/*
* TipDateSamplingComponentGenerator.java
*
* Copyright (c) 2002-2015 Alexei Drummond, Andrew Rambaut and Marc Suchard
*
* This file is part of BEAST.
* See the NOTICE file distributed with this work for additional
* information regarding copyright ownership and licensing.
*
* BEAST is free software; you can redistribute it and/or modify
* it under the terms of the GNU Lesser General Public License as
* published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* BEAST is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU Lesser General Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with BEAST; if not, write to the
* Free Software Foundation, Inc., 51 Franklin St, Fifth Floor,
* Boston, MA 02110-1301 USA
*/
package dr.app.beauti.components.tipdatesampling;
import dr.app.beauti.options.AbstractPartitionData;
import dr.app.beauti.options.PartitionTreeModel;
import dr.app.beauti.util.XMLWriter;
import dr.app.beauti.types.TipDateSamplingType;
import dr.app.beauti.generator.BaseComponentGenerator;
import dr.app.beauti.options.BeautiOptions;
import dr.evolution.util.Date;
import dr.evolution.util.Taxa;
import dr.evolution.util.Taxon;
import dr.evolution.util.TaxonList;
import dr.evoxml.TaxonParser;
import dr.inference.model.ParameterParser;
import dr.util.Attribute;
import dr.xml.XMLParser;
import java.util.HashSet;
import java.util.Set;
/**
* @author Andrew Rambaut
* @version $Id$
*/
public class TipDateSamplingComponentGenerator extends BaseComponentGenerator {
public TipDateSamplingComponentGenerator(final BeautiOptions options) {
super(options);
}
public boolean usesInsertionPoint(final InsertionPoint point) {
TipDateSamplingComponentOptions comp = (TipDateSamplingComponentOptions)options.getComponentOptions(TipDateSamplingComponentOptions.class);
if (comp.tipDateSamplingType == TipDateSamplingType.NO_SAMPLING) {
return false;
}
switch (point) {
case IN_TREE_MODEL:
case IN_FILE_LOG_PARAMETERS:
return true;
case AFTER_TREE_MODEL:
return options.getPartitionTreeModels().size() > 1 || comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_JOINT;
case IN_MCMC_PRIOR:
return comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_JOINT;
default:
return false;
}
}
protected void generate(final InsertionPoint point, final Object item, final String prefix, final XMLWriter writer) {
TipDateSamplingComponentOptions comp = (TipDateSamplingComponentOptions)options.getComponentOptions(TipDateSamplingComponentOptions.class);
TaxonList taxa = comp.getTaxonSet();
switch (point) {
case IN_TREE_MODEL: {
writeLeafHeightParameters(writer, (PartitionTreeModel)item, taxa);
} break;
case AFTER_TREE_MODEL:
if (options.getPartitionTreeModels().size() > 1) {
// we have multiple treeModels with some or all the same taxa - create a JointParameter for each...
writeJointParameters(writer, taxa);
}
if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_JOINT) {
writer.writeOpenTag("compoundParameter",
new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, "treeModel.tipDates"),
}
);
for (int i = 0; i < taxa.getTaxonCount(); i++) {
Taxon taxon = taxa.getTaxon(i);
writer.writeIDref(ParameterParser.PARAMETER, "age(" + taxon.getId() + ")");
}
writer.writeCloseTag("compoundParameter");
}
break;
case IN_MCMC_PRIOR:
if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_INDIVIDUALLY ||
comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_PRECISION) {
// nothing to do - individual parameter priors are written automatically
} else if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_JOINT) {
}
break;
case IN_FILE_LOG_PARAMETERS:
if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_INDIVIDUALLY ||
comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_PRECISION) {
for (int i = 0; i < taxa.getTaxonCount(); i++) {
Taxon taxon = taxa.getTaxon(i);
writer.writeIDref(ParameterParser.PARAMETER, "age(" + taxon.getId() + ")");
}
} else if (comp.tipDateSamplingType == TipDateSamplingType.SAMPLE_JOINT) {
writer.writeIDref(ParameterParser.PARAMETER, "treeModel.tipDates");
}
break;
default:
throw new IllegalArgumentException("This insertion point is not implemented for " + this.getClass().getName());
}
}
private void writeJointParameters(XMLWriter writer, TaxonList taxa) {
for (int i = 0; i < taxa.getTaxonCount(); i++) {
Taxon taxon = taxa.getTaxon(i);
Set<PartitionTreeModel> treeModels = new HashSet<PartitionTreeModel>();
for (PartitionTreeModel treeModel : options.getPartitionTreeModels()) {
for (AbstractPartitionData data : options.getDataPartitions(treeModel)) {
if (data.getTaxonList().asList().contains(taxon)) {
treeModels.add(treeModel);
}
}
}
// if we are sampling within precisions then only include this leaf if precision > 0
if (treeModels.size() > 0) {
writer.writeOpenTag("jointParameter",
new Attribute[]{
new Attribute.Default<String>(XMLParser.ID, "age(" + taxon.getId() + ")")
}
);
for (PartitionTreeModel treeModel : treeModels) {
writer.writeTag(ParameterParser.PARAMETER, new Attribute.Default<String>(XMLParser.IDREF, treeModel.getPrefix() + "age(" + taxon.getId() + ")"), true);
}
writer.writeCloseTag("jointParameter");
}
}
}
private void writeLeafHeightParameters(XMLWriter writer, PartitionTreeModel item, TaxonList taxa) {
// only include this taxon as a leaf height if it found in this partition.
PartitionTreeModel treeModel = (PartitionTreeModel)item;
Set<Taxon> taxonSet = new HashSet<Taxon>();
for (AbstractPartitionData data : options.getDataPartitions(treeModel)) {
if (data.getTaxonList() != null) {
for (Taxon taxon : data.getTaxonList()) {
taxonSet.add(taxon);
}
}
}
for (int i = 0; i < taxa.getTaxonCount(); i++) {
Taxon taxon = taxa.getTaxon(i);
if (taxonSet.contains(taxon)) {
// if we are sampling within precisions then only include this leaf if precision > 0
writer.writeOpenTag("leafHeight",
new Attribute[]{
new Attribute.Default<String>(TaxonParser.TAXON, taxon.getId()),
}
);
writer.writeTag(ParameterParser.PARAMETER, new Attribute.Default<String>(XMLParser.ID, treeModel.getPrefix() + "age(" + taxon.getId() + ")"), true);
writer.writeCloseTag("leafHeight");
}
}
}
protected String getCommentLabel() {
return "Tip date sampling";
}
}