org.sbml.jsbml.ext.layout.Point 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.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;
/**
* The representation of a point in the "layout" package.
*
* A {@link Point} is specified via the required attributes 'x', 'y' and an optional
* attribute 'z', all of which are of type double. If the attribute z is not
* specified, the object is a two dimensional object. The {@link Point} 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
* @author Clemens Wrzodek
* @since 1.0
*/
public class Point extends AbstractNamedSBase implements UniqueNamedSBase {
/**
*
*/
private static final long serialVersionUID = -7464572763198848890L;
/**
* A {@link Logger} for this class.
*/
private static final transient Logger logger = Logger.getLogger(Point.class);
/**
* the x coordinate
*/
private double x;
/**
* the y coordinate
*/
private double y;
/**
* the z coordinate
*/
private double z;
/**
* The name to be used when writing this point to XML.
*/
private String xmlElementName;
/**
* Creates a new {@link Point} instance with all coordinates set to {@link Double#NaN}.
*
*/
public Point() {
super();
initDefaults();
}
/**
* Creates a new {@link Point} instance with the given x and y coordinates. z is set to {@link Double#NaN}.
*
* @param x the x coordinate
* @param y the y coordinate
*/
public Point(double x, double y) {
this();
this.x = x;
this.y = y;
z = Double.NaN;
}
/**
* Creates a new {@link Point} instance with the given coordinates.
*
* @param x the x coordinate
* @param y the y coordinate
* @param z the z coordinate
*/
public Point(double x, double y, double z) {
this();
this.x = x;
this.y = y;
this.z = z;
}
/**
* Creates a new {@link Point} instance with the given coordinates and level and version.
*
* @param x the x coordinate
* @param y the y coordinate
* @param z the z coordinate
* @param level the SBML level
* @param version the SBML version
*/
public Point(double x, double y, double z, int level, int version) {
this(level, version);
this.x = x;
this.y = y;
this.z = z;
}
/**
* Creates a new {@link Point} instance with the given level and version, all coordinates are set to {@link Double#NaN}.
*
* @param level the SBML level
* @param version the SBML version
*/
public Point(int level, int version) {
super(level, version);
initDefaults();
}
/**
* Creates a new {@link Point} instance with all attributes cloned from the given {@link Point}.
*
* @param point the {@link Point} instance to clone.
*/
public Point(Point point) {
super(point);
clonePointAttributes(point, this);
setElementName(point.getElementName());
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#clone()
*/
@Override
public Point clone() {
return new Point(this);
}
/**
* Clones the x, y and z coordinates from point to cloned.
*
* @param point
* @param cloned
*/
protected void clonePointAttributes(Point point, Point cloned) {
if (point.isSetX()) {
cloned.setX(point.getX());
} else {
cloned.setX(Double.NaN);
}
if (point.isSetY()) {
cloned.setY(point.getY());
} else {
cloned.setY(Double.NaN);
}
if (point.isSetZ()) {
cloned.setZ(point.getZ());
} else {
cloned.setZ(Double.NaN);
}
}
/**
* Initializes the default values using the namespace.
*/
public void initDefaults() {
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
x = y = z = 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) {
Point p = (Point) object;
equals &= p.isSetX() == isSetX();
if (equals && isSetX()) {
equals &= Double.valueOf(p.getX()).equals(Double.valueOf(getX()));
}
equals &= p.isSetY() == isSetY();
if (equals && isSetY()) {
equals &= Double.valueOf(p.getY()).equals(Double.valueOf(getY()));
}
equals &= p.isSetZ() == isSetZ();
if (equals && isSetZ()) {
equals &= Double.valueOf(p.getZ()).equals(Double.valueOf(getZ()));
}
}
return equals;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#getElementName()
*/
@Override
public String getElementName() {
return xmlElementName;
}
/**
* Gets the x coordinate.
*
*
Returns {@link Double#NaN} if {@link #isSetX()}
* return false.
*
* @return the x coordinate.
*/
public double getX() {
return x;
}
/**
* Gets the y coordinate.
*
*
Returns {@link Double#NaN} if {@link #isSetY()}
* return false.
*
* @return the y coordinate.
*/
public double getY() {
return y;
}
/**
* Gets the z coordinate.
*
*
Returns {@link Double#NaN} if {@link #isSetZ()}
* return false.
*
* @return the z coordinate.
*/
public double getZ() {
return z;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 947;
int hashCode = super.hashCode();
hashCode += prime * Double.valueOf(x).hashCode();
hashCode += prime * Double.valueOf(y).hashCode();
hashCode += prime * Double.valueOf(z).hashCode();
return hashCode;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.NamedSBase#isIdMandatory()
*/
@Override
public boolean isIdMandatory() {
return false;
}
/**
* Returns {@code true} if the x coordinate is set.
*
* @return {@code true} if the x coordinate is set.
*/
public boolean isSetX() {
return !Double.isNaN(x);
}
/**
* Returns {@code true} if the y coordinate is set.
*
* @return {@code true} if the y coordinate is set.
*/
public boolean isSetY() {
return !Double.isNaN(y);
}
/**
* Returns {@code true} if the z coordinate is set.
*
* @return {@code true} if the z coordinate is set.
*/
public boolean isSetZ() {
return !Double.isNaN(z);
}
/* (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.x)) {
setX(StringTools.parseSBMLDouble(value));
}
else if (attributeName.equals(LayoutConstants.y))
{
setY(StringTools.parseSBMLDouble(value));
}
else if (attributeName.equals(LayoutConstants.z))
{
setZ(StringTools.parseSBMLDouble(value));
}
else {
return false;
}
}
return isAttributeRead;
}
/**
* Sets the name to be used when writing this {@link Point} to XML.
*
*
This method should only be used internally.
*
* @param elementName the xml element name.
*/
void setElementName(String elementName) {
xmlElementName = elementName;
}
/**
* Sets the x coordinate.
*
*
The general {@link Point} class specifies the x, y, and z (optional) attributes
* which defines the graphical location with respect to the coordinate system
* of the {@link Layout} extension. The x attribute is required.
*
* @param x the x coordinate to be set.
*/
public void setX(double x) {
Double oldX = this.x;
this.x = x;
firePropertyChange(LayoutConstants.x, oldX, this.x);
}
/**
* Sets the y coordinate.
*
*
The y attribute is required. For a more general description of the dimension
* attributes, see {@link #setX(double)}.
*
* @param y the y coordinate to be set.
*/
public void setY(double y) {
Double oldY = this.y;
this.y = y;
firePropertyChange(LayoutConstants.y, oldY, this.y);
}
/**
* Sets the z coordinate.
*
*
The z attribute is optional. The layout is 2-dimensional if the z attribute is
* not specified.
*
* @param z the z coordinate to be set.
*/
public void setZ(double z) {
Double oldZ = this.z;
this.z = z;
firePropertyChange(LayoutConstants.z, oldZ, this.z);
}
/* (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 (isSetX()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.x, StringTools.toString(Locale.ENGLISH, x));
}
if (isSetY()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.y, StringTools.toString(Locale.ENGLISH, y));
}
if (isSetZ()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.z, StringTools.toString(Locale.ENGLISH, z));
}
return attributes;
}
/**
* Gets the x coordinate.
*
* @return the x coordinate.
* @see #getX()
* @libsbml.deprecated
*/
public double x() {
return getX();
}
/**
* Gets the y coordinate.
*
* @return the y coordinate.
* @see #getY()
* @libsbml.deprecated
*/
public double y() {
return getY();
}
/**
* Gets the z coordinate.
*
* @return the z coordinate.
* @see #getZ()
* @libsbml.deprecated
*/
public double z() {
return getZ();
}
}