/*
* PartitionParser.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.beagle.tools.parsers;
import dr.evomodel.branchmodel.BranchModel;
import dr.evomodel.branchmodel.HomogeneousBranchModel;
import dr.evomodel.siteratemodel.GammaSiteRateModel;
import dr.evomodel.substmodel.FrequencyModel;
import dr.evomodel.substmodel.SubstitutionModel;
import dr.app.beagle.tools.Partition;
import dr.evolution.sequence.Sequence;
import dr.evomodel.branchratemodel.BranchRateModel;
import dr.evomodel.branchratemodel.DefaultBranchRateModel;
import dr.evomodel.tree.TreeModel;
import dr.xml.AbstractXMLObjectParser;
import dr.xml.AttributeRule;
import dr.xml.ElementRule;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
import dr.xml.XMLSyntaxRule;
import dr.xml.XORRule;
/**
* @author Filip Bielejec
* @version $Id$
*/
public class PartitionParser extends AbstractXMLObjectParser {
public static final String PARTITION = "partition";
public static final String FROM = "from";
public static final String TO = "to";
public static final String EVERY = "every";
@Override
public String getParserName() {
return PARTITION;
}
@Override
public String getParserDescription() {
return "Partition element";
}
@Override
public Class<Partition> getReturnType() {
return Partition.class;
}
@Override
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
int from = 0;
int to = -1;
int every = xo.getAttribute(EVERY, 1);
if (xo.hasAttribute(FROM)) {
from = xo.getIntegerAttribute(FROM) - 1;
if (from < 0) {
throw new XMLParseException(
"Illegal 'from' attribute in patterns element");
}
}// END: from check
if (xo.hasAttribute(TO)) {
to = xo.getIntegerAttribute(TO) - 1;
if (to < 0 || to < from) {
throw new XMLParseException(
"Illegal 'to' attribute in patterns element");
}
}// END: to check
if (every <= 0) {
throw new XMLParseException(
"Illegal 'every' attribute in patterns element");
}// END: every check
TreeModel tree = (TreeModel) xo.getChild(TreeModel.class);
GammaSiteRateModel siteModel = (GammaSiteRateModel) xo.getChild(GammaSiteRateModel.class);
FrequencyModel freqModel = (FrequencyModel) xo.getChild(FrequencyModel.class);
Sequence rootSequence = (Sequence) xo.getChild(Sequence.class);
BranchRateModel rateModel = (BranchRateModel) xo.getChild(BranchRateModel.class);
if (rateModel == null) {
rateModel = new DefaultBranchRateModel();
}
BranchModel branchModel = (BranchModel) xo.getChild(BranchModel.class);
if (branchModel == null) {
SubstitutionModel substitutionModel = (SubstitutionModel) xo.getChild(SubstitutionModel.class);
branchModel = new HomogeneousBranchModel(substitutionModel);
}
Partition partition = new Partition(tree, branchModel, siteModel, rateModel, freqModel, from, to, every);
if (rootSequence != null) {
partition.setRootSequence(rootSequence);
}// END: ancestralSequence check
return partition;
}//END: parseXMLObject
@Override
public XMLSyntaxRule[] getSyntaxRules() {
return new XMLSyntaxRule[] {
AttributeRule.newIntegerRule(FROM, true,
"The site position to start at, default is 1 (the first position)"), //
AttributeRule.newIntegerRule(TO, true,
"The site position to finish at, must be greater than <b>"
+ FROM
+ "</b>, default is number of sites"), //
AttributeRule.newIntegerRule(
EVERY,
true,
"Determines how many sites are selected. A value of 3 will select every third site starting from <b>"
+ FROM
+ "</b>, default is 1 (every site)"), //
new ElementRule(TreeModel.class), //
new XORRule(new ElementRule(BranchModel.class),
new ElementRule(SubstitutionModel.class), false), //
new ElementRule(GammaSiteRateModel.class), //
new ElementRule(BranchRateModel.class, true), //
new ElementRule(FrequencyModel.class), //
new ElementRule(Sequence.class, true) //
};
}// END: getSyntaxRules
}// END: class