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

Example 11 with Taxon

use of beast.evolution.alignment.Taxon in project beast2 by CompEvol.

the class MRCAPriorInputEditor method getTaxonCandidates.

Set<Taxon> getTaxonCandidates(MRCAPrior prior) {
    Set<Taxon> candidates = new HashSet<>();
    Tree tree = prior.treeInput.get();
    String[] taxa = null;
    if (tree.m_taxonset.get() != null) {
        try {
            TaxonSet set = tree.m_taxonset.get();
            set.initAndValidate();
            taxa = set.asStringList().toArray(new String[0]);
        } catch (Exception e) {
            taxa = prior.treeInput.get().getTaxaNames();
        }
    } else {
        taxa = prior.treeInput.get().getTaxaNames();
    }
    for (String taxon : taxa) {
        candidates.add(doc.getTaxon(taxon));
    }
    return candidates;
}

Example 12 with Taxon

use of beast.evolution.alignment.Taxon in project beast2 by CompEvol.

the class TaxonSetDialog method processEntry.

private void processEntry() {
    String filter = ".*" + filterEntry.getText() + ".*";
    listModel1.clear();
    for (Taxon taxon : _candidates) {
        if (taxon.getID().matches(filter)) {
            listModel1.addElement(taxon);
        }
    }
    for (int i = 0; i < listModel2.size(); i++) {
        listModel1.removeElement(listModel2.get(i));
    }
}

Example 13 with Taxon

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

the class TestBase method getTaxonSet.

public TaxonSet getTaxonSet(int nTaxa) {
    List<Taxon> taxonList = new ArrayList<>();
    for (int i = 0; i < nTaxa; i++) {
        try {
            taxonList.add(new Taxon("t" + i));
        } catch (Exception e) {
            System.out.println("Error creating test taxon.");
            System.exit(1);
        }
    }
    TaxonSet taxonSet = null;
    try {
        taxonSet = new TaxonSet(taxonList);
    } catch (Exception e) {
        System.out.println("Error creating test taxon set.");
        System.exit(1);
    }
    return taxonSet;
}

Example 14 with Taxon

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

the class AddRemoveConversion method main.

public static void main(String[] args) throws Exception {
    ConversionGraph acg = new ConversionGraph();
    ConstantPopulation popFunc = new ConstantPopulation();
    AddRemoveConversion operator = new AddRemoveConversion();
    operator.initByName("weight", 1.0, "acg", acg, "populationModel", popFunc, "rho", new RealParameter(Double.toString(1.0 / 10000.0)), "delta", new RealParameter("50.0"));
    popFunc.initByName("popSize", new RealParameter("1.0"));
    TaxonSet taxonSet = new TaxonSet();
    taxonSet.taxonsetInput.setValue(new Taxon("t1"), taxonSet);
    taxonSet.taxonsetInput.setValue(new Taxon("t2"), taxonSet);
    Locus locus = new Locus("locus", 10000);
    try (PrintStream ps = new PrintStream("out.txt")) {
        for (int i = 0; i < 100000; i++) {
            acg.initByName("locus", locus, "taxonset", taxonSet, "fromString", "(0:1.0,1:1.0)2:0.0;");
            operator.drawNewConversion();
            ps.println(acg.getConversions(locus).get(0).getStartSite() + " " + acg.getConversions(locus).get(0).getEndSite());
        }
    }
}

Example 15 with Taxon

use of beast.evolution.alignment.Taxon in project beast2 by CompEvol.

the class FilteredAlignmentTest method testWeightedSitesReordered.

public void testWeightedSitesReordered() throws Exception {
    // reorder taxa
    Alignment data = getAlignmentNoTInHuman();
    data.setID("data");
    List<Taxon> taxa = new ArrayList<>();
    taxa.add(new Taxon("1chimp"));
    taxa.add(new Taxon("0human"));
    TaxonSet set = new TaxonSet(taxa);
    data.taxonSetInput.setValue(set, data);
    data.siteWeightsInput.setValue("11232, 2, 3, 4 ,1123,2,3,4,112,2,3,4,11,2,3,	4 ", data);
    data.initAndValidate();
    String weights = Arrays.toString(data.getWeights());
    System.out.println(weights + "\n0human\t" + alignmentToString(data, data.getTaxonIndex("0human")) + "\n1chimp\t" + alignmentToString(data, data.getTaxonIndex("1chimp")));
    assertEquals("[11243, 1123, 112, 4, 2, 2, 6, 3, 3, 8, 4, 4]", weights);
}