Examples with Taxa dr.evolution.util.Taxa used on opensource projects

Example 31 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class TreesTableModel method applyTaxa.

// END: setRow
public void applyTaxa(Tree tree) {
    // set attributes to be parsed later in Taxa panel
    Taxa taxa = new Taxa();
    for (Taxon taxon : tree.asList()) {
        double absoluteHeight = Utils.getAbsoluteTaxonHeight(taxon, tree);
        taxon.setAttribute(Utils.ABSOLUTE_HEIGHT, absoluteHeight);
        taxon.setAttribute(Utils.TREE_FILENAME, tree.getId());
        taxa.addTaxon(taxon);
        dataList.allTaxa.addTaxon(taxon);
    }
// END: taxon loop
}

Example 32 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class Utils method importTaxaFromFile.

// END: countLines
public static Taxa importTaxaFromFile(File file) throws IOException {
    Taxa taxa = new Taxa();
    Taxon taxon;
    String[] lines = Utils.loadStrings(file.getAbsolutePath());
    for (int i = 0; i < lines.length; i++) {
        String[] line = lines[i].split("\\s+");
        taxon = new Taxon(line[TaxaEditorTableModel.NAME_INDEX]);
        taxon.setAttribute(Utils.ABSOLUTE_HEIGHT, Double.valueOf(line[TaxaEditorTableModel.HEIGHT_INDEX]));
        taxa.addTaxon(taxon);
    }
    return taxa;
}

Example 33 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class TestCalibratedYuleModel method createTreeModel.

protected DefaultTreeModel createTreeModel(int treeSize) throws Exception {
    taxa = new Taxa();
    for (int i = 0; i < treeSize; i++) {
        taxa.addTaxon(new Taxon("T" + Integer.toString(i)));
    }
    // System.out.println("taxaSubSet_size = " + taxaSubSet.getTaxonCount());
    Parameter popSize = new Parameter.Default(treeSize);
    popSize.setId(ConstantPopulationModelParser.POPULATION_SIZE);
    ConstantPopulationModel startingTree = new ConstantPopulationModel(popSize, Units.Type.YEARS);
    Tree tree = calibration(taxa, startingTree);
    // treeModel
    return new DefaultTreeModel(tree);
}

Example 34 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class FilteredTreeTraitTest method testBackboneFilter.

public void testBackboneFilter() {
    Taxa taxonList = new Taxa();
    taxonList.addTaxon(taxa[0]);
    taxonList.addTaxon(taxa[1]);
    TreeTrait backboneFilter = new TreeTrait.FilteredD(dummyTrait, new BackboneNodeFilter("backbone", tree, taxonList, true, true));
    treeTraitProvider.addTrait(backboneFilter);
    TreeTrait sumTrait = new TreeTrait.SumOverTreeD(backboneFilter);
    treeTraitProvider.addTrait(sumTrait);
    System.out.println("BackboneFilter Test");
    StringBuffer buffer = new StringBuffer();
    TreeUtils.newick(tree, tree.getRoot(), false, TreeUtils.BranchLengthType.LENGTHS_AS_TIME, // format
    null, // branchRates,
    null, new TreeTraitProvider[] { treeTraitProvider }, // idMap,
    null, buffer);
    System.out.println("Tree: " + buffer.toString());
    double traitValue = (Double) sumTrait.getTrait(tree, null);
    System.out.println("Trait: " + traitValue);
    // TODO Get real result
    assertEquals(traitValue, 7.0);
}

Example 35 with Taxa

use of dr.evolution.util.Taxa in project beast-mcmc by beast-dev.

the class GhostTreeModelTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    Taxa ghostTaxa = new Taxa("ghost");
    ghostTaxa.addTaxon(new Taxon("g1"));
    ghostTaxa.addTaxon(new Taxon("g2"));
    Taxa corporealTaxa = new Taxa("corporeal");
    corporealTaxa.addTaxon(new Taxon("0"));
    corporealTaxa.addTaxon(new Taxon("1"));
    corporealTaxa.addTaxon(new Taxon("2"));
    Taxa allTaxa = new Taxa(ghostTaxa);
    allTaxa.addTaxa(corporealTaxa);
    NewickImporter importer = new NewickImporter("(((g1:0.5,0:1):0.5,1:1):1,(g2:1,2:1):0.5)");
    Tree superTree = importer.importTree(allTaxa);
    ghostTree = new GhostTreeModel(superTree, ghostTaxa);
    corporealTree = ghostTree.getCorporealTreeModel();
}