use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.
the class MsatFullLikelihoodTest method setUpExample3.
private void setUpExample3() throws Exception {
//taxa
ArrayList<Taxon> taxonList3 = new ArrayList<Taxon>();
Collections.addAll(taxonList3, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"), new Taxon("taxon4"), new Taxon("taxon5"), new Taxon("taxon6"), new Taxon("taxon7"));
Taxa taxa3 = new Taxa(taxonList3);
//msat datatype
Microsatellite msat = new Microsatellite(1, 4);
Patterns msatPatterns = new Patterns(msat, taxa3);
//pattern in the correct code form.
msatPatterns.addPattern(new int[] { 0, 3, 1, 2, 3, 0, 1 });
//create tree
NewickImporter importer = new NewickImporter("(((taxon1:0.3,taxon2:0.3):0.6,taxon3:0.9):0.9,((taxon4:0.5,taxon5:0.5):0.3,(taxon6:0.7,taxon7:0.7):0.1):1.0);");
Tree tree = importer.importTree(null);
//treeModel
TreeModel treeModel = new TreeModel(tree);
//msatsubstModel
AsymmetricQuadraticModel aqm3 = new AsymmetricQuadraticModel(msat, null);
//siteModel
GammaSiteModel siteModel = new GammaSiteModel(aqm3);
//treeLikelihood
treeLikelihood3 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
}
use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.
the class BirthDeathLikelihoodTest method setUp.
public void setUp() throws Exception {
super.setUp();
NewickImporter importer = new NewickImporter("((1:1.0,2:1.0):1.0,3:2.0);");
tree = (FlexibleTree) importer.importTree(null);
}
use of dr.evolution.io.NewickImporter in project beast-mcmc by beast-dev.
the class AncestralStateTreeLikelihoodTest method setUp.
public void setUp() throws Exception {
super.setUp();
MathUtils.setSeed(666);
NewickImporter importer = new NewickImporter("(0:2.0,(1:1.0,2:1.0):1.0);");
tree = (FlexibleTree) importer.importTree(null);
}
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