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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) 2009-2017 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.Locale;
import java.util.Map;
import org.apache.log4j.Logger;
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.UniqueNamedSBase;
import org.sbml.jsbml.util.ResourceManager;
import org.sbml.jsbml.util.StringTools;
/**
* A {@link Dimensions} is specified via the required attributes width,
* height and an optional attribute depth, all of which are of type double.
* If the attribute depth is not specified, the object is a two dimensional object.
* The width attribute of {@link Dimensions} specifies the size of the object
* in the direction of the positive x axis, the height attribute specifies the
* size of the object along the positive y axis and the depth attribute specifies
* the size of the object along the positive z axis. All sizes for {@link Dimensions}
* objects are positive values, and so the attributes are not allowed to take
* negative values. The {@link Dimensions} class also has an optional attribute
* id of type SId. While not used in the {@link Layout} package, it can be used by
* programs to refer to the elements.
*
* @author Nicolas Rodriguez
* @author Sebastian Frölich
* @author Andreas Dräger
* @since 1.0
*/
public class Dimensions extends AbstractNamedSBase implements UniqueNamedSBase {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -6114634391235520057L;
/**
* A {@link Logger} for this class.
*/
private static final transient Logger logger = Logger.getLogger(Dimensions.class);
/**
*
*/
private double depth;
/**
*
*/
private double height;
/**
*
*/
private double width;
/**
*
*/
public Dimensions() {
initDefaults();
}
/**
*
* @param dimensions
*/
public Dimensions(Dimensions dimensions) {
super(dimensions);
depth = height = width = Double.NaN;
if (dimensions.isSetDepth()) {
setDepth(dimensions.getDepth());
} else {
depth = Double.NaN;
}
if (dimensions.isSetHeight()) {
setHeight(dimensions.getHeight());
} else {
height = Double.NaN;
}
if (dimensions.isSetWidth()) {
setWidth(dimensions.getWidth());
} else {
width = Double.NaN;
}
}
/**
*
* @param width
* @param height
* @param depth
* @param level
* @param version
*/
public Dimensions(double width, double height, double depth, int level, int version) {
this(level, version);
this.width = width;
this.height = height;
this.depth = depth;
}
/**
*
* @param level
* @param version
*/
public Dimensions(int level, int version) {
super(level, version);
initDefaults();
}
/**
*
* @param id
* @param level
* @param version
*/
public Dimensions(String id, int level, int version) {
super(id, level, version);
initDefaults();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#clone()
*/
@Override
public Dimensions clone() {
return new Dimensions(this);
}
/**
*
*/
private void initDefaults() {
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
depth = height = width = Double.NaN;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#equals(java.lang.Object)
*/
@Override
public boolean equals(Object object) {
boolean equals = super.equals(object);
if (equals) {
Dimensions d = (Dimensions) object;
equals &= d.isSetDepth() == isSetDepth();
if (equals && isSetDepth()) {
equals &= Double.valueOf(d.getDepth()).equals(Double.valueOf(getDepth()));
}
equals &= d.isSetHeight() == isSetHeight();
if (equals && isSetHeight()) {
equals &= Double.valueOf(d.getHeight()).equals(Double.valueOf(getHeight()));
}
equals &= d.isSetWidth() == isSetWidth();
if (equals && isSetWidth()) {
equals &= Double.valueOf(d.getWidth()).equals(Double.valueOf(getWidth()));
}
}
return equals;
}
/**
*
* @return
*/
public double getDepth() {
return depth;
}
/**
*
* @return
*/
public double getHeight() {
return height;
}
/**
*
* @return
*/
public double getWidth() {
return width;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 941;
int hashCode = super.hashCode();
hashCode += prime * Double.valueOf(depth).hashCode();
hashCode += prime * Double.valueOf(height).hashCode();
hashCode += prime * Double.valueOf(width).hashCode();
return hashCode;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.NamedSBase#isIdMandatory()
*/
@Override
public boolean isIdMandatory() {
return false;
}
/**
* @return
*/
public boolean isSetDepth() {
return !Double.isNaN(depth);
}
/**
* @return
*/
public boolean isSetHeight() {
return !Double.isNaN(height);
}
/**
* @return
*/
public boolean isSetWidth() {
return !Double.isNaN(width);
}
/* (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.width))
{
Double valueDouble = StringTools.parseSBMLDouble(value);
// If the value is NaN, we could have encountered a NumberFormatExpection
// So we parse it again to be sure as StringTools.parseSBMLDouble does not propagate the exception.
if (valueDouble.isNaN()) {
try {
Double.parseDouble(value);
} catch (NumberFormatException e) {
// The value is a wrong double so don't set it and return false so that it is put in the unknown attributes
return false;
}
}
setWidth(valueDouble);
}
else if (attributeName.equals(LayoutConstants.height))
{
Double valueDouble = StringTools.parseSBMLDouble(value);
// If the value is NaN, we could have encountered a NumberFormatExpection
// So we parse it again to be sure as StringTools.parseSBMLDouble does not propagate the exception.
if (valueDouble.isNaN()) {
try {
Double.parseDouble(value);
} catch (NumberFormatException e) {
// The value is a wrong double so don't set it and return false so that it is put in the unknown attributes
return false;
}
}
setHeight(valueDouble);
}
else if (attributeName.equals(LayoutConstants.depth))
{
Double valueDouble = StringTools.parseSBMLDouble(value);
// If the value is NaN, we could have encountered a NumberFormatExpection
// So we parse it again to be sure as StringTools.parseSBMLDouble does not propagate the exception.
if (valueDouble.isNaN()) {
try {
Double.parseDouble(value);
} catch (NumberFormatException e) {
// The value is a wrong double so don't set it and return false so that it is put in the unknown attributes
return false;
}
}
setDepth(valueDouble);
}
else
{
return false;
}
return true;
}
return isAttributeRead;
}
/**
* Depth is an optional attribute and specifies the size along the positive z axis.
*
* @param depth
*/
public void setDepth(double depth) {
Double oldDepth = this.depth;
this.depth = depth;
firePropertyChange(LayoutConstants.depth, oldDepth, this.depth);
}
/**
* Height is a required attribute and specifies the size along the positive y axis.
*
* @param height
*/
public void setHeight(double height) {
Double oldHeight = this.height;
this.height = height;
firePropertyChange(LayoutConstants.height, oldHeight, this.height);
}
/**
* Width is a required attribute and specifies the size along the positive x axis.
*
* @param width
*/
public void setWidth(double width) {
Double oldWidth = this.width;
this.width = width;
firePropertyChange(LayoutConstants.width, oldWidth, this.width);
}
/* (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!
}
if (isSetDepth()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.depth, StringTools.toString(Locale.ENGLISH, depth));
}
if (isSetHeight()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.height, StringTools.toString(Locale.ENGLISH, height));
}
if (isSetWidth()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.width, StringTools.toString(Locale.ENGLISH, width));
}
return attributes;
}
}
