        // 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
        1);
        //			Sequence ancestralSequence = new Sequence();
        //			ancestralSequence.appendSequenceString("TCAAGTGAGG");
        //			partition1.setRootSequence(ancestralSequence);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        SimpleAlignment alignment = simulator.simulate(simulateInPar, true);
        // alignment.setOutputType(SimpleAlignment.OutputType.NEXUS);
        alignment.setOutputType(SimpleAlignment.OutputType.XML);
        System.out.println(alignment.toString());
    } catch (Exception e) {
        e.printStackTrace();
    }
// END: try-catch
}

Example 18 with Tree

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

the class CoalGenFrame method generateFile.

protected void generateFile(File outFile) throws IOException {
    PrintWriter writer = new PrintWriter(new FileWriter(outFile));
    dr.evolution.coalescent.CoalescentSimulator simulator = new dr.evolution.coalescent.CoalescentSimulator();
    int count = 0;
    while (data.hasNext()) {
        DemographicFunction demo = data.nextDemographic();
        Tree tree = simulator.simulateTree(data.taxonList, demo);
        writer.println(count + "\t" + TreeUtils.newick(tree));
        count += 1;
    }
    writer.close();
}

Example 19 with Tree

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

the class TreesTableModel method loadTreeFile.

// END: doLoadTreeFile
private void loadTreeFile(final File file, final int row) {
    frame.setBusy();
    SwingWorker<Void, Void> worker = new SwingWorker<Void, Void>() {

        // Executed in background thread
        public Void doInBackground() {
            try {
                Tree tree = Utils.importTreeFromFile(file);
                tree.setId(file.getName());
                setRow(row, new TreesTableRecord(tree.getId(), tree));
            } catch (Exception e) {
                Utils.handleException(e);
            }
            return null;
        }

        // END: doInBackground()
        // Executed in event dispatch thread
        public void done() {
            frame.setIdle();
            frame.fireTaxaChanged();
        }
    };
    worker.execute();
}

Example 20 with Tree

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

the class BirthDeathCollapseModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    final Units.Type units = XMLUnits.Utils.getUnitsAttr(xo);
    final double collH = xo.getDoubleAttribute(COLLAPSE_HEIGHT);
    XMLObject cxo = xo.getChild(TREE);
    final Tree tree = (Tree) cxo.getChild(Tree.class);
    final Parameter birthMinusDeath = (Parameter) xo.getElementFirstChild(BIRTHDIFF_RATE);
    final Parameter relativeDeathRate = (Parameter) xo.getElementFirstChild(RELATIVE_DEATH_RATE);
    final Parameter originHeight = (Parameter) xo.getElementFirstChild(ORIGIN_HEIGHT);
    final Parameter collapseWeight = (Parameter) xo.getElementFirstChild(COLLAPSE_WEIGHT);
    final String modelName = xo.getId();
    return new BirthDeathCollapseModel(modelName, tree, units, birthMinusDeath, relativeDeathRate, originHeight, collapseWeight, collH);
}