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/*
* $Id$
* $URL$
* ----------------------------------------------------------------------------
* 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
*
* 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.ext.layout;
import java.text.MessageFormat;
import java.util.Map;
import javax.swing.tree.TreeNode;
import org.apache.log4j.Logger;
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.UniqueNamedSBase;
import org.sbml.jsbml.util.ResourceManager;
/**
* All the more specific layout elements ({@link CompartmentGlyph}, {@link GeneralGlyph},
* {@link SpeciesGlyph}, {@link ReactionGlyph}, {@link ReferenceGlyph}, {@link TextGlyph},
* and {@link SpeciesReferenceGlyph}) are derived from the class {@link GraphicalObject}.
* Each object of class {@link GraphicalObject} has a mandatory {@link BoundingBox}, which
* specifies the position and the size of the object. While {@link GraphicalObject} is the
* base class for most elements in the {@link Layout} package, it is not an abstract class.
* It can be instantiated when used in the listOfAdditionalGraphicalObjects to describe
* additional elements and relationships. Since it only describes a {@link BoundingBox},
* programs are encouraged to add {@link org.sbml.jsbml.Annotation} objects that describe program-specific
* graphical information.
*
* @author Nicolas Rodriguez
* @author Sebastian Frölich
* @author Andreas Dräger
* @author Clemens Wrzodek
* @since 1.0
* @version $Rev$
*/
public class GraphicalObject extends AbstractNamedSBase implements UniqueNamedSBase {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 7587814013754302901L;
/**
* A {@link Logger} for this class.
*/
private static final transient Logger logger = Logger.getLogger(GraphicalObject.class);
/**
*
*/
private BoundingBox boundingBox;
/**
*
*/
private String metaidRef;
/**
*
*/
public GraphicalObject() {
super();
initDefaults();
}
/**
*
* @param graphicalObject
*/
public GraphicalObject(GraphicalObject graphicalObject) {
super(graphicalObject);
if (graphicalObject.isSetBoundingBox()) {
setBoundingBox(graphicalObject.getBoundingBox().clone());
}
if (graphicalObject.isSetMetaidRef()) {
setMetaidRef(graphicalObject.getMetaidRef());
}
}
/**
*
* @param level
* @param version
*/
public GraphicalObject(int level, int version) {
super(level, version);
initDefaults();
}
/**
* @param id
*/
public GraphicalObject(String id) {
super(id);
initDefaults();
}
/**
*
* @param id
* @param level
* @param version
*/
public GraphicalObject(String id, int level, int version) {
super(id, level, version);
initDefaults();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#clone()
*/
@Override
public GraphicalObject clone() {
return new GraphicalObject(this);
}
/**
* Initializes the default values using the namespace.
*/
public void initDefaults() {
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
/**
* Creates and sets a {@link BoundingBox} for this object.
* @return {@link BoundingBox}.
*/
public BoundingBox createBoundingBox() {
BoundingBox bb = new BoundingBox();
setBoundingBox(bb);
return bb;
}
/**
*
* @param dimensions
* @return
*/
public BoundingBox createBoundingBox(Dimensions dimensions) {
BoundingBox bb = createBoundingBox();
bb.setDimensions(dimensions);
return bb;
}
/**
* Creates and sets a {@link BoundingBox} for this object, with the
* given parameters for {@link Dimensions}.
* @param width
* @param height
* @param depth
* @return {@link BoundingBox}.
*/
public BoundingBox createBoundingBox(double width, double height, double depth) {
BoundingBox bb = createBoundingBox();
bb.createDimensions(width, height, depth);
return bb;
}
/**
* Creates and sets a {@link BoundingBox} for this object, with the
* given parameters for {@link Dimensions} and {@link Point}.
* @param width
* @param height
* @param depth
* @param x
* @param y
* @param z
* @return {@link BoundingBox}.
*/
public BoundingBox createBoundingBox(double width, double height, double depth,
double x, double y, double z) {
BoundingBox bb = createBoundingBox(width, height, depth);
bb.createPosition(x, y, z);
return bb;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#equals(java.lang.Object)
*/
@Override
public boolean equals(Object object) {
boolean equals = super.equals(object);
if (equals) {
GraphicalObject graphicalObject = (GraphicalObject) object;
equals &= graphicalObject.isSetBoundingBox() == isSetBoundingBox();
if (equals && isSetBoundingBox()) {
equals &= graphicalObject.getBoundingBox().equals(getBoundingBox());
}
}
return equals;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#getAllowsChildren()
*/
@Override
public boolean getAllowsChildren() {
return true;
}
/**
*
* @return
*/
public BoundingBox getBoundingBox() {
return boundingBox;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#getChildAt(int)
*/
@Override
public TreeNode getChildAt(int index) {
if (index < 0) {
throw new IndexOutOfBoundsException(Integer.toString(index));
}
int count = super.getChildCount(), pos = 0;
if (index < count) {
return super.getChildAt(index);
} else {
index -= count;
}
if (isSetBoundingBox()) {
if (pos == index) {
return getBoundingBox();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#getChildCount()
*/
@Override
public int getChildCount() {
int count = super.getChildCount();
if (isSetBoundingBox()) {
count++;
}
return count;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 941;
int hashCode = super.hashCode();
if (isSetBoundingBox()) {
hashCode += prime * getBoundingBox().hashCode();
}
return hashCode;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.NamedSBase#isIdMandatory()
*/
@Override
public boolean isIdMandatory() {
// See Layout Extension (April 25, 2005) page 9, SId use="required"
return true;
}
/**
* @return
*/
public boolean isSetBoundingBox() {
return boundingBox != null;
}
/**
* This is the only required element (besides the SId) of the {@link GraphicalObject}. Because
* this class is not an abstract class and can be instantiated, {@link org.sbml.jsbml.Annotation} objects are
* encouraged to be added.
*
* @param boundingBox
*/
public void setBoundingBox(BoundingBox boundingBox) {
unsetBoundingBox();
this.boundingBox = boundingBox;
registerChild(this.boundingBox);
}
/**
*
*/
public void unsetBoundingBox() {
if (isSetBoundingBox()) {
BoundingBox oldValue = boundingBox;
boundingBox = null;
oldValue.fireNodeRemovedEvent();
}
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetId()) {
attributes.remove("id");
attributes.put(LayoutConstants.shortLabel + ":id", getId());
}
if (isSetName()) {
attributes.remove("name");
logger.warn(MessageFormat.format(
ResourceManager.getBundle("org.sbml.jsbml.resources.cfg.Messages").getString("UNDEFINED_ATTRIBUTE"),
"name", getLevel(), getVersion(), getElementName()));
// TODO: This must be generally solved. Here we have an SBase with ID but without name!
// TODO: This does not have to be done at this level, however... also, why is this AbstractNamedSbase?
}
if (isSetMetaidRef())
{
attributes.put(LayoutConstants.shortLabel + ':' + LayoutConstants.metaidRef, getMetaidRef());
}
return attributes;
}
/**
* Returns the value of metaidRef
*
* @return the value of metaidRef
*/
public String getMetaidRef()
{
if (isSetMetaidRef()) {
return metaidRef;
}
return "";
}
/**
* Returns whether metaidRef is set
*
* @return whether metaidRef is set
*/
public boolean isSetMetaidRef() {
return metaidRef != null;
}
/**
* Sets the value of metaidRef which uniquely references elements in the model.
*
* @param metaidRef
*/
public void setMetaidRef(String metaidRef) {
String oldMetaidRef = this.metaidRef;
this.metaidRef = metaidRef;
firePropertyChange(LayoutConstants.metaidRef, oldMetaidRef, this.metaidRef);
}
/**
* Unsets the variable metaidRef
*
* @return {@code true}, if metaidRef was set before,
* otherwise {@code false}
*/
public boolean unsetMetaidRef() {
if (isSetMetaidRef()) {
String oldMetaidRef = metaidRef;
metaidRef = null;
firePropertyChange(LayoutConstants.metaidRef, oldMetaidRef, metaidRef);
return true;
}
return false;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#readAttribute(java.lang.String, java.lang.String, java.lang.String)
*/
@Override
public boolean readAttribute(String attributeName, String prefix, String value)
{
boolean isAttributeRead = super.readAttribute(attributeName, prefix, value);
if (!isAttributeRead) {
isAttributeRead = true;
if (attributeName.equals(LayoutConstants.metaidRef))
{
setMetaidRef(value);
}
else
{
isAttributeRead = false;
}
}
return isAttributeRead;
}
}
