Examples with DefaultTreeModel dr.evomodel.tree.DefaultTreeModel used on opensource projects

Example 6 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class BeagleSeqSimTest method simulateTwoPartitions.

// END: simulateOnePartition
static void simulateTwoPartitions() {
    try {
        System.out.println("Test case 3: simulateTwoPartitions");
        MathUtils.setSeed(666);
        int sequenceLength = 11;
        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);
        DefaultTreeModel treeModel = new DefaultTreeModel(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
        3, // every
        1);
        // create partition
        Partition Partition = new // 
        Partition(// 
        treeModel, // 
        substitutionModel, // 
        siteRateModel, // 
        branchRateModel, // 
        freqModel, // from
        4, // to
        sequenceLength - 1, // every
        1);
        Sequence ancestralSequence = new Sequence();
        ancestralSequence.appendSequenceString("TCAAGTG");
        Partition.setRootSequence(ancestralSequence);
        partitionsList.add(partition1);
        partitionsList.add(Partition);
        // 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 block
}

Example 7 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel 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);
        DefaultTreeModel treeModel = new DefaultTreeModel(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 8 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class Coevolve method runModel2.

private void runModel2(PatternList patternList, PrintWriter pw, Tree tree, SubstitutionModel substModel, final Parameter betaParameter) {
    final Parameter muParameter = new Parameter.Default(1.0);
    muParameter.setId("mu");
    SiteModel siteModel = new GammaSiteModel(substModel, muParameter, null, 1, null);
    DefaultTreeModel treeModel = new DefaultTreeModel(tree);
    final TreeLikelihood treeLikelihood = new TreeLikelihood(patternList, treeModel, siteModel, null, null, false, false, true, false, false);
    treeLikelihood.setId("likelihood");
    MultivariateFunction function = new MultivariateFunction() {

        public double evaluate(double[] argument) {
            betaParameter.setParameterValue(0, argument[0]);
            betaParameter.setParameterValue(1, argument[1]);
            muParameter.setParameterValue(0, argument[2]);
            double lnL = -treeLikelihood.getLogLikelihood();
            // System.err.println("" + argument[0] + "\t" + argument[1] + "\t" + argument[2] + "\t" + lnL);
            return lnL;
        }

        public int getNumArguments() {
            return 3;
        }

        public double getLowerBound(int n) {
            return 0.0;
        }

        public double getUpperBound(int n) {
            return 100.0;
        }
    };
    MultivariateMinimum optimizer = new ConjugateGradientSearch();
    double lnL = optimizer.findMinimum(function, new double[] { 1.0, 1.0, 1.0 }, 6, 6);
    pw.write(betaParameter.getParameterValue(0) + "\t");
    pw.write(betaParameter.getParameterValue(1) + "\t");
    pw.write(muParameter.getParameterValue(0) + "\t");
    pw.write(lnL + "\n");
    pw.flush();
    System.out.println("" + betaParameter.getParameterValue(0) + "\t" + betaParameter.getParameterValue(1) + "\t" + muParameter.getParameterValue(0) + "\t" + lnL);
}

Example 9 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class AncestralSequenceAnnotator method sampleTree.

private FlexibleTree sampleTree(Tree tree, PatternList alignment, GammaSiteRateModel siteModel, BranchRateModel rateModel) {
    FlexibleTree flexTree = new FlexibleTree(tree, true);
    flexTree.adoptTreeModelOrdering();
    FlexibleTree finalTree = new FlexibleTree(tree);
    finalTree.adoptTreeModelOrdering();
    TreeModel treeModel = new DefaultTreeModel(tree);
    // Turn off noisy logging by TreeLikelihood constructor
    Logger logger = Logger.getLogger("dr.evomodel");
    boolean useParentHandlers = logger.getUseParentHandlers();
    logger.setUseParentHandlers(false);
    // AncestralStateTreeLikelihood likelihood = new AncestralStateTreeLikelihood(
    // alignment,
    // treeModel,
    // siteModel,
    // rateModel,
    // false, true,
    // alignment.getDataType(),
    // TAG,
    // false);
    AncestralStateBeagleTreeLikelihood likelihood = new AncestralStateBeagleTreeLikelihood(alignment, treeModel, new HomogeneousBranchModel(siteModel.getSubstitutionModel()), siteModel, rateModel, null, false, PartialsRescalingScheme.DEFAULT, true, null, alignment.getDataType(), TAG, false, true);
    // PatternList patternList, TreeModel treeModel,
    // BranchSiteModel branchSiteModel,
    // SiteRateModel siteRateModel,
    // BranchRateModel branchRateModel,
    // boolean useAmbiguities,
    // PartialsRescalingScheme scalingScheme,
    // Map<Set<String>, Parameter> partialsRestrictions,
    // final DataType dataType,
    // final String tag,
    // SubstitutionModel substModel,
    // boolean useMAP,
    // boolean returnML) {
    // PatternList patternList, TreeModel treeModel,
    // SiteModel siteModel, BranchRateModel branchRateModel,
    // boolean useAmbiguities, boolean storePartials,
    // final DataType dataType,
    // final String tag,
    // boolean forceRescaling,
    // boolean useMAP,
    // boolean returnML) {
    logger.setUseParentHandlers(useParentHandlers);
    // Sample internal nodes
    likelihood.makeDirty();
    double logLikelihood = likelihood.getLogLikelihood();
    System.out.println("The new and old Likelihood (this value should be roughly the same, debug?): " + logLikelihood + ", " + Double.parseDouble(tree.getAttribute(LIKELIHOOD).toString()));
    if (Double.parseDouble(tree.getAttribute(LIKELIHOOD).toString()) != logLikelihood) {
    /* Newly written check, not sure if this is correct. May need to round values at least */
    // throw new RuntimeException("The values of likelihood are not identical");
    }
    // System.err.printf("New logLikelihood = %4.1f\n", logLikelihood);
    flexTree.setAttribute(LIKELIHOOD, logLikelihood);
    TreeTrait ancestralStates = likelihood.getTreeTrait(TAG);
    for (int i = 0; i < treeModel.getNodeCount(); i++) {
        NodeRef node = treeModel.getNode(i);
        String sample = ancestralStates.getTraitString(treeModel, node);
        String oldSeq = (String) flexTree.getNodeAttribute(flexTree.getNode(i), SEQ_STRING);
        if (oldSeq != null) {
            char[] seq = (sample.substring(1, sample.length() - 1)).toCharArray();
            int length = oldSeq.length();
            for (int j = 0; j < length; j++) {
                if (oldSeq.charAt(j) == GAP)
                    seq[j] = GAP;
            }
            String newSeq = new String(seq);
            // if( newSeq.contains("MMMMMMM") ) {
            // System.err.println("bad = "+newSeq);
            // System.exit(-1);
            // }
            finalTree.setNodeAttribute(finalTree.getNode(i), NEW_SEQ, newSeq);
        }
    // Taxon taxon = finalTree.getNodeTaxon(finalTree.getNode(i));
    // System.err.println("node: "+(taxon == null ? "null" : taxon.getId())+" "+
    // finalTree.getNodeAttribute(finalTree.getNode(i),NEW_SEQ));
    }
    return finalTree;
}

Example 10 with DefaultTreeModel

use of dr.evomodel.tree.DefaultTreeModel in project beast-mcmc by beast-dev.

the class NarrowExchangeTest method testNarrow.

/**
 * Test method for {@link dr.evomodel.operators.ExchangeOperator#narrow()}.
 */
public void testNarrow() throws IOException, ImportException {
    // probability of picking B node is 1/(2n-4) = 1/6
    // probability of swapping it with C is 1/1
    // total = 1/6
    System.out.println("Test 1: Forward");
    String treeMatch = "((((A,C),B),D),E);";
    int count = 0;
    int reps = 100000;
    for (int i = 0; i < reps; i++) {
        DefaultTreeModel treeModel = new DefaultTreeModel("treeModel", tree5);
        ExchangeOperator operator = new ExchangeOperator(ExchangeOperator.NARROW, treeModel, 1);
        operator.doOperation();
        String tree = TreeUtils.newickNoLengths(treeModel);
        if (tree.equals(treeMatch)) {
            count += 1;
        }
    }
    double p_1 = (double) count / (double) reps;
    System.out.println("Number of proposals:\t" + count);
    System.out.println("Number of tries:\t" + reps);
    System.out.println("Number of ratio:\t" + p_1);
    System.out.println("Number of expected ratio:\t" + 1.0 / 6.0);
    assertExpectation(1.0 / 6.0, p_1, reps);
}