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

Example 81 with Taxon

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

the class TreeSummary method buildConsensusTree.

private Tree buildConsensusTree(CladeSystem cladeSystem) {
    List<BitSet> bitSets = new ArrayList<BitSet>(cladeSystem.getCladeMap().keySet());
    Collections.sort(bitSets, new Comparator<BitSet>() {

        @Override
        public int compare(BitSet b1, BitSet b2) {
            return b1.cardinality() - b2.cardinality();
        }
    });
    SimpleNode root = null;
    for (int i = 0; i < bitSets.size(); i++) {
        BitSet key1 = bitSets.get(i);
        CladeSystem.Clade clade1 = cladeSystem.getCladeMap().get(key1);
        if (key1.cardinality() == 1) {
            Taxon taxon = cladeSystem.getTaxon(key1.nextSetBit(0));
            clade1.node = new SimpleNode();
            clade1.node.setTaxon(taxon);
            clade1.node.setAttribute("clade", clade1);
        }
        if (clade1.credibility >= posteriorLimit) {
            for (int j = i + 1; j < bitSets.size(); j++) {
                BitSet key2 = bitSets.get(j);
                if (isSubSet(key1, key2) && cladeSystem.getCladeCredibility(key2) >= posteriorLimit) {
                    // the clades are ordered by size so this is the smallest clade for which
                    // clade1 is a subset and has high credibility.
                    CladeSystem.Clade clade2 = cladeSystem.getCladeMap().get(key2);
                    if (clade2.node == null) {
                        clade2.node = new SimpleNode();
                    }
                    if (clade1.node == null) {
                        throw new RuntimeException("null node");
                    }
                    clade2.node.addChild(clade1.node);
                    clade2.node.setAttribute("credibility", clade2.credibility);
                    clade2.node.setAttribute("clade", clade2);
                    if (key2.cardinality() == cladeSystem.taxonList.getTaxonCount()) {
                        root = clade2.node;
                    }
                    break;
                }
            }
        }
    }
    SimpleTree tree = new SimpleTree(root);
    return tree;
}

Example 82 with Taxon

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

the class STARBEASTGenerator method writeMultiSpecies.

/**
     * write tag <sp>
     *
     * @param taxonList TaxonList
     * @param writer    XMLWriter
     */
private void writeMultiSpecies(TaxonList taxonList, XMLWriter writer) {
    List<String> species = options.starBEASTOptions.getSpeciesList();
    String sp;
    // used in private String getIndicatorsParaValue()
    numOfSpecies = species.size();
    for (String eachSp : species) {
        writer.writeOpenTag(SpeciesBindingsSPinfoParser.SP, new Attribute[] { new Attribute.Default<String>(XMLParser.ID, eachSp) });
        for (int i = 0; i < taxonList.getTaxonCount(); i++) {
            Taxon taxon = null;
            try {
                taxon = taxonList.getTaxon(i);
                sp = taxon.getAttribute(TraitData.TRAIT_SPECIES).toString();
            } catch (Exception e) {
                throw new IllegalArgumentException("Cannot get value from Taxon " + taxon.getId());
            }
            if (sp.equals(eachSp)) {
                writer.writeIDref(TaxonParser.TAXON, taxon.getId());
            }
        }
        writer.writeCloseTag(SpeciesBindingsSPinfoParser.SP);
    }
    writeGeneTrees(writer);
}

Example 83 with Taxon

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

the class TraitData method getStatesListOfTrait.

public static Set<String> getStatesListOfTrait(Taxa taxonList, String traitName) {
    Set<String> states = new TreeSet<String>();
    if (taxonList == null) {
        throw new IllegalArgumentException("taxon list is null");
    }
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        Taxon taxon = taxonList.getTaxon(i);
        String attr = (String) taxon.getAttribute(traitName);
        // ? is used to denote missing data so is not a state...
        if (attr != null && !attr.equals("?")) {
            states.add(attr);
        }
    }
    return states;
}

Example 84 with Taxon

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

the class TraitData method getEmptyStateIndex.

public static int getEmptyStateIndex(Taxa taxonList, String traitName) {
    if (taxonList == null) {
        throw new IllegalArgumentException("taxon list is null");
    }
    for (int i = 0; i < taxonList.getTaxonCount(); i++) {
        Taxon taxon = taxonList.getTaxon(i);
        String attr = (String) taxon.getAttribute(traitName);
        // ? is used to denote missing data so is not a state...
        if (attr == null || attr.equals("?")) {
            return i;
        }
    }
    return -1;
}

Example 85 with Taxon

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

the class DateGuesser method guessDates.

public void guessDates(TaxonList taxonList) {
    // To avoid duplicating code, add all the taxa into a list and
    // pass it to guessDates(List<Taxon> taxonList)
    List<Taxon> taxa = new ArrayList<Taxon>();
    for (Taxon taxon : taxonList) {
        taxa.add(taxon);
    }
    guessDates(taxa);
}