Examples with CladeSystem beast.app.treeannotator.CladeSystem used on opensource projects

Example 1 with CladeSystem

use of beast.app.treeannotator.CladeSystem in project beast2 by CompEvol.

the class TreeAnnotatorTest method setUp.

@Before
public void setUp() throws Exception {
    final String[] treesString = new String[] { "((A:1,B:1):1,(C:1,D:1):1);", "(((A:1,B:1):1,C:2):2,D:3);", "((A:2,(B:1,C:1):1):2,D:3);" };
    final String[] treesSAString = new String[] { "((((0:0.5,1:1.0):1.0,2:2.0):1.0,3:0.0):2.0,4:4.0);", "((((0:1.0,2:1.5):1.0,1:2.5):0.5,3:0.0):2.0,4:4.0);", "(((0:0.5,2:1.0):1.0,1:2.0):3.0,(3:0.2,4:2.2):1.8);", "((((0:1.0,2:1.5):1.0,1:2.5):0.2,4:1.7):0.3,3:0.0):0.0;" };
    treeAnnotator = new TreeAnnotator();
    treeAnnotatorSA = new TreeAnnotator();
    trees = new Tree[treesString.length];
    for (int i = 0; i < trees.length; i++) {
        trees[i] = new TreeParser(treesString[i], false, false, true, 1);
    }
    treesSA = new Tree[treesSAString.length];
    for (int i = 0; i < treesSA.length; i++) {
        treesSA[i] = new TreeParser(treesSAString[i], false, false, false, 0);
    }
    cladeSystem = new CladeSystem();
    cladeSystemSA = new CladeSystem();
}