org.sbml.jsbml.ext.layout.CompartmentGlyph Maven / Gradle / Ivy
/*
* ----------------------------------------------------------------------------
* This file is part of JSBML. Please visit
* for the latest version of JSBML and more information about SBML.
*
* Copyright (C) 2009-2017 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.util.Locale;
import java.util.Map;
import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.CompartmentalizedSBase;
import org.sbml.jsbml.NamedSBase;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.util.StringTools;
import org.sbml.jsbml.util.TreeNodeChangeEvent;
/**
* The {@link CompartmentGlyph} class is derived from {@link GraphicalObject}
* and inherits its attributes. Additionally it has tow optional attributes:
* compartment and order.
*
* @author Nicolas Rodriguez
* @author Andreas Dräger
* @since 1.0
*/
public class CompartmentGlyph extends AbstractReferenceGlyph implements CompartmentalizedSBase {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -831178362695634919L;
/**
*
*/
private Double order;
/**
* Creates a new instance of {@link CompartmentGlyph}.
*/
public CompartmentGlyph() {
super();
initDefaults();
}
/**
* Creates a new instance of {@link CompartmentGlyph}.
*
* @param compartmentGlyph the {@link CompartmentGlyph} to clone.
*/
public CompartmentGlyph(CompartmentGlyph compartmentGlyph) {
super(compartmentGlyph);
initDefaults();
}
/**
* Creates a new instance of {@link CompartmentGlyph}.
*
* @param level the SBML level
* @param version the SBML version
*/
public CompartmentGlyph(int level, int version) {
super(level, version);
initDefaults();
}
/**
* Creates a new instance of {@link CompartmentGlyph}.
*
* @param id the id
*/
public CompartmentGlyph(String id) {
super(id);
initDefaults();
}
/**
* Creates a new instance of {@link CompartmentGlyph}.
*
* @param id the id
* @param level the SBML level
* @param version the SBML version
*/
public CompartmentGlyph(String id, int level, int version) {
super(id, level, version);
initDefaults();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#clone()
*/
@Override
public CompartmentGlyph clone() {
return new CompartmentGlyph(this);
}
/**
* Initializes the default values using the namespace.
*/
public void initDefaults() {
setPackageVersion(-1);
packageName = LayoutConstants.shortLabel;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.CompartmentalizedSBase#getCompartment()
*/
@Override
public String getCompartment() {
return getReference();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.CompartmentalizedSBase#getCompartmentInstance()
*/
@Override
public NamedSBase getCompartmentInstance() {
return getNamedSBaseInstance();
}
/**
* Returns the value of order
*
* @return the value of order
*/
public double getOrder()
{
if (isSetOrder()) {
return order;
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(LayoutConstants.order, this);
}
/* (non-Javadoc)
* @see org.sbml.jsbml.CompartmentalizedSBase#isCompartmentMandatory()
*/
@Override
public boolean isCompartmentMandatory() {
return false;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.CompartmentalizedSBase#isSetCompartment()
*/
@Override
public boolean isSetCompartment() {
return isSetReference();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.CompartmentalizedSBase#isSetCompartmentInstance()
*/
@Override
public boolean isSetCompartmentInstance() {
return getCompartmentInstance() != null;
}
/**
* Returns whether order is set
*
* @return whether order is set
*/
public boolean isSetOrder() {
return order != null;
}
/* (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) {
if (attributeName.equals(LayoutConstants.compartment))
{
setCompartment(value);
}
else if (attributeName.equals(LayoutConstants.order))
{
Double valueDbl = 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 (valueDbl.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;
}
}
setOrder(valueDbl);
}
else
{
return false;
}
return true;
}
return isAttributeRead;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.CompartmentalizedSBase#setCompartment(org.sbml.jsbml.Compartment)
*/
@Override
public boolean setCompartment(Compartment compartment) {
return setCompartment(compartment.getId());
}
/* (non-Javadoc)
* @see org.sbml.jsbml.CompartmentalizedSBase#setCompartment(java.lang.String)
*/
@Override
public boolean setCompartment(String compartment) {
return setReference(compartment, TreeNodeChangeEvent.compartment);
}
/**
* Sets the oder.
*
* The order attribute is an optional attribute of type {@link Double}. It is there
* to handle the case where compartments in a layout overlap, and tools want to
* clearly disambiguate which {@link CompartmentGlyph} is on top of the other.
* The order attribute follows the coordinate system. There are z dimension points
* into a screen; thus, an element with a lower order value will be in front
* of an elements with a higher value. If not specified, the order is undefined
* and tools are free to display the compartment glyphs in the order that best fits their
* needs.
*
* Note: if z coordinates are used (and this order is seemingly redundant), the order
* can still be used to disambiguate drawing order.
*
* @param order the oder
*/
public void setOrder(double order) {
Double oldOrder = this.order;
this.order = order;
firePropertyChange(LayoutConstants.order, oldOrder, this.order);
}
/* (non-Javadoc)
* @see org.sbml.jsbml.CompartmentalizedSBase#unsetCompartment()
*/
@Override
public boolean unsetCompartment() {
return unsetReference();
}
/**
* Unsets the variable order
*
* @return {@code true}, if order was set before,
* otherwise {@code false}
*/
public boolean unsetOrder() {
if (isSetOrder()) {
Double oldOrder = order;
order = null;
firePropertyChange(LayoutConstants.order, oldOrder, order);
return true;
}
return false;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.layout.GraphicalObject#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetCompartment()) {
attributes.put(LayoutConstants.shortLabel + ':'
+ LayoutConstants.compartment, getCompartment());
}
if (isSetOrder()) {
attributes.put(LayoutConstants.shortLabel + ':' + LayoutConstants.order,
StringTools.toString(Locale.ENGLISH, order.doubleValue()));
}
return attributes;
}
}