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/*
*
* ----------------------------------------------------------------------------
* This file is part of JSBML. Please visit
* for the latest version of JSBML and more information about SBML.
*
* Copyright (C) 2009-2016 jointly by the following organizations:
* 1. The University of Tuebingen, Germany
* 2. EMBL European Bioinformatics Institute (EBML-EBI), Hinxton, UK
* 3. The California Institute of Technology, Pasadena, CA, USA
* 4. The University of California, San Diego, La Jolla, CA, USA
* 5. The Babraham Institute, Cambridge, UK
* 6. The University of Utah, Salt Lake City, UT, USA
*
* This library 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. A copy of the license agreement is provided
* in the file named "LICENSE.txt" included with this software distribution
* and also available online as .
* ----------------------------------------------------------------------------
*/
package org.sbml.jsbml.xml.parsers;
import java.util.List;
import org.apache.log4j.Logger;
import org.mangosdk.spi.ProviderFor;
import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.SBase;
import org.sbml.jsbml.ext.ASTNodePlugin;
import org.sbml.jsbml.ext.SBasePlugin;
import org.sbml.jsbml.ext.arrays.ArraysConstants;
import org.sbml.jsbml.ext.arrays.ArraysSBasePlugin;
import org.sbml.jsbml.ext.arrays.Dimension;
import org.sbml.jsbml.ext.arrays.Index;
import org.sbml.jsbml.xml.stax.SBMLObjectForXML;
/**
* @author Leandro Watanabe
* @since 1.0
*/
@ProviderFor(ReadingParser.class)
public class ArraysParser extends AbstractReaderWriter implements PackageParser {
/**
* A {@link Logger} for this class.
*/
private static final transient Logger logger = Logger.getLogger(ArraysParser.class);
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.ReadingParser#getNamespaces()
*/
@Override
public List getNamespaces() {
return ArraysConstants.namespaces;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.PackageParser#createPluginFor(org.sbml.jsbml.SBase)
*/
@Override
public SBasePlugin createPluginFor(SBase sbase) {
if (sbase != null) {
//if (sbase instanceof Model) {
return new ArraysSBasePlugin(sbase);
//}
}
return null;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.PackageParser#getNamespaceFor(int, int, int)
*/
@Override
public String getNamespaceFor(int level, int version, int packageVersion) {
if (level == 3 && version == 1 && packageVersion == 1) {
return ArraysConstants.namespaceURI_L3V1V1;
}
return null;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.PackageParser#getPackageNamespaces()
*/
@Override
public List getPackageNamespaces() {
return getNamespaces();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.PackageParser#getPackageName()
*/
@Override
public String getPackageName() {
return ArraysConstants.shortLabel;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.PackageParser#isRequired()
*/
@Override
public boolean isRequired() {
return true;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#processStartElement(java.lang.String, java.lang.String, java.lang.String, boolean, boolean, java.lang.Object)
*/
@Override
public Object processStartElement(String elementName, String uri,
String prefix, boolean hasAttributes, boolean hasNamespaces,
Object contextObject) {
if (contextObject instanceof ListOf)
{
@SuppressWarnings("unchecked")
ListOf listOf = (ListOf) contextObject;
SBase sBase = listOf.getParent();
ArraysSBasePlugin arraysPlugin = (ArraysSBasePlugin) sBase.getPlugin(ArraysConstants.shortLabel);
if (elementName.equals("dimension")) {
Dimension dimension = new Dimension();
arraysPlugin.addDimension(dimension);
return dimension;
}
else if (elementName.equals("index")) {
Index index = new Index();
arraysPlugin.addIndex(index);
return index;
}
}
else if (contextObject instanceof SBase)
{
SBase sBase = (SBase) contextObject;
if (elementName.equals("listOfDimensions")) {
ArraysSBasePlugin arraysPlugin = (ArraysSBasePlugin) sBase.getPlugin(ArraysConstants.shortLabel);
return arraysPlugin.getListOfDimensions();
}
else if (elementName.equals("listOfIndices")) {
ArraysSBasePlugin arraysPlugin = (ArraysSBasePlugin) sBase.getPlugin(ArraysConstants.shortLabel);
return arraysPlugin.getListOfIndices();
}
}
return contextObject;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#getShortLabel()
*/
@Override
public String getShortLabel() {
return ArraysConstants.shortLabel;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#getNamespaceURI()
*/
@Override
public String getNamespaceURI() {
return ArraysConstants.namespaceURI;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.xml.parsers.AbstractReaderWriter#writeElement(org.sbml.jsbml.xml.stax.SBMLObjectForXML, java.lang.Object)
*/
@Override
public void writeElement(SBMLObjectForXML xmlObject, Object sbmlElementToWrite) {
super.writeElement(xmlObject, sbmlElementToWrite);
String name = xmlObject.getName();
if (name.equals("listOfIndexs")) {
xmlObject.setName(ArraysConstants.listOfIndices);
}
}
@Override
public ASTNodePlugin createPluginFor(ASTNode astNode) {
// This package does not extends ASTNode
return null;
}
}
