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

Example 26 with NewickImporter

use of dr.evolution.io.NewickImporter 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 27 with NewickImporter

use of dr.evolution.io.NewickImporter 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
}

Example 28 with NewickImporter

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

the class BeagleSeqSimTest method ancestralSequenceTree.

//END: simulateRandomBranchAssignment
static void ancestralSequenceTree() {
    try {
        LinkedHashMap<NodeRef, int[]> sequenceMap = new LinkedHashMap<NodeRef, int[]>();
        DataType dataType = Nucleotides.INSTANCE;
        // 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);
        for (NodeRef node : treeModel.getNodes()) {
            if (treeModel.isExternal(node)) {
                int[] seq = new int[] { 1, 1, 1 };
                sequenceMap.put(node, seq);
            } else {
                int[] seq = new int[] { 2, 2, 2 };
                sequenceMap.put(node, seq);
            }
        }
        // END: nodes loop
        AncestralSequenceTrait ancestralSequence = new AncestralSequenceTrait(sequenceMap, dataType);
        TreeTraitProvider[] treeTraitProviders = new TreeTraitProvider[] { ancestralSequence };
        StringBuffer buffer = new StringBuffer();
        NumberFormat format = NumberFormat.getNumberInstance(Locale.ENGLISH);
        boolean useTipLabels = true;
        //
        TreeUtils.newick(//
        treeModel, //
        treeModel.getRoot(), //
        useTipLabels, //
        TreeUtils.BranchLengthType.LENGTHS_AS_TIME, //
        format, //
        null, //
        treeTraitProviders, null, buffer);
        System.out.println(buffer);
    } catch (IOException e) {
        e.printStackTrace();
    } catch (ImportException e) {
        e.printStackTrace();
    }
// END: try-catch
}

Example 29 with NewickImporter

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

the class BeagleSeqSimTest method simulateTopology.

// END: annotateTree
static void simulateTopology() {
    try {
        System.out.println("Test case 1: simulateTopology");
        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);
        // set demographic function
        ExponentialGrowth exponentialGrowth = new ExponentialGrowth(Units.Type.YEARS);
        exponentialGrowth.setN0(10);
        exponentialGrowth.setGrowthRate(0.5);
        Taxa taxa = new Taxa();
        for (Taxon taxon : tree.asList()) {
            double absoluteHeight = Utils.getAbsoluteTaxonHeight(taxon, tree);
            taxon.setAttribute(Utils.ABSOLUTE_HEIGHT, absoluteHeight);
            // taxon.setAttribute("date", new Date(absoluteHeight,
            // Units.Type.YEARS, true));
            taxa.addTaxon(taxon);
        }
        // END: taxon loop
        CoalescentSimulator topologySimulator = new CoalescentSimulator();
        TreeModel treeModel = new TreeModel(topologySimulator.simulateTree(taxa, exponentialGrowth));
        System.out.println(treeModel.toString());
        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
        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 block
}

Example 30 with NewickImporter

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

the class BeagleSeqSimTest method simulateOnePartition.

// END: simulate topology
static void simulateOnePartition() {
    try {
        MathUtils.setSeed(666);
        System.out.println("Test case 2: simulateOnePartition");
        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 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
        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, false);
        // alignment.setOutputType(SimpleAlignment.OutputType.NEXUS);
        alignment.setOutputType(SimpleAlignment.OutputType.XML);
        System.out.println(alignment.toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}