org.sbml.jsbml.ext.layout.BoundingBox Maven / Gradle / Ivy
/*
*
* ----------------------------------------------------------------------------
* 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;
/**
* The {@link BoundingBox} class specifies the required elements position and dimension.
* The class describes the rectangular area by which other classes of the Layout package
* will be situated.
*
* @author Nicolas Rodriguez
* @author Sebastian Frölich
* @author Andreas Dräger
* @author Clemens Wrzodek
* @since 1.0
*/
public class BoundingBox extends AbstractNamedSBase implements UniqueNamedSBase {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -6371039558611201798L;
/**
* A {@link Logger} for this class.
*/
private static final transient Logger logger = Logger.getLogger(BoundingBox.class);
/**
*
*/
private Dimensions dimensions;
/**
*
*/
private Point position;
/**
* Creates a new instance of {@link BoundingBox}.
*/
public BoundingBox() {
super();
init();
}
/**
* Creates a new instance of {@link BoundingBox}.
*
* @param boundingBox the {@link BoundingBox} to clone.
*/
public BoundingBox(BoundingBox boundingBox) {
super(boundingBox);
if (boundingBox.isSetDimensions()) {
setDimensions(boundingBox.getDimensions().clone());
}
if (boundingBox.isSetPosition()) {
setPosition(boundingBox.getPosition().clone());
}
}
/**
* Creates a new instance of {@link BoundingBox}.
*
* @param level the SBML level
* @param version the SBML version
*/
public BoundingBox(int level, int version) {
super(level, version);
init();
}
/**
* Creates a new instance of {@link BoundingBox}.
*
* @param id the id
*/
public BoundingBox(String id) {
super(id);
init();
}
/**
* Creates a new instance of {@link BoundingBox}.
*
* @param id the id
* @param level the SBML level
* @param version the SBML version
*/
public BoundingBox(String id, int level, int version) {
super(id, level, version);
init();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#clone()
*/
@Override
public BoundingBox clone() {
return new BoundingBox(this);
}
/**
* Creates, sets and returns a {@link Dimensions}
*
* @return new {@link Dimensions} object.
*/
public Dimensions createDimensions() {
Dimensions d = new Dimensions(getLevel(), getVersion());
setDimensions(d);
return d;
}
/**
* Creates, sets and returns {@link Dimensions} based on the
* given values.
*
* @param width
* @param height
* @param depth
* @return new {@link Dimensions} object.
*/
public Dimensions createDimensions(double width, double height, double depth) {
Dimensions d = new Dimensions(width, height, depth, getLevel(), getVersion());
setDimensions(d);
return d;
}
/**
* Creates, sets and returns a {@link Point}
*
* @return new {@link Point} object.
*/
public Point createPosition() {
Point p = new Point(getLevel(), getVersion());
setPosition(p);
return p;
}
/**
* Creates, sets and returns a {@link Point} based on the
* given values.
*
* @param x
* @param y
* @param z
* @return new {@link Point} object.
*/
public Point createPosition(double x, double y, double z) {
Point p = new Point(x, y, z, getLevel(), getVersion());
setPosition(p);
return p;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#equals(java.lang.Object)
*/
@Override
public boolean equals(Object object) {
// Check all child elements recursively in super class first:
boolean equals = super.equals(object);
if (equals) {
// Cast is possible because super class checks the class attributes
BoundingBox bb = (BoundingBox) object;
// compare position and dimensions
equals &= bb.isSetPosition() == isSetPosition();
if (equals && isSetPosition()) {
equals &= bb.getPosition().equals(getPosition());
}
equals &= bb.isSetDimensions() == isSetDimensions();
if (equals && isSetDimensions()) {
equals &= bb.getDimensions().equals(getDimensions());
}
}
return equals;
}
/* (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 (isSetPosition()) {
if (pos == index) {
return getPosition();
}
pos++;
}
if (isSetDimensions()) {
if (pos == index) {
return getDimensions();
}
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 (isSetPosition()) {
count++;
}
if (isSetDimensions()) {
count++;
}
return count;
}
/**
*
* @return
*/
public Dimensions getDimensions() {
return dimensions;
}
/**
*
* @return
*/
public Point getPosition() {
return position;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 7;
int hashCode = super.hashCode();
hashCode += prime * getId().hashCode();
return hashCode;
}
/**
*
*/
private void init() {
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.NamedSBase#isIdMandatory()
*/
@Override
public boolean isIdMandatory() {
return false;
}
/**
* @return
*/
public boolean isSetDimensions() {
return dimensions != null;
}
/**
* @return
*/
public boolean isSetPosition() {
return position != null;
}
/**
* Sets the {@link Dimensions}.
*
* The dimensions element is required and of type {@link Dimensions}. It represents
* the size of the {@link BoundingBox}.
*
* @param dimensions
*/
public void setDimensions(Dimensions dimensions) {
if (this.dimensions != null) {
Dimensions oldValue = this.dimensions;
this.dimensions = null;
oldValue.fireNodeRemovedEvent();
}
this.dimensions = dimensions;
registerChild(this.dimensions);
}
/**
* Sets the position.
*
* Position always specifies the upper left corner of the {@link BoundingBox}.
* The position is of type {@link Point}.
*
* @param point
*/
public void setPosition(Point point) {
Point oldValue = position;
position = point;
if (oldValue != null) {
oldValue.fireNodeRemovedEvent();
}
if (position != null) {
position.setElementName(LayoutConstants.position);
}
registerChild(position);
}
/* (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!
}
return attributes;
}
}