/*
* SitePatternsParser.java
*
* Copyright (C) 2002-2006 Alexei Drummond and Andrew Rambaut
*
* 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.alignment.PatternList;
import dr.evolution.alignment.Patterns;
import dr.evolution.datatype.DataType;
import dr.evolution.util.Taxon;
import dr.evolution.util.TaxonList;
import dr.evoxml.util.DataTypeUtils;
import dr.xml.*;
import java.util.logging.Logger;
/**
* @author Alexei Drummond
* @author Andrew Rambaut
*
* @version $Id: SitePatternsParser.java,v 1.3 2005/07/11 14:06:25 rambaut Exp $
*/
public class AttributePatternsParser extends AbstractXMLObjectParser {
public static final String ATTRIBUTE = "attribute";
public static final String PATTERNS = "Patterns";
public static final String ATTRIBUTE_PATTERNS = ATTRIBUTE + PATTERNS;
public String getParserName() { return ATTRIBUTE_PATTERNS; }
public Object parseXMLObject(XMLObject xo) throws XMLParseException {
String attributeName = xo.getStringAttribute(ATTRIBUTE);
TaxonList taxa = (TaxonList)xo.getChild(TaxonList.class);
DataType dataType = DataTypeUtils.getDataType(xo);
if (dataType == null) {
throw new XMLParseException("dataType expected for attributePatterns element");
}
Patterns patterns = new Patterns(dataType, taxa);
int[] pattern = new int[taxa.getTaxonCount()];
boolean attributeFound = false;
for (int i = 0; i < taxa.getTaxonCount(); i++) {
Taxon taxon = taxa.getTaxon(i);
Object value = taxon.getAttribute(attributeName);
if (value != null) {
int state = dataType.getState(value.toString());
if (state < 0) {
throw new XMLParseException("State for attribute, " + attributeName + ", in taxon, " + taxon.getId() + ", is unknown: " + value.toString());
}
pattern[i] = state;
attributeFound = true;
} else {
pattern[i] = dataType.getUnknownState();
}
}
if (!attributeFound) {
throw new XMLParseException("The attribute, " + attributeName + " was missing in all taxa. Check the name of the attribute.");
}
patterns.addPattern(pattern);
if (xo.hasAttribute(XMLParser.ID)) {
Logger.getLogger("dr.evoxml").info("Read attribute patterns, '" + xo.getId() + "' for attribute, "+ attributeName);
} else {
Logger.getLogger("dr.evoxml").info("Read attribute patterns for attribute, "+ attributeName);
}
return patterns;
}
//************************************************************************
// AbstractXMLObjectParser implementation
//************************************************************************
public XMLSyntaxRule[] getSyntaxRules() { return rules; }
private XMLSyntaxRule[] rules = new XMLSyntaxRule[] {
new XORRule(
new StringAttributeRule(
DataType.DATA_TYPE,
"The data type",
DataType.getRegisteredDataTypeNames(), false),
new ElementRule(DataType.class)
),
AttributeRule.newStringRule(ATTRIBUTE),
new ElementRule(TaxonList.class, "The taxon set")
};
public String getParserDescription() {
return "A site pattern defined by an attribute in a set of taxa.";
}
public Class getReturnType() { return PatternList.class; }
}