Examples with EmpiricalAminoAcidModel dr.evomodel.substmodel.aminoacid.EmpiricalAminoAcidModel used on opensource projects

Example 1 with EmpiricalAminoAcidModel

use of dr.evomodel.substmodel.aminoacid.EmpiricalAminoAcidModel 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
}