Examples with ApSpInfo dr.evomodel.alloppnet.speciation.AlloppSpeciesBindings.ApSpInfo used on opensource projects

Example 1 with ApSpInfo

use of dr.evomodel.alloppnet.speciation.AlloppSpeciesBindings.ApSpInfo in project beast-mcmc by beast-dev.

the class AlloppSpeciesNetworkModelTEST method testNetworkToMulLabTree.

public void testNetworkToMulLabTree() {
    ApSpInfo[] apspecies = new ApSpInfo[5];
    apspecies[0] = new ApSpInfo("a", 2, new Individual[0]);
    apspecies[1] = new ApSpInfo("b", 4, new Individual[0]);
    apspecies[2] = new ApSpInfo("c", 4, new Individual[0]);
    apspecies[3] = new ApSpInfo("d", 4, new Individual[0]);
    apspecies[4] = new ApSpInfo("e", 2, new Individual[0]);
    AlloppSpeciesBindings testASB = new AlloppSpeciesBindings(apspecies);
    AlloppSpeciesNetworkModel testASNM = new AlloppSpeciesNetworkModel(testASB);
    System.out.println("Tests of Network To MulLabTree conversion with dips a,e and tets b,c,d");
    String newick;
    newick = testASNM.testExampleNetworkToMulLabTree(1);
    System.out.println(newick + "\n\n");
    assertEquals(0, newick.compareTo("((((b0,c0),d0),a),(((b1,c1),d1),e))"));
    newick = testASNM.testExampleNetworkToMulLabTree(2);
    System.out.println(newick + "\n\n");
    assertEquals(0, newick.compareTo("(((((b0,c0),d0),a),((b1,c1),d1)),e)"));
    newick = testASNM.testExampleNetworkToMulLabTree(3);
    System.out.println(newick + "\n\n");
    assertEquals(0, newick.compareTo("(((((b0,c0),d0),((b1,c1),d1)),a),e)"));
    newick = testASNM.testExampleNetworkToMulLabTree(4);
    System.out.println(newick + "\n\n");
    assertEquals(0, newick.compareTo("((((b0,c0),a),(d0,d1)),((b1,c1),e))"));
    newick = testASNM.testExampleNetworkToMulLabTree(5);
    System.out.println(newick + "\n\n");
    assertEquals(0, newick.compareTo("(((((a,b0),c0),c1),(d0,d1)),(b1,e))"));
    System.out.println("");
    System.out.println("");
}

Example 2 with ApSpInfo

use of dr.evomodel.alloppnet.speciation.AlloppSpeciesBindings.ApSpInfo in project beast-mcmc by beast-dev.

the class AlloppSpeciesNetworkModelTEST method testLhoodMulLabTree.

public void testLhoodMulLabTree() {
    ApSpInfo[] apspecies = new ApSpInfo[3];
    apspecies[0] = new ApSpInfo("a", 2, new Individual[0]);
    apspecies[1] = new ApSpInfo("b", 2, new Individual[0]);
    apspecies[2] = new ApSpInfo("z", 4, new Individual[0]);
    AlloppSpeciesBindings testASB = new AlloppSpeciesBindings(apspecies);
    AlloppMulLabTree testamlt = new AlloppMulLabTree(testASB);
    double llhood = testamlt.testGeneTreeInMULTreeLogLikelihood();
    assertEquals(llhood, -13.562218135041552713, 1e-10);
    System.out.println(llhood);
}