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

Example 26 with Taxon

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

the class AlloppDiploidHistory method simpletree2dhtesttree.

// for testing
private void simpletree2dhtesttree(SimpleNode snode) {
    if (snode.getChildCount() == 2) {
        simpletree2dhtesttree(snode.getChild(0));
        int lft = nextn - 1;
        simpletree2dhtesttree(snode.getChild(1));
        int rgt = nextn - 1;
        dhnodes[nextn].lft = lft;
        dhnodes[lft].anc = nextn;
        dhnodes[nextn].rgt = rgt;
        dhnodes[rgt].anc = nextn;
    }
    dhnodes[nextn].height = snode.getHeight();
    dhnodes[nextn].taxon = new Taxon(snode.getTaxon().getId());
    dhnodes[nextn].union = apsp.speciesseqEmptyUnion();
    nextn++;
}

Example 27 with Taxon

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

the class MoveLinkageGroup method doOperation.

public double doOperation() {
    // pick a read uniformly at random, add it to a linkage group uniformly at random
    int r = MathUtils.nextInt(readCount);
    Taxon read = hlm.getData().getReadsTaxa().getTaxon(r);
    int g = hlm.getLinkageGroupId(read);
    int newGroup = MathUtils.nextInt(groupCount);
    hlm.moveReadGroup(read, g, newGroup);
    // moves are symmetric -- same forward and backward proposal probabilities
    double logHastings = 0.0;
    return logHastings;
}

Example 28 with Taxon

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

the class LinkageGroupSwap method doOperation.

@Override
public double doOperation() {
    if (MathUtils.nextBoolean()) {
        // swap all taxa in one group to a new group
        int A = MathUtils.nextInt(groupCount);
        int B = MathUtils.nextInt(groupCount);
        HashSet<Taxon> aTaxa = new HashSet<Taxon>(hlm.getGroup(A));
        HashSet<Taxon> bTaxa = new HashSet<Taxon>(hlm.getGroup(B));
        for (Taxon taxon : aTaxa) {
            hlm.moveReadGroup(taxon, A, B);
        }
        for (Taxon taxon : bTaxa) {
            hlm.moveReadGroup(taxon, B, A);
        }
    } else {
        // pick two linkage groups uniformly A, B
        // pick an alignment column uniformly X
        // move all reads in group A that are defined in column X to group B, and
        // vice versa from B to A.
        // pick a read uniformly at random, add it to a linkage group uniformly at random
        ArrayList<Taxon> aTaxa = new ArrayList<Taxon>();
        ArrayList<Taxon> bTaxa = new ArrayList<Taxon>();
        int A = 0, B = 0;
        // choice of X and Y to groups that have something in col X.
        while (aTaxa.size() == 0 && bTaxa.size() == 0) {
            int X = MathUtils.nextInt(columnCount);
            A = MathUtils.nextInt(groupCount);
            B = MathUtils.nextInt(groupCount);
            if (A == B)
                // nothing to do.
                continue;
            // find all reads intersecting column X
            Alignment aln = hlm.getData().getAlignment();
            for (int i = 0; i < aln.getTaxonCount(); i++) {
                int state = aln.getPatternState(i, X);
                if (state == hlm.getDataType().getGapState() || state == hlm.getDataType().getUnknownState())
                    // seq undefined in this column
                    continue;
                if (hlm.getGroup(A).contains(aln.getTaxon(i))) {
                    aTaxa.add(aln.getTaxon(i));
                }
                if (hlm.getGroup(B).contains(aln.getTaxon(i))) {
                    bTaxa.add(aln.getTaxon(i));
                }
            }
        }
        // move taxa from A to B and from B to A
        for (Taxon taxon : aTaxa) {
            hlm.moveReadGroup(taxon, A, B);
        }
        for (Taxon taxon : bTaxa) {
            hlm.moveReadGroup(taxon, B, A);
        }
    }
    return 0;
}

Example 29 with Taxon

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

the class TreeDataLikelihoodParser method createTreeDataLikelihood.

protected Likelihood createTreeDataLikelihood(List<PatternList> patternLists, List<BranchModel> branchModels, List<SiteRateModel> siteRateModels, TreeModel treeModel, BranchRateModel branchRateModel, TipStatesModel tipStatesModel, boolean useAmbiguities, PartialsRescalingScheme scalingScheme, boolean delayRescalingUntilUnderflow) throws XMLParseException {
    if (tipStatesModel != null) {
        throw new XMLParseException("Tip State Error models are not supported yet with TreeDataLikelihood");
    }
    List<Taxon> treeTaxa = treeModel.asList();
    List<Taxon> patternTaxa = patternLists.get(0).asList();
    if (!patternTaxa.containsAll(treeTaxa)) {
        throw new XMLParseException("TreeModel contains more taxa than the partition pattern list.");
    }
    if (!treeTaxa.containsAll(patternTaxa)) {
        throw new XMLParseException("TreeModel contains fewer taxa than the partition pattern list.");
    }
    //        DataLikelihoodDelegate dataLikelihoodDelegate = new BeagleDataLikelihoodDelegate(
    //                treeModel,
    //                patternLists.get(0),
    //                branchModel,
    //                siteRateModel,
    //                useAmbiguities,
    //                scalingScheme,
    //                delayRescalingUntilUnderflow);
    boolean useBeagle3 = Boolean.parseBoolean(System.getProperty("USE_BEAGLE3", "true"));
    boolean useJava = Boolean.parseBoolean(System.getProperty("java.only", "false"));
    if (useBeagle3 && MultiPartitionDataLikelihoodDelegate.IS_MULTI_PARTITION_COMPATIBLE() && !useJava) {
        DataLikelihoodDelegate dataLikelihoodDelegate = new MultiPartitionDataLikelihoodDelegate(treeModel, patternLists, branchModels, siteRateModels, useAmbiguities, scalingScheme, delayRescalingUntilUnderflow);
        return new TreeDataLikelihood(dataLikelihoodDelegate, treeModel, branchRateModel);
    } else {
        // The multipartition data likelihood isn't available so make a set of single partition data likelihoods
        List<Likelihood> treeDataLikelihoods = new ArrayList<Likelihood>();
        for (int i = 0; i < patternLists.size(); i++) {
            DataLikelihoodDelegate dataLikelihoodDelegate = new BeagleDataLikelihoodDelegate(treeModel, patternLists.get(i), branchModels.get(i), siteRateModels.get(i), useAmbiguities, scalingScheme, delayRescalingUntilUnderflow);
            treeDataLikelihoods.add(new TreeDataLikelihood(dataLikelihoodDelegate, treeModel, branchRateModel));
        }
        if (treeDataLikelihoods.size() == 1) {
            return treeDataLikelihoods.get(0);
        }
        return new CompoundLikelihood(treeDataLikelihoods);
    }
}

Example 30 with Taxon

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

the class MonophylyStatisticParser method parseTaxonListOrTaxa.

public static TaxonList parseTaxonListOrTaxa(XMLObject cxo) {
    TaxonList taxa = (TaxonList) cxo.getChild(TaxonList.class);
    if (taxa == null) {
        Taxa taxa1 = new Taxa();
        for (int i = 0; i < cxo.getChildCount(); i++) {
            Object ccxo = cxo.getChild(i);
            if (ccxo instanceof Taxon) {
                taxa1.addTaxon((Taxon) ccxo);
            }
        }
        taxa = taxa1;
    }
    return taxa;
}