/*
* DataTypeUtils.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.util;
import dr.evolution.datatype.DataType;
import dr.evolution.datatype.GeneticCode;
import dr.xml.XMLObject;
import dr.xml.XMLParseException;
/**
* @author Alexei Drummond
*
* @version $Id$
*/
public class DataTypeUtils {
public static DataType getDataType(XMLObject xo) throws XMLParseException {
DataType dataType = null;
if (xo.hasAttribute(DataType.DATA_TYPE)) {
String dataTypeStr = xo.getStringAttribute(DataType.DATA_TYPE);
if (xo.hasAttribute(GeneticCode.GENETIC_CODE)) {
dataTypeStr += "-" + xo.getStringAttribute(GeneticCode.GENETIC_CODE);
}
dataType = DataType.getRegisteredDataTypeByName(dataTypeStr);
}
for (int i = 0; i < xo.getChildCount(); i++) {
Object child = xo.getChild(i);
if (child instanceof DataType) {
if (dataType != null) {
throw new XMLParseException("Multiple dataTypes defined for alignment element");
}
dataType = (DataType) child;
}
}
return dataType;
}
}