Examples with SimpleAlignment dr.evolution.alignment.SimpleAlignment used on opensource projects

Example 16 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class BeagleSeqSimTest method simulateOnePartition.

// END: simulate topology
static void simulateOnePartition() {
    try {
        MathUtils.setSeed(666);
        System.out.println("Test case 2: simulateOnePartition");
        int sequenceLength = 10;
        ArrayList<Partition> partitionsList = new ArrayList<Partition>();
        // create tree
        NewickImporter importer = new NewickImporter("(SimSeq1:73.7468,(SimSeq2:25.256989999999995,SimSeq3:45.256989999999995):18.48981);");
        Tree tree = importer.importTree(null);
        TreeModel treeModel = new TreeModel(tree);
        // create Frequency Model
        Parameter freqs = new Parameter.Default(new double[] { 0.25, 0.25, 0.25, 0.25 });
        FrequencyModel freqModel = new FrequencyModel(Nucleotides.INSTANCE, freqs);
        // create substitution model
        Parameter kappa = new Parameter.Default(1, 10);
        HKY hky = new HKY(kappa, freqModel);
        HomogeneousBranchModel substitutionModel = new HomogeneousBranchModel(hky);
        // create site model
        GammaSiteRateModel siteRateModel = new GammaSiteRateModel("siteModel");
        // create branch rate model
        BranchRateModel branchRateModel = new DefaultBranchRateModel();
        // create partition
        Partition partition1 = new //
        Partition(//
        treeModel, //
        substitutionModel, //
        siteRateModel, //
        branchRateModel, //
        freqModel, // from
        0, // to
        sequenceLength - 1, // every
        1);
        Sequence ancestralSequence = new Sequence();
        ancestralSequence.appendSequenceString("TCAAGTGAGG");
        partition1.setRootSequence(ancestralSequence);
        partitionsList.add(partition1);
        // feed to sequence simulator and generate data
        BeagleSequenceSimulator simulator = new BeagleSequenceSimulator(partitionsList);
        SimpleAlignment alignment = simulator.simulate(simulateInPar, false);
        // alignment.setOutputType(SimpleAlignment.OutputType.NEXUS);
        alignment.setOutputType(SimpleAlignment.OutputType.XML);
        System.out.println(alignment.toString());
    } catch (Exception e) {
        e.printStackTrace();
        System.exit(-1);
    }
// END: try-catch block
}

Example 17 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class IstvanOperator method doOperation.

public double doOperation() {
    Tree tree = likelihood.getTreeModel();
    alignment = likelihood.getAlignment();
    //System.out.println("Incoming alignment");
    //System.out.println(alignment);
    //System.out.println();
    SubstitutionModel substModel = likelihood.getSiteModel().getSubstitutionModel();
    // initialize the iParent and iTau arrays based on the given tree.
    initTree(tree, likelihood.getSiteModel().getMu());
    int[] treeIndex = new int[tree.getTaxonCount()];
    for (int i = 0; i < treeIndex.length; i++) {
        treeIndex[i] = tree.getTaxonIndex(alignment.getTaxonId(i));
    }
    // initialize the iAlignment array from the given alignment.
    initAlignment(alignment, treeIndex);
    // initialize the iProbs array from the substitution model -- must be called after populating tree!
    initSubstitutionModel(substModel);
    DataType dataType = substModel.getDataType();
    proposal.setGapSymbol(dataType.getGapState());
    int[][] returnedAlignment = new int[iAlignment.length][];
    //System.out.println("Initialization done, starting proposal proper...");
    double logq = proposal.propose(iAlignment, iProbs, iBaseFreqs, iParent, iTau, returnedAlignment, tuning, exponent, gapPenalty);
    //System.out.println("Proposal finished, logq=" + logq);
    //create new alignment object
    SimpleAlignment newAlignment = new SimpleAlignment();
    for (int i = 0; i < alignment.getTaxonCount(); i++) {
        StringBuffer seqBuffer = new StringBuffer();
        for (int j = 0; j < returnedAlignment[i].length; j++) {
            seqBuffer.append(dataType.getChar(returnedAlignment[treeIndex[i]][j]));
        }
        // add sequences in order of tree
        String seqString = seqBuffer.toString();
        Sequence sequence = new Sequence(alignment.getTaxon(i), seqString);
        newAlignment.addSequence(sequence);
        String oldunaligned = alignment.getUnalignedSequenceString(i);
        String unaligned = newAlignment.getUnalignedSequenceString(i);
        if (!unaligned.equals(oldunaligned)) {
            System.err.println("Sequence changed from:");
            System.err.println("old:'" + oldunaligned + "'");
            System.err.println("new:'" + unaligned + "'");
            throw new RuntimeException();
        }
    }
    //System.out.println("Outgoing alignment");
    //System.out.println(newAlignment);
    //System.out.println();
    likelihood.setAlignment(newAlignment);
    return logq;
}

Example 18 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class AncestralStateBeagleTreeLikelihoodTest method testJointLikelihood.

public void testJointLikelihood() {
    TreeModel treeModel = new TreeModel("treeModel", tree);
    Sequence[] sequence = new Sequence[3];
    sequence[0] = new Sequence(new Taxon("0"), "A");
    sequence[1] = new Sequence(new Taxon("1"), "C");
    sequence[2] = new Sequence(new Taxon("2"), "C");
    Taxa taxa = new Taxa();
    for (Sequence s : sequence) {
        taxa.addTaxon(s.getTaxon());
    }
    SimpleAlignment alignment = new SimpleAlignment();
    for (Sequence s : sequence) {
        alignment.addSequence(s);
    }
    Parameter mu = new Parameter.Default(1, 1.0);
    Parameter kappa = new Parameter.Default(1, 1.0);
    double[] pi = { 0.25, 0.25, 0.25, 0.25 };
    Parameter freqs = new Parameter.Default(pi);
    FrequencyModel f = new FrequencyModel(Nucleotides.INSTANCE, freqs);
    HKY hky = new HKY(kappa, f);
    GammaSiteRateModel siteRateModel = new GammaSiteRateModel("gammaModel", mu, null, -1, null);
    siteRateModel.setSubstitutionModel(hky);
    BranchModel branchModel = new HomogeneousBranchModel(siteRateModel.getSubstitutionModel());
    BranchRateModel branchRateModel = null;
    AncestralStateBeagleTreeLikelihood treeLikelihood = new AncestralStateBeagleTreeLikelihood(alignment, treeModel, branchModel, siteRateModel, branchRateModel, null, false, PartialsRescalingScheme.DEFAULT, true, null, hky.getDataType(), "stateTag", // useMap = true
    true, false);
    double logLike = treeLikelihood.getLogLikelihood();
    StringBuffer buffer = new StringBuffer();
    //        Tree.Utils.newick(treeModel, treeModel.getRoot(), false, Tree.BranchLengthType.LENGTHS_AS_TIME,
    //                null, null, new NodeAttributeProvider[]{treeLikelihood}, null, null, buffer);
    TreeUtils.newick(treeModel, treeModel.getRoot(), false, TreeUtils.BranchLengthType.LENGTHS_AS_TIME, null, null, new TreeTraitProvider[] { treeLikelihood }, null, buffer);
    System.out.println(buffer);
    System.out.println("t_CA(2) = " + t(false, 2.0));
    System.out.println("t_CC(1) = " + t(true, 1.0));
    double trueValue = 0.25 * t(false, 2.0) * Math.pow(t(true, 1.0), 3.0);
    assertEquals(logLike, Math.log(trueValue), 1e-6);
}

Example 19 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class NexusImporter method readCharactersBlock.

/**
     * Reads a 'CHARACTERS' block.
     */
private Alignment readCharactersBlock(TaxonList taxonList) throws ImportException, IOException {
    siteCount = 0;
    dataType = null;
    readDataBlockHeader("MATRIX", CHARACTERS_BLOCK);
    SimpleAlignment alignment = new SimpleAlignment();
    readSequenceData(alignment, taxonList);
    alignment.updateSiteCount();
    findEndBlock();
    return alignment;
}

Example 20 with SimpleAlignment

use of dr.evolution.alignment.SimpleAlignment in project beast-mcmc by beast-dev.

the class PhylipSequentialImporter method importAlignment.

/**
	 * importAlignment. 
	 */
public Alignment importAlignment() throws IOException, Importer.ImportException {
    SimpleAlignment alignment = null;
    try {
        int taxonCount = readInteger();
        int siteCount = readInteger();
        String firstSeq = null;
        for (int i = 0; i < taxonCount; i++) {
            StringBuffer name = new StringBuffer();
            char ch = read();
            int n = 0;
            while (!Character.isWhitespace(ch) && (maxNameLength < 1 || n < maxNameLength)) {
                name.append(ch);
                ch = read();
                n++;
            }
            StringBuffer seq = new StringBuffer(siteCount);
            readSequence(seq, dataType, "", siteCount, "-", "?", ".", firstSeq);
            if (firstSeq == null) {
                firstSeq = seq.toString();
            }
            if (alignment == null) {
                alignment = new SimpleAlignment();
            }
            alignment.addSequence(new Sequence(new Taxon(name.toString()), seq.toString()));
        }
    } catch (EOFException e) {
    }
    return alignment;
}