/*
* SplitBySiteTraitLogger.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.evomodel.treelikelihood;
import dr.evolution.tree.NodeRef;
import dr.evolution.tree.Tree;
import dr.evolution.tree.TreeTrait;
import dr.evolution.tree.TreeTraitProvider;
import dr.evomodel.tree.TreeModel;
import dr.oldevomodel.treelikelihood.AncestralStateTreeLikelihood;
import dr.util.Citable;
import dr.util.Citation;
import dr.util.CommonCitations;
import dr.xml.*;
import java.util.*;
import java.util.logging.Logger;
/**
* Takes a TreeTraitProvider that returns multiple-site traits and provides a new Trait for logging by site
*
* @author Marc A. Suchard
*/
public class SplitBySiteTraitLogger extends TreeTraitProvider.Helper implements Citable {
public static final String TRAIT_LOGGER = "splitTraitBySite";
public static final String TRAIT_NAME = "traitName";
public static final String SCALE = "scaleByBranchLength";
public SplitBySiteTraitLogger(final AncestralStateTraitProvider treeLikelihood, String traitName, boolean scale) throws XMLParseException {
TreeTrait trait = treeLikelihood.getTreeTrait(traitName);
if (trait == null) {
throw new XMLParseException("TreeTraitProvider does not provide trait named '" + traitName + ".");
}
TreeModel tree = treeLikelihood.getTreeModel();
int length;
Object obj = trait.getTrait(tree, tree.getNode(0));
boolean isDoubleArray = false;
boolean isIntegerArray = false;
if (obj instanceof double[]) {
length = ((double[]) obj).length;
isDoubleArray = true;
} else if (obj instanceof int[]) {
length = ((int[]) obj).length;
isIntegerArray = true;
} else {
throw new XMLParseException("Unknown trait type to split");
}
TreeTrait[] partitionedTraits = new TreeTrait[length];
if (isDoubleArray) {
for (int i = 0; i < length; i++) {
if (scale) {
partitionedTraits[i] = new TreeTrait.PickEntryDAndScale(trait, i);
} else {
partitionedTraits[i] = new TreeTrait.PickEntryD(trait, i);
}
}
} else if (isIntegerArray) {
for (int i = 0; i < length; ++i) {
if (traitName.compareTo(AncestralStateTreeLikelihood.STATES_KEY) == 0) {
partitionedTraits[i] = new TreeTrait.PickEntryI(trait, i) {
public String getTraitString(Tree tree, NodeRef node) {
int[] state = new int[1];
state[0] = getTrait(tree, node);
return treeLikelihood.formattedState(state);
}
};
} else {
partitionedTraits[i] = new TreeTrait.PickEntryI(trait, i);
}
}
}
addTraits(partitionedTraits);
Logger.getLogger("dr.app.beagle").info("\tConstructing a split logger with " + length + " partitions; please cite:\n"
+ Citable.Utils.getCitationString(this));
}
public static XMLObjectParser PARSER = new AbstractXMLObjectParser() {
public String getParserName() {
return TRAIT_LOGGER;
}
/**
* @return an object based on the XML element it was passed.
*/
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
String traitName = xo.getStringAttribute(TRAIT_NAME);
AncestralStateTraitProvider tree = (AncestralStateTraitProvider) xo.getChild(AncestralStateTraitProvider.class);
boolean scale = xo.getAttribute(SCALE, false);
return new SplitBySiteTraitLogger(tree, traitName, scale);
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
private final XMLSyntaxRule[] rules = {
new ElementRule(AncestralStateTraitProvider.class, "The tree which is to be logged"),
AttributeRule.newStringRule(TRAIT_NAME),
AttributeRule.newBooleanRule(SCALE, true),
};
public String getParserDescription() {
return null;
}
public String getExample() {
return null;
}
public Class getReturnType() {
return TreeTraitProvider.class;
}
};
@Override
public Citation.Category getCategory() {
return Citation.Category.COUNTING_PROCESSES;
}
@Override
public String getDescription() {
return "Split by site trait logger";
}
public List<Citation> getCitations() {
return Collections.singletonList(CommonCitations.LEMEY_2012_RENAISSANCE);
}
}