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

Example 86 with Tree

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

the class BeagleBranchLikelihood method main.

// END: LikelihoodColumn class
// ////////////
// ---TEST---//
// ////////////
public static void main(String[] args) {
    try {
        MathUtils.setSeed(666);
        int sequenceLength = 1000;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("((SimSeq1:22.0,SimSeq2:22.0):12.0,(SimSeq3:23.1,SimSeq4:23.1):10.899999999999999);");
        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 branch model
        Parameter kappa1 = new Parameter.Default(1, 1);
        HKY hky1 = new HKY(kappa1, freqModel);
        BranchModel homogeneousBranchModel = new HomogeneousBranchModel(hky1);
        List<SubstitutionModel> substitutionModels = new ArrayList<SubstitutionModel>();
        substitutionModels.add(hky1);
        List<FrequencyModel> freqModels = new ArrayList<FrequencyModel>();
        freqModels.add(freqModel);
        // create branch rate model
        Parameter rate = new Parameter.Default(1, 1.000);
        BranchRateModel branchRateModel = new StrictClockBranchRates(rate);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        homogeneousBranchModel, //
        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(false, false);
        System.out.println(alignment);
        BeagleTreeLikelihood btl = new BeagleTreeLikelihood(alignment, treeModel, homogeneousBranchModel, siteRateModel, branchRateModel, null, false, PartialsRescalingScheme.DEFAULT, true);
        System.out.println("BTL(homogeneous) = " + btl.getLogLikelihood());
        BeagleBranchLikelihood bbl = new BeagleBranchLikelihood(alignment, treeModel, homogeneousBranchModel, siteRateModel, freqModel, branchRateModel);
        int branchIndex = 4;
        System.out.println(bbl.getBranchLogLikelihood(branchIndex));
        bbl.finalizeBeagle();
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    } catch (Throwable e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}

Example 87 with Tree

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

the class IndependentCoalescentSampler method doOperation.

/**
	 * change the parameter and return the hastings ratio.
     */
public double doOperation() {
    CoalescentSimulator simulator = new CoalescentSimulator();
    List<TaxonList> taxonLists = new ArrayList<TaxonList>();
    double rootHeight = -1.0;
    double oldLikelihood = 0.0;
    double newLikelihood = 0.0;
    // should have one child that is node
    for (int i = 0; i < xo.getChildCount(); i++) {
        final Object child = xo.getChild(i);
        //careful: Trees are TaxonLists ... (AER); see OldCoalescentSimulatorParser
        if (child instanceof Tree) {
        //do nothing
        } else if (child instanceof TaxonList) {
            //taxonLists.add((TaxonList) child);
            taxonLists.add((Taxa) child);
            //taxa added
            break;
        }
    }
    try {
        Tree[] trees = new Tree[taxonLists.size()];
        // simulate each taxonList separately
        for (int i = 0; i < taxonLists.size(); i++) {
            trees[i] = simulator.simulateTree(taxonLists.get(i), demoModel);
        }
        oldLikelihood = coalescent.getLogLikelihood();
        SimpleTree simTree = simulator.simulateTree(trees, demoModel, rootHeight, trees.length != 1);
        //this would be the normal way to do it
        treeModel.beginTreeEdit();
        //now it's allowed to adjust the tree structure
        treeModel.adoptTreeStructure(simTree);
        //endTreeEdit() would then fire the events
        treeModel.endTreeEdit();
        newLikelihood = coalescent.getLogLikelihood();
    } catch (IllegalArgumentException iae) {
        try {
            throw new XMLParseException(iae.getMessage());
        } catch (XMLParseException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    return oldLikelihood - newLikelihood;
}

Example 88 with Tree

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

the class DataLikelihoodTester method createSpecifiedTree.

private static TreeModel createSpecifiedTree(String t) throws Exception {
    NewickImporter importer = new NewickImporter(t);
    Tree tree = importer.importTree(null);
    //treeModel
    return new TreeModel(tree);
}

Example 89 with Tree

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

the class ProgressiveScalarTreeTransform method main.

// TODO Move to JUnitTest
public static void main(String[] args) throws Exception {
    NewickImporter importer = new NewickImporter("((((A:2,B:1):0.5,C:3):1.5,(D:1.5,E:1):3.5):1,F:5);");
    Tree tree = importer.importTree(null);
    Parameter scale = new Parameter.Default(0.5);
    TreeTransform xform = new ProgressiveScalarTreeTransform(scale);
    TreeModel treeModel = new TreeModel("original", tree);
    TransformedTreeModel model = new TransformedTreeModel("tree", treeModel, xform);
    System.err.println(model.toString());
    TreeTransform xform2 = new SingleScalarTreeTransform(scale);
    TransformedTreeModel model2 = new TransformedTreeModel("tree2", treeModel, xform2);
    System.err.println(model2.toString());
}

Example 90 with Tree

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

the class TreeTransform method setupTraits.

private void setupTraits() {
    TreeTrait baseTrait = new TreeTrait.D() {

        public String getTraitName() {
            return TREE_TRANSFORM_PREFIX;
        }

        public Intent getIntent() {
            return Intent.BRANCH;
        }

        public Double getTrait(Tree tree, NodeRef node) {
            return getScaleForNode(tree, node);
        }

        public boolean getLoggable() {
            return true;
        }
    };
    treeTraits.addTrait(baseTrait);
}