/* * 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"; } }