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

Example 16 with TaxonList

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

the class MetagenomeDataParser method parseXMLObject.

@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    TaxonList taxa = null;
    taxa = (TaxonList) xo.getChild(TaxonList.class);
    if (taxa == null)
        taxa = (Tree) xo.getChild(Tree.class);
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    LinkageConstraints lc = (LinkageConstraints) xo.getChild(LinkageConstraints.class);
    boolean fixedReferenceTree = false;
    if (xo.hasAttribute("fixedReferenceTree")) {
        fixedReferenceTree = xo.getBooleanAttribute("fixedReferenceTree");
    }
    MetagenomeData md = new MetagenomeData(taxa, alignment, lc, fixedReferenceTree);
    return md;
}

Example 17 with TaxonList

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

the class HiddenLinkageLikelihood method getLogLikelihood.

public double getLogLikelihood() {
    double logL = 0;
    // first check whether the reads are linked together
    // according to the linkage constraints provided as data in the
    // input file
    ArrayList<LinkedGroup> linkedGroups = hlm.getData().getConstraints();
    for (LinkedGroup lg : linkedGroups) {
        TaxonList tl = lg.getLinkedReads();
        int found = 0;
        for (int l = 0; l < hlm.getLinkageGroupCount(); l++) {
            Set<Taxon> group = hlm.getGroup(l);
            for (int i = 0; i < tl.getTaxonCount(); i++) {
                if (group.contains(tl.getTaxon(i)))
                    found++;
            }
            if (found == tl.getTaxonCount()) {
                logL += Math.log(lg.getLinkageProbability());
                break;
            } else if (found > 0) {
                logL += Math.log(1.0 - lg.getLinkageProbability());
                break;
            }
        }
    }
    // reference tree topology
    if (hlm.getData().getFixedReferenceTree()) {
        // not yet implemented.
        logL += Double.NEGATIVE_INFINITY;
    }
    return logL;
}

Example 18 with TaxonList

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

the class ParsimonyStatisticParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String name = xo.getAttribute(Statistic.NAME, xo.getId());
    Tree tree = (Tree) xo.getChild(Tree.class);
    XMLObject cxo = xo.getChild(STATE);
    TaxonList taxa = (TaxonList) cxo.getChild(TaxonList.class);
    try {
        return new ParsimonyStatistic(name, tree, taxa);
    } catch (TreeUtils.MissingTaxonException mte) {
        throw new XMLParseException("Taxon, " + mte + ", in " + getParserName() + "was not found in the tree.");
    }
}

Example 19 with TaxonList

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

the class LineageSitePatternsParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Alignment alignment = (Alignment) xo.getChild(Alignment.class);
    TaxonList taxa = null;
    int from = 0;
    int to = -1;
    int every = xo.getAttribute(EVERY, 1);
    boolean strip = xo.getAttribute(STRIP, true);
    boolean unique = xo.getAttribute(UNIQUE, true);
    if (xo.hasAttribute(FROM)) {
        from = xo.getIntegerAttribute(FROM) - 1;
        if (from < 0)
            throw new XMLParseException("illegal 'from' attribute in patterns element");
    }
    if (xo.hasAttribute(TO)) {
        to = xo.getIntegerAttribute(TO) - 1;
        if (to < 0 || to < from)
            throw new XMLParseException("illegal 'to' attribute in patterns element");
    }
    if (every <= 0)
        throw new XMLParseException("illegal 'every' attribute in patterns element");
    if (xo.hasChildNamed(TAXON_LIST)) {
        taxa = (TaxonList) xo.getElementFirstChild(TAXON_LIST);
    }
    if (from > alignment.getSiteCount())
        throw new XMLParseException("illegal 'from' attribute in patterns element");
    if (to > alignment.getSiteCount())
        throw new XMLParseException("illegal 'to' attribute in patterns element");
    LineageSitePatterns patterns = new LineageSitePatterns(alignment, taxa, from, to, every, strip, unique);
    int f = from + 1;
    // fixed a *display* error by adding + 1 for consistency with f = from + 1
    int t = to + 1;
    if (to == -1)
        t = alignment.getSiteCount();
    if (xo.hasAttribute(XMLParser.ID)) {
        final Logger logger = Logger.getLogger("dr.evoxml");
        logger.info("Site patterns '" + xo.getId() + "' created from positions " + Integer.toString(f) + "-" + Integer.toString(t) + " of alignment '" + alignment.getId() + "'");
        if (every > 1) {
            logger.info("  only using every " + every + " site");
        }
        logger.info("  pattern count = " + patterns.getPatternCount());
    }
    return patterns;
}

Example 20 with TaxonList

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

the class TaxonSetPanel method setCurrentTaxonSet.

protected void setCurrentTaxonSet(Taxa taxonSet) {
    this.currentTaxonSet = taxonSet;
    includedTaxa.clear();
    excludedTaxa.clear();
    if (currentTaxonSet != null) {
        for (int i = 0; i < taxonSet.getTaxonCount(); i++) {
            includedTaxa.add(taxonSet.getTaxon(i));
        }
        Collections.sort(includedTaxa);
        // get taxa associated to each tree
        PartitionTreeModel treeModel = options.taxonSetsTreeModel.get(currentTaxonSet);
        TaxonList alignment = options.getDataPartitions(treeModel).get(0).getTaxonList();
        Taxa taxa = new Taxa(alignment);
        for (int i = 0; i < taxa.getTaxonCount(); i++) {
            excludedTaxa.add(taxa.getTaxon(i));
        }
        excludedTaxa.removeAll(includedTaxa);
        Collections.sort(excludedTaxa);
    }
    setTaxonSetTitle();
    setupTaxonSetsComboBoxes();
    includedTaxaTableModel.fireTableDataChanged();
    excludedTaxaTableModel.fireTableDataChanged();
}