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

Example 46 with Taxon

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

the class SingleTipObservationProcessParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    Parameter mu = (Parameter) xo.getElementFirstChild(AnyTipObservationProcessParser.DEATH_RATE);
    Parameter lam = (Parameter) xo.getElementFirstChild(AnyTipObservationProcessParser.IMMIGRATION_RATE);
    TreeModel treeModel = (TreeModel) xo.getChild(TreeModel.class);
    PatternList patterns = (PatternList) xo.getChild(PatternList.class);
    Taxon sourceTaxon = (Taxon) xo.getChild(Taxon.class);
    SiteModel siteModel = (SiteModel) xo.getChild(SiteModel.class);
    BranchRateModel branchRateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
    Logger.getLogger("dr.evomodel.MSSD").info("Creating SingleTipObservationProcess model. All traits are assumed extant in " + sourceTaxon.getId() + "Initial mu = " + mu.getParameterValue(0) + " initial lam = " + lam.getParameterValue(0));
    return new SingleTipObservationProcess(treeModel, patterns, siteModel, branchRateModel, mu, lam, sourceTaxon);
}

Example 47 with Taxon

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

the class AdvancedTreeLikelihood method addDeltaParameter.

private void addDeltaParameter(Parameter deltaParameter, TaxonList taxa) {
    this.deltaParameter = deltaParameter;
    this.deltaTips = new HashSet<Integer>();
    if (taxa != null) {
        boolean first = true;
        StringBuffer sb = new StringBuffer("Delta parameter added for tips: {");
        for (int i = 0; i < treeModel.getExternalNodeCount(); i++) {
            NodeRef node = treeModel.getExternalNode(i);
            Taxon taxon = treeModel.getNodeTaxon(node);
            if (taxa.getTaxonIndex(taxon) != -1) {
                if (!first) {
                    sb.append(", ");
                } else {
                    first = false;
                }
                sb.append(taxon.getId());
                deltaTips.add(node.getNumber());
            }
        }
        sb.append("}");
        Logger.getLogger("dr.evomodel").info(sb.toString());
    } else {
        Logger.getLogger("dr.evomodel").info("Delta parameter added for all tips.");
    }
    addVariable(deltaParameter);
}

Example 48 with Taxon

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

the class PopTreeModel method mergeSubtreePopulation.

protected void mergeSubtreePopulation(NodeRef parent) {
    /*
        merge the subtree below node into a new population
         */
    LinkedList<NodeRef> sequenceNodes;
    sequenceNodes = new LinkedList<NodeRef>();
    if (this.getNodeTaxon(parent) == null) {
        this.setNodeTaxon(parent, new Taxon("popNode" + populations.size()));
    }
    if (this.isExternal(parent)) {
    }
    //push(parent);
    sequenceNodes.addFirst(parent);
    while (true) {
        NodeRef currentNode = sequenceNodes.removeFirst();
        if (this.isExternal(currentNode)) {
            //push(currentNode);
            sequenceNodes.addFirst(currentNode);
            //this.setNodeAttribute(parent,"sequenceNodes",sequenceNodes);
            populations.put(parent, sequenceNodes);
            return;
        }
        int numChildren = this.getChildCount(currentNode);
        for (int i = 0; getChildCount(currentNode) > 0; ) {
            NodeRef child = this.getChild(currentNode, i);
            //push(child);
            sequenceNodes.addFirst(child);
            this.removeChild(currentNode, child);
        }
    }
}

Example 49 with Taxon

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

the class TaxonSetPanel method excludeSelectedTaxa.

private void excludeSelectedTaxa() {
    int[] rows = includedTaxaTable.getSelectedRows();
    List<Taxon> transfer = new ArrayList<Taxon>();
    for (int r : rows) {
        transfer.add(includedTaxa.get(r));
    }
    excludedTaxa.addAll(transfer);
    Collections.sort(excludedTaxa);
    includedTaxa.removeAll(excludedTaxa);
    includedTaxaTableModel.fireTableDataChanged();
    excludedTaxaTableModel.fireTableDataChanged();
    excludedTaxaTable.getSelectionModel().clearSelection();
    for (Taxon taxon : transfer) {
        int row = excludedTaxa.indexOf(taxon);
        excludedTaxaTable.getSelectionModel().addSelectionInterval(row, row);
    }
    taxonSetChanged();
}

Example 50 with Taxon

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

the class TaxonSetPanel method includeSelectedTaxa.

private void includeSelectedTaxa() {
    int[] rows = excludedTaxaTable.getSelectedRows();
    List<Taxon> transfer = new ArrayList<Taxon>();
    for (int r : rows) {
        transfer.add(excludedTaxa.get(r));
    }
    includedTaxa.addAll(transfer);
    Collections.sort(includedTaxa);
    excludedTaxa.removeAll(includedTaxa);
    includedTaxaTableModel.fireTableDataChanged();
    excludedTaxaTableModel.fireTableDataChanged();
    includedTaxaTable.getSelectionModel().clearSelection();
    for (Taxon taxon : transfer) {
        int row = includedTaxa.indexOf(taxon);
        includedTaxaTable.getSelectionModel().addSelectionInterval(row, row);
    }
    taxonSetChanged();
}