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

Example 51 with Alignment

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

the class SerializationDeserializationTest method testString.

@Test
public void testString() 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(0);
    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);
    // Write ACG out to string
    String argString = acg.toStringOld();
    // Read ACG back in from string
    ConversionGraph argNew = new ConversionGraph();
    argNew.initByName("locus", locus, "fromString", argString);
    // Check that new ACG matches old
    Conversion newConv1 = argNew.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 = argNew.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());
// Note that there are minor differences in the tree due to
// rounding errors.  Is this normal!?
}

Example 52 with Alignment

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

the class TestBase method createMarginalAlignment.

/**
 * Create Alignment object representing alignment of a region
 * corresponding to a single marginal tree.
 *
 * @param alignment
 * @param region
 * @return
 * @throws Exception
 */
public Alignment createMarginalAlignment(Alignment alignment, Region region) throws Exception {
    List<Sequence> sequences = Lists.newArrayList();
    for (int leafIdx = 0; leafIdx < alignment.getTaxonCount(); leafIdx++) {
        List<Integer> stateSequence;
        stateSequence = alignment.getCounts().get(leafIdx).subList(region.leftBoundary, region.rightBoundary);
        String taxonName = alignment.getTaxaNames().get(leafIdx);
        String charSequence = alignment.getDataType().encodingToString(stateSequence);
        sequences.add(new Sequence(taxonName, charSequence));
    }
    return new Alignment(sequences, alignment.getDataType().getTypeDescription());
}

Example 53 with Alignment

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

the class ACGLikelihoodApproxTest method testACGHeightMap.

@Test
public void testACGHeightMap() 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);
    Conversion conversion = new Conversion();
    conversion.setNode1(acg.getNode(0));
    conversion.setHeight1(0.5);
    conversion.setNode2(acg.getNode(2));
    conversion.setHeight2(1.5);
    conversion.setStartSite(0);
    conversion.setEndSite(9);
    conversion.setLocus(locus);
    acg.addConversion(conversion);
    ACGLikelihoodApprox likelihoodApprox = new ACGLikelihoodApprox();
    likelihoodApprox.initByName("acg", acg, "substitutionRate", "1.0", "alignment", alignment, "locus", locus);
    Map<Double, Coalescence> heightMap = likelihoodApprox.getCoalescenceHeights();
    Assert.assertEquals(3, heightMap.size());
    Assert.assertTrue(heightMap.containsKey(1.0));
    Assert.assertTrue(heightMap.containsKey(1.5));
    Assert.assertTrue(heightMap.containsKey(2.0));
    Assert.assertTrue("height map contains incorrect coalescence.", heightMap.get(1.0).equals(new Coalescence("[10,20]{0}{1}")));
    Assert.assertTrue("height map contains incorrect coalescence.", heightMap.get(1.5).equals(new Coalescence("[0,10]{0}{2}")));
    Assert.assertTrue("height map contains incorrect coalescence.", heightMap.get(2.0).equals(new Coalescence("[0,10]{0,2}{1} [10,20]{0,1}{2}")));
}

Example 54 with Alignment

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

the class SimulatedAlignmentTest method test.

@Test
public void test() throws Exception {
    // Randomizer.setSeed(26);
    Randomizer.setSeed(7);
    Locus locus = new Locus("locus", 100000);
    TaxonSet taxonSet = getTaxonSet(10);
    ConstantPopulation popFunc = new ConstantPopulation();
    popFunc.initByName("popSize", new RealParameter("1.0"));
    ConversionGraph acg = new SimulatedACG();
    acg.initByName("rho", 1.0 / 100000, "delta", 1000.0, "populationModel", popFunc, "locus", locus, "taxonset", taxonSet);
    System.out.println(acg);
    // Site model:
    JukesCantor jc = new JukesCantor();
    jc.initByName();
    SiteModel siteModel = new SiteModel();
    siteModel.initByName("mutationRate", new RealParameter("1.0"), "substModel", jc);
    // Simulate alignment:
    SimulatedAlignment alignment = new SimulatedAlignment();
    alignment.initByName("acg", acg, "siteModel", siteModel, "outputFileName", "simulated_alignment.nexus", "useNexus", true);
    for (Region region : acg.getRegions(locus)) System.out.println(new MarginalTree(acg, region));
    // (Should be enough info here for precise agreement)
    for (Region region : acg.getRegions(locus)) {
        Alignment margAlign = createMarginalAlignment(alignment, region);
        ClusterTree upgmaTree = new ClusterTree();
        upgmaTree.initByName("clusterType", "upgma", "taxa", margAlign);
        MarginalTree marginalTree = new MarginalTree(acg, region);
        // outfMarg.println(marginalTree.getRoot() + ";");
        // outfMarg.flush();
        // 
        // outfUPGMA.println(upgmaTree.getRoot() + ";");
        // outfUPGMA.flush();
        assertTrue(topologiesEquivalent(marginalTree.getRoot(), upgmaTree.getRoot()));
    }
// outfMarg.close();
// outfUPGMA.close();
}

Example 55 with Alignment

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

the class ACGLikelihoodSlow method createMarginalAlignment.

/**
 * Create Alignment object representing alignment of a region
 * corresponding to a single marginal tree.
 *
 * @param alignment
 * @param acg
 * @param region
 * @return
 * @throws Exception
 */
public Alignment createMarginalAlignment(Alignment alignment, ConversionGraph acg, Region region) {
    List<Sequence> sequences = new ArrayList<>();
    for (int leafIdx = 0; leafIdx < alignment.getTaxonCount(); leafIdx++) {
        List<Integer> stateSequence;
        stateSequence = alignment.getCounts().get(leafIdx).subList(region.leftBoundary, region.rightBoundary);
        String taxonName = alignment.getTaxaNames().get(leafIdx);
        String charSequence = alignment.getDataType().encodingToString(stateSequence);
        sequences.add(new Sequence(taxonName, charSequence));
    }
    return new Alignment(sequences, alignment.getDataType().getTypeDescription());
}