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

Example 51 with Tree

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

the class SpeciesTreeModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    SpeciesBindings spb = (SpeciesBindings) xo.getChild(SpeciesBindings.class);
    Parameter coalPointsPops = null;
    Parameter coalPointsIndicators = null;
    final Boolean cr = xo.getAttribute(CONST_ROOT_POPULATION, false);
    final Boolean cp = xo.getAttribute(CONSTANT_POPULATION, false);
    final Boolean bmp = xo.getAttribute(BMPRIOR, false);
    {
        XMLObject cxo = xo.getChild(COALESCENT_POINTS_POPULATIONS);
        if (cxo != null) {
            final double value = cxo.getAttribute(Attributable.VALUE, 1.0);
            coalPointsPops = SpeciesTreeModel.createCoalPointsPopParameter(spb, cxo.getAttribute(Attributable.VALUE, value), bmp);
            ParameterParser.replaceParameter(cxo, coalPointsPops);
            coalPointsPops.addBounds(new Parameter.DefaultBounds(Double.MAX_VALUE, 0, coalPointsPops.getDimension()));
            cxo = xo.getChild(COALESCENT_POINTS_INDICATORS);
            if (cxo == null) {
                throw new XMLParseException("Must have indicators");
            }
            coalPointsIndicators = new Parameter.Default(coalPointsPops.getDimension(), 0);
            ParameterParser.replaceParameter(cxo, coalPointsIndicators);
        } else {
        // assert ! bmp;
        }
    }
    final XMLObject cxo = xo.getChild(SPP_SPLIT_POPULATIONS);
    final double value = cxo.getAttribute(Attributable.VALUE, 1.0);
    final boolean nonConstRootPopulation = coalPointsPops == null && !cr;
    final Parameter sppSplitPopulations = SpeciesTreeModel.createSplitPopulationsParameter(spb, value, nonConstRootPopulation, cp);
    ParameterParser.replaceParameter(cxo, sppSplitPopulations);
    final Parameter.DefaultBounds bounds = new Parameter.DefaultBounds(Double.MAX_VALUE, 0, sppSplitPopulations.getDimension());
    sppSplitPopulations.addBounds(bounds);
    final Tree startTree = (Tree) xo.getChild(Tree.class);
    return new SpeciesTreeModel(spb, sppSplitPopulations, coalPointsPops, coalPointsIndicators, startTree, bmp, nonConstRootPopulation, cp);
}

Example 52 with Tree

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

the class BetaSplittingModelParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    XMLObject cxo = xo.getChild(PHI);
    Parameter phiParameter = (Parameter) cxo.getChild(Parameter.class);
    cxo = xo.getChild(TREE);
    Tree tree = (Tree) cxo.getChild(Tree.class);
    return new BetaSplittingModel(phiParameter, tree);
}

Example 53 with Tree

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

the class CompatibilityStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree1 = (Tree) xo.getChild(Tree.class);
    XMLObject cxo = xo.getChild(COMPATIBLE_WITH);
    Tree tree2 = (Tree) cxo.getChild(Tree.class);
    try {
        return new CompatibilityStatistic(name, tree1, tree2);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was in the source tree but not the constraints tree.");
    }
}

Example 54 with Tree

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

the class MsatFullLikelihoodTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    //taxa
    ArrayList<Taxon> taxonList1 = new ArrayList<Taxon>();
    Collections.addAll(taxonList1, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"));
    Taxa taxa1 = new Taxa(taxonList1);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 3);
    Patterns msatPatterns = new Patterns(msat, taxa1);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 2 });
    //create tree
    NewickImporter importer = new NewickImporter("(taxon1:7.5,(taxon2:5.3,taxon3:5.3):2.2);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel aqm1 = new AsymmetricQuadraticModel(msat, null);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm1);
    //treeLikelihood
    treeLikelihood1 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
    setUpExample2();
    setUpExample3();
}

Example 55 with Tree

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

the class MsatFullLikelihoodTest method setUpExample2.

private void setUpExample2() throws Exception {
    //taxa
    ArrayList<Taxon> taxonList2 = new ArrayList<Taxon>();
    Collections.addAll(taxonList2, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"), new Taxon("taxon4"), new Taxon("taxon5"));
    Taxa taxa2 = new Taxa(taxonList2);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 3);
    Patterns msatPatterns = new Patterns(msat, taxa2);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 2, 1, 2 });
    //create tree
    NewickImporter importer = new NewickImporter("(((taxon1:1.5,taxon2:1.5):1.5,(taxon3:2.1,taxon4:2.1):0.9):0.7,taxon5:3.7);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel aqm2 = new AsymmetricQuadraticModel(msat, null);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm2);
    //treeLikelihood
    treeLikelihood2 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
}