Examples with Alignment beast.evolution.alignment.Alignment used on opensource projects

Example 56 with Alignment

use of beast.evolution.alignment.Alignment in project bacter by tgvaughan.

the class SerializationDeserializationTest method testExtendedNewick.

@Test
public void testExtendedNewick() throws Exception {
    Alignment alignment = getAlignment();
    alignment.setID("alignment");
    Locus locus = new Locus("locus", alignment.getSiteCount());
    // ConversionGraph
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", alignment);
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    // Add recombination event 1
    Node node1 = acg.getExternalNodes().get(0);
    Node node2 = node1.getParent();
    double height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
    double height2 = 0.5 * (node2.getHeight() + node2.getParent().getHeight());
    int startLocus = 100;
    int endLocus = 200;
    Conversion conv1 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(conv1);
    // Add recombination event 2
    node1 = acg.getExternalNodes().get(8);
    node2 = acg.getRoot();
    height1 = 0.5 * (node1.getHeight() + node1.getParent().getHeight());
    height2 = node2.getHeight() + 1.0;
    startLocus = 300;
    endLocus = 400;
    Conversion conv2 = new Conversion(node1, height1, node2, height2, startLocus, endLocus, acg, locus);
    acg.addConversion(conv2);
    String newickString = acg.getExtendedNewick();
    System.out.println(newickString);
    ConversionGraph acgNew = new ConversionGraph();
    acgNew.initByName("locus", locus);
    acgNew.fromExtendedNewick(newickString);
    // Check that new ACG matches old
    Conversion newConv1 = acgNew.getConversions(locus).get(0);
    assertEquals(newConv1.getNode1().getNr(), conv1.getNode1().getNr());
    assertEquals(newConv1.getNode2().getNr(), conv1.getNode2().getNr());
    assertEquals(newConv1.getHeight1(), conv1.getHeight1(), 1e-15);
    assertEquals(newConv1.getHeight2(), conv1.getHeight2(), 1e-15);
    assertEquals(newConv1.getStartSite(), conv1.getStartSite());
    assertEquals(newConv1.getEndSite(), conv1.getEndSite());
    Conversion newConv2 = acgNew.getConversions(locus).get(1);
    assertEquals(newConv2.getNode1().getNr(), conv2.getNode1().getNr());
    assertEquals(newConv2.getNode2().getNr(), conv2.getNode2().getNr());
    assertEquals(newConv2.getHeight1(), conv2.getHeight1(), 1e-15);
    assertEquals(newConv2.getHeight2(), conv2.getHeight2(), 1e-15);
    assertEquals(newConv2.getStartSite(), conv2.getStartSite());
    assertEquals(newConv2.getEndSite(), conv2.getEndSite());
}

Example 57 with Alignment

use of beast.evolution.alignment.Alignment in project bacter by tgvaughan.

the class TestBase method getAlignment.

/**
 * @return An Alignment object containing primate data for unit tests.
 * @throws Exception
 */
public Alignment getAlignment() throws Exception {
    List<Sequence> sequences = new ArrayList<>();
    sequences.add(new Sequence("Tarsius_syrichta", "AAGTTTCATTGGAGCCACCARTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATTTTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGGCCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCTGGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTCATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTCCCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCATGCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACTATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAACATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TGCAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGATAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTATTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCGCCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAATAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT"));
    sequences.add(new Sequence("Lemur_catta", "AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATTCTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGGGATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCTAGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTCATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTCCCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAACCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATTTACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAACACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATGTATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGATAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAATAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTATAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTGCATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAACAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT"));
    sequences.add(new Sequence("Homo_sapiens", "AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATTCTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGGACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCTCGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTCCTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTCCCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAAACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCTATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTACCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCGCATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAGTTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT"));
    sequences.add(new Sequence("Pan", "AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATTCTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGGACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCTCGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTCCTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTCCCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAAGCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCTATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TATAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCACCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCGCGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAGCTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT"));
    sequences.add(new Sequence("Gorilla", "AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGGACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCTCGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTCCTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTCCCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAAACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCTATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAACATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CGTAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTACCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCGCATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAGCTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT"));
    sequences.add(new Sequence("Pongo", "AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTTCTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGGCCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCTTGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTCTTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTCTCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAAACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTTATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAACATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CACAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGATAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAACAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCGCTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCGCATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAACCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT"));
    sequences.add(new Sequence("Hylobates", "AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATTCTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGGGCTCCAAGCCTTACTCCCACTGATAGCYTTCTGATGACTCGCAGCAAGCCTCGCTAACCTCGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTCCTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTCCCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAAACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCTAACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAACATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CACAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAATAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAGCCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTGCCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAACCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT"));
    sequences.add(new Sequence("Macaca_fuscata", "AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGGACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTCCTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTCTCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAAGCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAACACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT"));
    sequences.add(new Sequence("M_mulatta", "AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTTCTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGGACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTCCTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTCCCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCTATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAACATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CGCGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTGCCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAATATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAACAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT"));
    sequences.add(new Sequence("M_fascicularis", "AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTTCTGCTTGGCCAATTCAAACTATGAGCGCACTCATAMCCGTACCATACTACTATCCCGAGGACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCTTGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTCCTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTCTCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAAACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCTATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAACATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CGCAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGATAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAATAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTGCCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAATATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAACAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT"));
    sequences.add(new Sequence("M_sylvanus", "AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTTCTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGVATCATACTACTATCCCGAGGACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCTTGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTCCTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTCTCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAAACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCTATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAACATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TGCAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGATAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAATAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCGCTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAATATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAACAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT"));
    sequences.add(new Sequence("Saimiri_sciureus", "AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTHTATGCTATTCTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAA-BACH-TTACTCGAGGGCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCTCGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTCTTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTCACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAAACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCTTACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAACATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CGCAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGATAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAATA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAGCTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCATCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAATCAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT"));
    return new Alignment(sequences, "nucleotide");
}

Example 58 with Alignment

use of beast.evolution.alignment.Alignment in project bacter by tgvaughan.

the class ACGLikelihoodApproxTest method testTreeHeightMap.

@Test
public void testTreeHeightMap() throws Exception {
    List<Sequence> sequences = new ArrayList<>();
    // 01234567890123456789
    sequences.add(new Sequence("t1", "GGGGGGGGGGGGGGGGGGGG"));
    sequences.add(new Sequence("t2", "CCCCCCCCCCCCCCCCCCCC"));
    sequences.add(new Sequence("t3", "TTTTTTTTTTTTTTTTTTTT"));
    Alignment alignment = new Alignment(sequences, "nucleotide");
    Locus locus = new Locus("locus", alignment);
    TreeParser tree = new TreeParser(alignment, "((t1:1,t2:1):1,t3:2):0;");
    ConversionGraph acg = new ConversionGraph();
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    ACGLikelihoodApprox likelihoodApprox = new ACGLikelihoodApprox();
    likelihoodApprox.initByName("acg", acg, "substitutionRate", "1.0", "alignment", alignment, "locus", locus);
    Map<Double, Coalescence> heightMap = likelihoodApprox.getCoalescenceHeights();
    Assert.assertEquals(2, heightMap.size());
    Assert.assertTrue(heightMap.containsKey(1.0));
    Assert.assertTrue(heightMap.containsKey(2.0));
    Assert.assertTrue(heightMap.get(1.0).equals(new Coalescence("[0,20]{0}{1}")));
    Assert.assertTrue(heightMap.get(2.0).equals(new Coalescence("[0,20]{0,1}{2}")));
}

Example 59 with Alignment

use of beast.evolution.alignment.Alignment in project bacter by tgvaughan.

the class ACGLikelihoodApproxTest method testPairwiseDistances.

@Test
public void testPairwiseDistances() throws Exception {
    List<Sequence> sequences = new ArrayList<>();
    // 01234567890123456789
    sequences.add(new Sequence("t1", "AAAAAAAAAAAAAAAAAAAA"));
    sequences.add(new Sequence("t2", "AAAACAAAAAAGAAAAAAAA"));
    sequences.add(new Sequence("t3", "CCCCCCCCCCCCCCCCCCCC"));
    Alignment alignment = new Alignment(sequences, "nucleotide");
    Locus locus = new Locus("locus", alignment);
    ConversionGraph acg = new ConversionGraph();
    ClusterTree tree = new ClusterTree();
    tree.initByName("clusterType", "upgma", "taxa", locus.getAlignment());
    acg.assignFrom(tree);
    acg.initByName("locus", locus);
    ACGLikelihoodApprox likelihoodApprox = new ACGLikelihoodApprox();
    likelihoodApprox.initByName("acg", acg, "substitutionRate", "1.0", "alignment", alignment, "locus", locus);
    Assert.assertEquals(0, likelihoodApprox.getPairwiseDistance(0, 1, 0, 4));
    Assert.assertEquals(1, likelihoodApprox.getPairwiseDistance(0, 1, 0, 5));
    Assert.assertEquals(1, likelihoodApprox.getPairwiseDistance(0, 1, 0, 11));
    Assert.assertEquals(2, likelihoodApprox.getPairwiseDistance(0, 1, 0, 12));
    Assert.assertEquals(2, likelihoodApprox.getPairwiseDistance(0, 1, 0, 20));
    Assert.assertEquals(5, likelihoodApprox.getPairwiseDistance(1, 2, 2, 8));
    Assert.assertEquals(19, likelihoodApprox.getPairwiseDistance(1, 2, 0, 20));
    Assert.assertEquals(6, likelihoodApprox.getPairwiseDistance(0, 2, 2, 8));
    Assert.assertEquals(20, likelihoodApprox.getPairwiseDistance(0, 2, 0, 20));
}

Example 60 with Alignment

use of beast.evolution.alignment.Alignment in project bacter by tgvaughan.

the class ACGLikelihoodBeagle method setPartials.

/**
 * Set leaf partials in a Beagle instance
 *
 * @param beagle beagle instance object
 * @param patterns leaf state patterns
 */
protected void setPartials(Beagle beagle, Multiset<int[]> patterns) {
    for (Node node : acg.getExternalNodes()) {
        Alignment data = dataInput.get();
        int nStates = data.getDataType().getStateCount();
        double[] partials = new double[patterns.elementSet().size() * nStates * siteModel.getCategoryCount()];
        int k = 0;
        int iTaxon = alignment.getTaxonIndex(node.getID());
        for (int[] pattern : patterns.elementSet()) {
            int code = pattern[iTaxon];
            boolean[] stateSet = alignment.getDataType().getStateSet(code);
            for (int iState = 0; iState < nStates; iState++) {
                partials[k++] = (stateSet[iState] ? 1.0 : 0.0);
            }
        }
        int n = patterns.elementSet().size() * siteModel.getCategoryCount();
        for (int cIdx = 1; cIdx < siteModel.getCategoryCount(); cIdx++) {
            System.arraycopy(partials, 0, partials, n * cIdx, n);
        }
        beagle.setTipPartials(node.getNr(), partials);
    }
}