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

Example 1 with Taxon

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

the class BeautiDoc method getTaxon.

/**
 * create Taxon with given name, reuse if a taxon
 *  with this name already exists
 */
public Taxon getTaxon(String taxaName) {
    if (taxaset.keySet().contains(taxaName)) {
        return taxaset.get(taxaName);
    } else {
        try {
            Taxon taxon = new Taxon(taxaName);
            registerPlugin(taxon);
            return taxon;
        } catch (Exception e) {
            e.printStackTrace();
        }
    }
    return null;
}

Example 2 with Taxon

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

the class NodeReheight method initAndValidate.

@Override
public void initAndValidate() {
    /**
     * maps gene taxa names to species number *
     */
    final Map<String, Integer> taxonMap = new HashMap<>();
    final List<Taxon> list = taxonSetInput.get().taxonsetInput.get();
    if (list.size() <= 1) {
        Log.err.println("NodeReheight operator requires at least 2 taxa while the taxon set (id=" + taxonSetInput.get().getID() + ") has only " + list.size() + " taxa. " + "If the XML file was set up in BEAUti, this probably means a taxon assignment needs to be set up in the taxonset panel.");
        // assume we are in BEAUti, back off for now
        return;
    }
    for (int i = 0; i < list.size(); i++) {
        final Taxon taxa = list.get(i);
        // cast should be ok if taxon-set is the set for the species tree
        final TaxonSet set = (TaxonSet) taxa;
        for (final Taxon taxon : set.taxonsetInput.get()) {
            taxonMap.put(taxon.getID(), i);
        }
    }
    /**
     * build the taxon map for each gene tree *
     */
    m_taxonMap = new ArrayList<>();
    for (final Tree tree : geneTreesInput.get()) {
        final Map<Integer, Integer> map = new HashMap<>();
        setupTaxaMap(tree.getRoot(), map, taxonMap);
        m_taxonMap.add(map);
    }
    nrOfGeneTrees = geneTreesInput.get().size();
    nrOfSpecies = treeInput.get().getLeafNodeCount();
}

Example 3 with Taxon

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

the class MRCAPriorTest method testMRCATimePrior.

@Test
public void testMRCATimePrior() throws Exception {
    Alignment data = BEASTTestCase.getAlignment();
    TreeParser tree = new TreeParser();
    tree.initByName("taxa", data, "newick", "((human:0.024003,(chimp:0.010772,bonobo:0.010772):0.013231):0.012035," + "(gorilla:0.024003,(orangutan:0.010772,siamang:0.010772):0.013231):0.012035);", "IsLabelledNewick", true);
    Taxon human = new Taxon();
    human.setID("human");
    Taxon bonobo = new Taxon();
    bonobo.setID("bonobo");
    Taxon chimp = new Taxon();
    chimp.setID("chimp");
    Taxon gorilla = new Taxon();
    gorilla.setID("gorilla");
    Taxon orangutan = new Taxon();
    orangutan.setID("orangutan");
    Taxon siamang = new Taxon();
    siamang.setID("siamang");
    MRCAPrior prior = new MRCAPrior();
    TaxonSet set = new TaxonSet();
    set.initByName("taxon", human, "taxon", bonobo, "taxon", chimp);
    Exponential exp = new Exponential();
    /* get distribution for set (human, bonobo, chimp) */
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true, "distr", exp);
    double logP = prior.calculateLogP();
    assertEquals(-0.024003, logP, BEASTTestCase.PRECISION);
    /* get distribution for set (human, chimp), do not require the set to by monophyletic */
    set = new TaxonSet();
    set.initByName("taxon", human, "taxon", chimp);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", false);
    logP = prior.calculateLogP();
    assertEquals(-0.024003, logP, BEASTTestCase.PRECISION);
    /* get distribution for set (human, chimp), DO require the set to by monophyletic */
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(Double.NEGATIVE_INFINITY, logP, 0);
    /* get distribution for set (human, gorilla) = root, not monophyletic */
    set = new TaxonSet();
    set.initByName("taxon", human, "taxon", gorilla);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", false);
    logP = prior.calculateLogP();
    assertEquals(-0.024003 - 0.012035, logP, BEASTTestCase.PRECISION);
}

Example 4 with Taxon

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

the class MRCAPriorTest method testSingleMonophyleticConstraint.

@Test
public void testSingleMonophyleticConstraint() throws Exception {
    Alignment data = BEASTTestCase.getAlignment();
    TreeParser tree = new TreeParser();
    tree.initByName("taxa", data, "newick", "((human:0.024003,(chimp:0.010772,bonobo:0.010772):0.013231):0.012035," + "(gorilla:0.024003,(orangutan:0.010772,siamang:0.010772):0.013231):0.012035);", "IsLabelledNewick", true);
    Taxon human = new Taxon();
    human.setID("human");
    Taxon bonobo = new Taxon();
    bonobo.setID("bonobo");
    Taxon chimp = new Taxon();
    chimp.setID("chimp");
    Taxon gorilla = new Taxon();
    gorilla.setID("gorilla");
    Taxon orangutan = new Taxon();
    orangutan.setID("orangutan");
    Taxon siamang = new Taxon();
    siamang.setID("siamang");
    MRCAPrior prior = new MRCAPrior();
    /* check (human, bonobo, chimp) is monophyletic **/
    TaxonSet set = new TaxonSet();
    set.initByName("taxon", human, "taxon", bonobo, "taxon", chimp);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    double logP = prior.calculateLogP();
    assertEquals(logP, 0, 0);
    /* check (gorilla, siamang) is NOT monophyletic **/
    set = new TaxonSet();
    set.initByName("taxon", gorilla, "taxon", siamang);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(logP, Double.NEGATIVE_INFINITY, 0);
    /* check (gorilla, orangutan, siamang) is monophyletic **/
    set = new TaxonSet();
    set.initByName("taxon", gorilla, "taxon", orangutan, "taxon", siamang);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(logP, 0, 0);
    /* check (human, gorilla) is NOT monophyletic **/
    set = new TaxonSet();
    set.initByName("taxon", human, "taxon", gorilla);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true);
    logP = prior.calculateLogP();
    assertEquals(logP, Double.NEGATIVE_INFINITY, 0);
    set.setID("test");
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    PrintStream ps = new PrintStream(baos);
    prior.init(ps);
    String log = new String(baos.toByteArray(), StandardCharsets.UTF_8);
    assertEquals(log, "mrcatime(test)\t");
    baos = new ByteArrayOutputStream();
    ps = new PrintStream(baos);
    prior.initByName("tree", tree, "taxonset", set, "monophyletic", true, "useOriginate", true);
    prior.init(ps);
    log = new String(baos.toByteArray(), StandardCharsets.UTF_8);
    assertEquals(log, "mrcatime(test.originate)\t");
}

Example 5 with Taxon

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

the class TaxonSetInputEditor method guessTaxonSets.

/**
 * guesses taxon sets based on pattern in regExp based on the taxa in
 * m_rawData
 */
public int guessTaxonSets(String regexp, int minSize) {
    m_taxonset.clear();
    HashMap<String, TaxonSet> map = new HashMap<>();
    Pattern m_pattern = Pattern.compile(regexp);
    Set<Taxon> taxa = new HashSet<>();
    Set<String> taxonIDs = new HashSet<>();
    for (Alignment alignment : getDoc().alignments) {
        for (String id : alignment.getTaxaNames()) {
            if (!taxonIDs.contains(id)) {
                Taxon taxon = getDoc().getTaxon(id);
                taxa.add(taxon);
                taxonIDs.add(id);
            }
        }
        for (Sequence sequence : alignment.sequenceInput.get()) {
            String id = sequence.taxonInput.get();
            if (!taxonIDs.contains(id)) {
                Taxon taxon = getDoc().getTaxon(sequence.taxonInput.get());
                // ensure sequence and taxon do not get same ID
                if (sequence.getID().equals(sequence.taxonInput.get())) {
                    sequence.setID("_" + sequence.getID());
                }
                taxa.add(taxon);
                taxonIDs.add(id);
            }
        }
    }
    List<String> unknowns = new ArrayList<>();
    for (Taxon taxon : taxa) {
        if (!(taxon instanceof TaxonSet)) {
            Matcher matcher = m_pattern.matcher(taxon.getID());
            String match;
            if (matcher.find()) {
                match = matcher.group(1);
            } else {
                match = "UNKNOWN";
                unknowns.add(taxon.getID());
            }
            try {
                if (map.containsKey(match)) {
                    TaxonSet set = map.get(match);
                    set.taxonsetInput.setValue(taxon, set);
                } else {
                    TaxonSet set = newTaxonSet(match);
                    set.taxonsetInput.setValue(taxon, set);
                    map.put(match, set);
                }
            } catch (Exception ex) {
                ex.printStackTrace();
            }
        }
    }
    if (unknowns.size() > 0) {
        showMisMatchMessage(unknowns);
    }
    // add taxon sets
    int ignored = 0;
    for (TaxonSet set : map.values()) {
        if (set.taxonsetInput.get().size() > minSize) {
            m_taxonset.add(set);
        } else {
            ignored += set.taxonsetInput.get().size();
        }
    }
    return ignored;
}