Examples with Taxon dr.evolution.util.Taxon used on opensource projects

Example 66 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class MsatFullLikelihoodTest method setUpExample2.

private void setUpExample2() throws Exception {
    //taxa
    ArrayList<Taxon> taxonList2 = new ArrayList<Taxon>();
    Collections.addAll(taxonList2, new Taxon("taxon1"), new Taxon("taxon2"), new Taxon("taxon3"), new Taxon("taxon4"), new Taxon("taxon5"));
    Taxa taxa2 = new Taxa(taxonList2);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 3);
    Patterns msatPatterns = new Patterns(msat, taxa2);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 2, 1, 2 });
    //create tree
    NewickImporter importer = new NewickImporter("(((taxon1:1.5,taxon2:1.5):1.5,(taxon3:2.1,taxon4:2.1):0.9):0.7,taxon5:3.7);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel aqm2 = new AsymmetricQuadraticModel(msat, null);
    //siteModel
    GammaSiteModel siteModel = new GammaSiteModel(aqm2);
    //treeLikelihood
    treeLikelihood2 = new TreeLikelihood(msatPatterns, treeModel, siteModel, null, null, false, false, true, false, false);
}

Example 67 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class MsatSamplingTreeLikelihoodTest method setUp.

public void setUp() throws Exception {
    super.setUp();
    //taxa
    ArrayList<Taxon> taxonList3 = new ArrayList<Taxon>();
    Collections.addAll(taxonList3, new Taxon("Taxon1"), new Taxon("Taxon2"), new Taxon("Taxon3"), new Taxon("Taxon4"), new Taxon("Taxon5"), new Taxon("Taxon6"), new Taxon("Taxon7"));
    Taxa taxa3 = new Taxa(taxonList3);
    //msat datatype
    Microsatellite msat = new Microsatellite(1, 6);
    Patterns msatPatterns = new Patterns(msat, taxa3);
    //pattern in the correct code form.
    msatPatterns.addPattern(new int[] { 0, 1, 3, 2, 4, 5, 1 });
    //create tree
    NewickImporter importer = new NewickImporter("(((Taxon1:0.3,Taxon2:0.3):0.6,Taxon3:0.9):0.9,((Taxon4:0.5,Taxon5:0.5):0.3,(Taxon6:0.7,Taxon7:0.7):0.1):1.0);");
    Tree tree = importer.importTree(null);
    //treeModel
    TreeModel treeModel = new TreeModel(tree);
    //msatsubstModel
    AsymmetricQuadraticModel eu1 = new AsymmetricQuadraticModel(msat, null);
    //create msatSamplerTreeModel
    Parameter internalVal = new Parameter.Default(new double[] { 2, 3, 4, 2, 1, 5 });
    int[] externalValues = msatPatterns.getPattern(0);
    HashMap<String, Integer> taxaMap = new HashMap<String, Integer>(externalValues.length);
    boolean internalValuesProvided = true;
    for (int i = 0; i < externalValues.length; i++) {
        taxaMap.put(msatPatterns.getTaxonId(i), i);
    }
    MicrosatelliteSamplerTreeModel msatTreeModel = new MicrosatelliteSamplerTreeModel("JUnitTestEx", treeModel, internalVal, msatPatterns, externalValues, taxaMap, internalValuesProvided);
    //create msatSamplerTreeLikelihood
    BranchRateModel branchRateModel = new StrictClockBranchRates(new Parameter.Default(1.0));
    eu1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, eu1, branchRateModel);
    //eu2
    TwoPhaseModel eu2 = new TwoPhaseModel(msat, null, eu1, new Parameter.Default(0.0), new Parameter.Default(0.4), null, false);
    eu2Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, eu2, branchRateModel);
    //ec1
    LinearBiasModel ec1 = new LinearBiasModel(msat, null, eu1, new Parameter.Default(0.48), new Parameter.Default(0.0), false, false, false);
    ec1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, ec1, branchRateModel);
    //ec2
    TwoPhaseModel ec2 = new TwoPhaseModel(msat, null, ec1, new Parameter.Default(0.0), new Parameter.Default(0.4), null, false);
    ec2Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, ec2, branchRateModel);
    //el1
    LinearBiasModel el1 = new LinearBiasModel(msat, null, eu1, new Parameter.Default(0.2), new Parameter.Default(-0.018), true, false, false);
    el1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, el1, branchRateModel);
    AsymmetricQuadraticModel pu1 = new AsymmetricQuadraticModel(msat, null, new Parameter.Default(1.0), new Parameter.Default(0.015), new Parameter.Default(0.0), new Parameter.Default(1.0), new Parameter.Default(0.015), new Parameter.Default(0.0), false);
    pu1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, pu1, branchRateModel);
    //ec2
    TwoPhaseModel pu2 = new TwoPhaseModel(msat, null, pu1, new Parameter.Default(0.0), new Parameter.Default(0.4), null, false);
    pu2Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, pu2, branchRateModel);
    //ec1
    LinearBiasModel pc1 = new LinearBiasModel(msat, null, pu1, new Parameter.Default(0.48), new Parameter.Default(0.0), false, false, false);
    pc1Likelihood = new MicrosatelliteSamplerTreeLikelihood(msatTreeModel, pc1, branchRateModel);
}

Example 68 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class SimpleTree method setTaxonId.

/**
     * Sets the ID of the taxon of the ith external node. If it doesn't have
     * a taxon, sets the ID of the node itself.
     */
public void setTaxonId(int taxonIndex, String id) {
    Taxon taxon = getTaxon(taxonIndex);
    if (taxon != null)
        taxon.setId(id);
    else
        getExternalNode(taxonIndex).setId(id);
    fireTreeChanged();
    fireTaxaChanged();
}

Example 69 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class TreeUtils method getLeafSet.

/**
     * @param tree the tree to retrieve leaf set of
     * @return a set of strings which are the taxa of the tree.
     */
public static Set<String> getLeafSet(Tree tree) {
    HashSet<String> leafSet = new HashSet<String>();
    int m = tree.getTaxonCount();
    for (int i = 0; i < m; i++) {
        Taxon taxon = tree.getTaxon(i);
        leafSet.add(taxon.getId());
    }
    return leafSet;
}

Example 70 with Taxon

use of dr.evolution.util.Taxon in project beast-mcmc by beast-dev.

the class BeagleSequenceSimulator method compileAlignment.

// END: SimulatePartitionCallable class
private SimpleAlignment compileAlignment() {
    SimpleAlignment simpleAlignment = new SimpleAlignment();
    simpleAlignment.setReportCountStatistics(false);
    simpleAlignment.setDataType(dataType);
    LinkedHashMap<Taxon, int[]> alignmentMap = new LinkedHashMap<Taxon, int[]>();
    // compile the alignment
    for (Partition partition : partitions) {
        Map<Taxon, int[]> sequenceMap = partition.getTaxonSequencesMap();
        Iterator<Entry<Taxon, int[]>> iterator = sequenceMap.entrySet().iterator();
        while (iterator.hasNext()) {
            Entry<Taxon, int[]> pairs = (Entry<Taxon, int[]>) iterator.next();
            Taxon taxon = pairs.getKey();
            int[] partitionSequence = pairs.getValue();
            if (alignmentMap.containsKey(taxon)) {
                int j = 0;
                for (int i = partition.from; i <= partition.to; i += partition.every) {
                    alignmentMap.get(taxon)[i] = partitionSequence[j];
                    j++;
                }
            // END: i loop
            } else {
                int[] sequence = new int[siteCount];
                // dirty solution for gaps when taxa between the tree
                // topologies don't match
                Arrays.fill(sequence, gapFlag);
                int j = 0;
                for (int i = partition.from; i <= partition.to; i += partition.every) {
                    sequence[i] = partitionSequence[j];
                    j++;
                }
                // END: i loop
                alignmentMap.put(taxon, sequence);
            }
        // END: key check
        }
    // END: iterate seqMap
    }
    // END: partitions loop
    Iterator<Entry<Taxon, int[]>> iterator = alignmentMap.entrySet().iterator();
    while (iterator.hasNext()) {
        Entry<Taxon, int[]> pairs = (Entry<Taxon, int[]>) iterator.next();
        Taxon taxon = (Taxon) pairs.getKey();
        int[] intSequence = (int[]) pairs.getValue();
        Sequence sequence = //
        Utils.intArray2Sequence(//
        taxon, //
        intSequence, //
        gapFlag, dataType);
        //			sequence.setDataType(dataType);
        simpleAlignment.addSequence(sequence);
        iterator.remove();
    }
    return simpleAlignment;
}