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

Example 21 with Taxon

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

the class TaxonSetDialog method createCancelOKButtons.

// createTaxonSelector
Component createCancelOKButtons() {
    Box cancelOkBox = Box.createHorizontalBox();
    cancelOkBox.setBorder(new EtchedBorder());
    JButton okButton = new JButton("Ok");
    okButton.setName("OK");
    okButton.addActionListener(e -> {
        taxonSet.setID(id);
        List<Taxon> taxa = taxonSet.taxonsetInput.get();
        while (taxa.size() > 0) {
            taxa.remove(0);
        }
        for (int i = 0; i < listModel2.size(); i++) {
            taxa.add(listModel2.get(i));
        }
        isOK = true;
        dispose();
    });
    JButton cancelButton = new JButton("Cancel");
    cancelButton.setName("Cancel");
    cancelButton.addActionListener(e -> {
        dispose();
    });
    cancelOkBox.add(Box.createHorizontalGlue());
    cancelOkBox.add(okButton);
    cancelOkBox.add(Box.createHorizontalGlue());
    cancelOkBox.add(cancelButton);
    cancelOkBox.add(Box.createHorizontalGlue());
    return cancelOkBox;
}

Example 22 with Taxon

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

the class TaxonSetInputEditor method guess.

private void guess() {
    GuessPatternDialog dlg = new GuessPatternDialog(this, m_sPattern);
    switch(dlg.showDialog("Guess taxon sets")) {
        case canceled:
            return;
        case pattern:
            String pattern = dlg.getPattern();
            try {
                guessTaxonSets(pattern, 0);
                m_sPattern = pattern;
                break;
            } catch (Exception e) {
                e.printStackTrace();
            }
        case trait:
            String trait = dlg.getTrait();
            parseTrait(trait);
            break;
    }
    m_lineageset.clear();
    for (Taxon taxonset2 : m_taxonset) {
        for (Taxon taxon : ((TaxonSet) taxonset2).taxonsetInput.get()) {
            m_lineageset.add(taxon);
            m_taxonMap.put(taxon.getID(), taxonset2.getID());
        }
    }
    taxonSetToModel();
    modelToTaxonset();
}

Example 23 with Taxon

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

the class PriorListInputEditor 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 24 with Taxon

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

the class GeneTreeForSpeciesTreeDistribution method getSetID.

/**
 * @param lineageID
 * @return species ID to which the lineage ID belongs according to the TaxonSets
 */
String getSetID(final String lineageID) {
    final TaxonSet taxonSuperset = speciesTreePriorInput.get().taxonSetInput.get();
    final List<Taxon> taxonSets = taxonSuperset.taxonsetInput.get();
    for (final Taxon taxonSet : taxonSets) {
        final List<Taxon> taxa = ((TaxonSet) taxonSet).taxonsetInput.get();
        for (final Taxon aTaxa : taxa) {
            if (aTaxa.getID().equals(lineageID)) {
                return taxonSet.getID();
            }
        }
    }
    return null;
}

Example 25 with Taxon

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

the class JSONTest method testAnnotatedConstructor.

@Test
public void testAnnotatedConstructor() throws Exception {
    List<Taxon> taxa = new ArrayList<>();
    taxa.add(new Taxon("first one"));
    taxa.add(new Taxon("second one"));
    AnnotatedRunnableTestClass t = new AnnotatedRunnableTestClass(3, taxa);
    JSONProducer producer = new JSONProducer();
    String json = producer.toJSON(t);
    assertEquals(3, (int) t.getParam1());
    FileWriter outfile = new FileWriter(new File("/tmp/JSONTest.json"));
    outfile.write(json);
    outfile.close();
    JSONParser parser = new JSONParser();
    BEASTInterface b = parser.parseFile(new File("/tmp/JSONTest.json"));
    assertEquals(3, (int) ((AnnotatedRunnableTestClass) b).getParam1());
    assertEquals(2, ((AnnotatedRunnableTestClass) b).getTaxon().size());
    // test that default value for param1 comes through
    String json2 = "{version: \"2.5\",\n" + "namespace: \"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\",\n" + "\n" + "beast: [\n" + "\n" + "\n" + "        {id: \"JSONTest\",\n" + "         spec: \"test.beast.util.AnnotatedRunnableTestClass\",\n" + "         taxon: [\n" + "                 {id: \"first one\" },\n" + "                 {id: \"second one\" }\n" + "          ]\n" + "        }\n" + "]\n" + "}";
    outfile = new FileWriter(new File("/tmp/JSONTest2.json"));
    outfile.write(json2);
    outfile.close();
    parser = new JSONParser();
    b = parser.parseFile(new File("/tmp/JSONTest2.json"));
    assertEquals(10, (int) ((AnnotatedRunnableTestClass) b).getParam1());
    assertEquals(2, ((AnnotatedRunnableTestClass) b).getTaxon().size());
    // test that array of doubles comes through in second constructor
    String json3 = "{version: \"2.5\",\n" + "namespace: \"beast.core:beast.evolution.alignment:beast.evolution.tree.coalescent:beast.core.util:beast.evolution.nuc:beast.evolution.operators:beast.evolution.sitemodel:beast.evolution.substitutionmodel:beast.evolution.likelihood\",\n" + "\n" + "beast: [\n" + "\n" + "\n" + "        {id: \"JSONTest\",\n" + "         spec: \"test.beast.util.AnnotatedRunnableTestClass\",\n" + "         array: [1.0, 2.0, 3.0]\n" + "        }\n" + "]\n" + "}";
    outfile = new FileWriter(new File("/tmp/JSONTest3.json"));
    outfile.write(json3);
    outfile.close();
    parser = new JSONParser();
    b = parser.parseFile(new File("/tmp/JSONTest3.json"));
    assertEquals(3, ((AnnotatedRunnableTestClass) b).getArray().size());
}