/*
* LinkedGroupParser.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.evoxml;
import dr.evolution.LinkedGroup;
import dr.evolution.util.Taxa;
import dr.evolution.util.TaxonList;
import dr.xml.*;
/**
* @author Aaron Darling
*/
public class LinkedGroupParser extends AbstractXMLObjectParser {
public String getParserDescription() {
return "A group of metagenome reads linked with some probability";
}
public Class getReturnType() {
return LinkedGroup.class;
}
public XMLSyntaxRule[] getSyntaxRules() {
return rules;
}
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
TaxonList taxa = null;
double linkageProbability = 0.9999999999;
if (xo.hasAttribute("probability")) {
linkageProbability = xo.getDoubleAttribute("probability");
}
taxa = (TaxonList)xo.getChild(TaxonList.class);
LinkedGroup lg = new LinkedGroup(taxa, linkageProbability);
return lg;
}
public String getParserName() {
return "LinkedGroup";
}
private XMLSyntaxRule[] rules = new XMLSyntaxRule[]{
new ElementRule(Taxa.class),
AttributeRule.newDoubleRule("probability", true, "the probability that the group of reads are linked to each other"),
};
}