org.sbml.jsbml.ext.multi.MultiCompartmentPlugin Maven / Gradle / Ivy
/*
* ----------------------------------------------------------------------------
* This file is part of JSBML. Please visit
* for the latest version of JSBML and more information about SBML.
*
* Copyright (C) 2009-2018 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.multi;
import java.text.MessageFormat;
import java.util.Map;
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.ext.AbstractSBasePlugin;
import org.sbml.jsbml.util.StringTools;
/**
*
* @author Nicolas Rodriguez
* @since 1.0
*/
public class MultiCompartmentPlugin extends AbstractSBasePlugin {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 4526455581462978178L;
/**
*
*/
private String compartmentType;
/**
*
*/
private Boolean isType;
/**
*
*/
private ListOf listOfCompartmentReferences;
/**
* Creates an MultiCompartmentPlugin instance.
*/
public MultiCompartmentPlugin() {
super();
initDefaults();
}
/**
* Creates a {@link MultiCompartmentPlugin} instance associated with the given
* {@link Compartment}.
*
* @param compartment
* the compartment to extend.
*/
public MultiCompartmentPlugin(Compartment compartment) {
super(compartment);
initDefaults();
}
/**
* Clone constructor.
*
* @param obj the {@link MultiCompartmentPlugin} to clone
*/
public MultiCompartmentPlugin(MultiCompartmentPlugin obj) {
super(obj);
if (obj.isSetListOfCompartmentReferences()) {
setListOfCompartmentReferences(obj.getListOfCompartmentReferences().clone());
}
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.AbstractSBasePlugin#clone()
*/
@Override
public MultiCompartmentPlugin clone() {
return new MultiCompartmentPlugin(this);
}
/**
* Initializes the default values using the namespace.
*/
public void initDefaults() {
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
*/
@Override
public String getPackageName() {
return MultiConstants.shortLabel;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
*/
@Override
public String getPrefix() {
return MultiConstants.shortLabel;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.SBasePlugin#getURI()
*/
@Override
public String getURI() {
return getElementNamespace();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractTreeNode#getParent()
*/
@Override
public Compartment getParent() {
return (Compartment) getExtendedSBase();
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
*/
@Override
public Compartment getParentSBMLObject() {
return getParent();
}
/**
* Returns {@code true} if {@link #listOfCompartmentReferences} contains at least
* one element.
*
* @return {@code true} if {@link #listOfCompartmentReferences} contains at least
* one element, otherwise {@code false}.
*/
public boolean isSetListOfCompartmentReferences() {
if (listOfCompartmentReferences == null) {
return false;
}
return true;
}
/**
* Returns the {@link #listOfCompartmentReferences}.
* Creates it if it does not already exist.
*
* @return the {@link #listOfCompartmentReferences}.
*/
public ListOf getListOfCompartmentReferences() {
if (listOfCompartmentReferences == null) {
listOfCompartmentReferences = new ListOf();
listOfCompartmentReferences.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfCompartmentReferences.setPackageName(null);
listOfCompartmentReferences.setPackageName(MultiConstants.shortLabel);
listOfCompartmentReferences.setSBaseListType(ListOf.Type.other);
listOfCompartmentReferences.setOtherListName(MultiConstants.listOfCompartmentReferences);
if (isSetExtendedSBase()) {
extendedSBase.registerChild(listOfCompartmentReferences);
}
}
return listOfCompartmentReferences;
}
/**
* Sets the given {@code ListOf}.
* If {@link #listOfCompartmentReferences} was defined before and contains some
* elements, they are all unset.
*
* @param listOfCompartmentReferences the list of {@link CompartmentReference}s to set
*/
public void setListOfCompartmentReferences(ListOf listOfCompartmentReferences) {
unsetListOfCompartmentReferences();
this.listOfCompartmentReferences = listOfCompartmentReferences;
if (listOfCompartmentReferences != null) {
listOfCompartmentReferences.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'multi'
listOfCompartmentReferences.setPackageName(null);
listOfCompartmentReferences.setPackageName(MultiConstants.shortLabel);
listOfCompartmentReferences.setSBaseListType(ListOf.Type.other);
listOfCompartmentReferences.setOtherListName(MultiConstants.listOfCompartmentReferences);
if (isSetExtendedSBase()) {
extendedSBase.registerChild(this.listOfCompartmentReferences);
}
}
}
/**
* Returns {@code true} if {@link #listOfCompartmentReferences} contains at least
* one element, otherwise {@code false}.
*
* @return {@code true} if {@link #listOfCompartmentReferences} contains at least
* one element, otherwise {@code false}.
*/
public boolean unsetListOfCompartmentReferences() {
if (isSetListOfCompartmentReferences()) {
ListOf oldCompartmentReferences = listOfCompartmentReferences;
listOfCompartmentReferences = null;
oldCompartmentReferences.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Adds a new {@link CompartmentReference} to the {@link #listOfCompartmentReferences}.
* The listOfCompartmentReferences is initialized if necessary.
*
* @param compartmentReference the element to add to the list
* @return {@code true} (as specified by {@link java.util.Collection#add})
* @see java.util.Collection#add(Object)
*/
public boolean addCompartmentReference(CompartmentReference compartmentReference) {
return getListOfCompartmentReferences().add(compartmentReference);
}
/**
* Removes an element from the {@link #listOfCompartmentReferences}.
*
* @param compartmentReference the element to be removed from the list.
* @return {@code true} if the list contained the specified element and it was
* removed.
* @see java.util.List#remove(Object)
*/
public boolean removeCompartmentReference(CompartmentReference compartmentReference) {
if (isSetListOfCompartmentReferences()) {
return getListOfCompartmentReferences().remove(compartmentReference);
}
return false;
}
/**
* Removes an element from the {@link #listOfCompartmentReferences}.
*
* @param compartmentReferenceId the id of the element to be removed from the list.
* @return the removed element, if it was successfully found and removed or
* {@code null}.
*/
public CompartmentReference removeCompartmentReference(String compartmentReferenceId) {
if (isSetListOfCompartmentReferences()) {
return getListOfCompartmentReferences().remove(compartmentReferenceId);
}
return null;
}
/**
* Removes an element from the {@link #listOfCompartmentReferences} at the given index.
*
* @param i the index where to remove the {@link CompartmentReference}.
* @return the specified element if it was successfully found and removed.
* @throws IndexOutOfBoundsException if the listOf is not set or if the index is
* out of bound ({@code (i < 0) || (i > listOfCompartmentReferences)}).
*/
public CompartmentReference removeCompartmentReference(int i) {
if (!isSetListOfCompartmentReferences()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
return getListOfCompartmentReferences().remove(i);
}
/**
* Creates a new CompartmentReference element and adds it to the
* {@link #listOfCompartmentReferences} list.
*
* @return the newly created element, i.e., the last item in the
* {@link #listOfCompartmentReferences}
*/
public CompartmentReference createCompartmentReference() {
return createCompartmentReference(null);
}
/**
* Creates a new {@link CompartmentReference} element and adds it to the
* {@link #listOfCompartmentReferences} list.
*
* @param id the identifier that is to be applied to the new element.
* @return the newly created {@link CompartmentReference} element, which is the last
* element in the {@link #listOfCompartmentReferences}.
*/
public CompartmentReference createCompartmentReference(String id) {
CompartmentReference compartmentReference = new CompartmentReference(id);
addCompartmentReference(compartmentReference);
return compartmentReference;
}
/**
* Gets an element from the {@link #listOfCompartmentReferences} at the given index.
*
* @param i the index of the {@link CompartmentReference} element to get.
* @return an element from the listOfCompartmentReferences at the given index.
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size).
*/
public CompartmentReference getCompartmentReference(int i) {
if (!isSetListOfCompartmentReferences()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
return getListOfCompartmentReferences().get(i);
}
/**
* Gets an element from the listOfCompartmentReferences, with the given id.
*
* @param compartmentReferenceId the id of the {@link CompartmentReference} element to get.
* @return an element from the listOfCompartmentReferences with the given id
* or {@code null}.
*/
public CompartmentReference getCompartmentReference(String compartmentReferenceId) {
if (isSetListOfCompartmentReferences()) {
return getListOfCompartmentReferences().get(compartmentReferenceId);
}
return null;
}
/**
* Returns the number of {@link CompartmentReference}s in this
* {@link MultiCompartmentPlugin}.
*
* @return the number of {@link CompartmentReference}s in this
* {@link MultiCompartmentPlugin}.
*/
public int getCompartmentReferenceCount() {
return isSetListOfCompartmentReferences() ? getListOfCompartmentReferences().size() : 0;
}
/**
* Returns the number of {@link CompartmentReference}s in this
* {@link MultiCompartmentPlugin}.
*
* @return the number of {@link CompartmentReference}s in this
* {@link MultiCompartmentPlugin}.
* @libsbml.deprecated same as {@link #getCompartmentReferenceCount()}
*/
public int getNumCompartmentReferences() {
return getCompartmentReferenceCount();
}
/**
* Returns the value of {@link #compartmentType}.
*
* @return the value of {@link #compartmentType}.
*/
public String getCompartmentType() {
if (isSetCompartmentType()) {
return compartmentType;
}
return null;
}
/**
* Returns whether {@link #compartmentType} is set.
*
* @return whether {@link #compartmentType} is set.
*/
public boolean isSetCompartmentType() {
return compartmentType != null;
}
/**
* Sets the value of compartmentType
*
* @param compartmentType the value of compartmentType to be set.
*/
public void setCompartmentType(String compartmentType) {
String oldCompartmentType = this.compartmentType;
this.compartmentType = compartmentType;
firePropertyChange(MultiConstants.compartmentType, oldCompartmentType, this.compartmentType);
}
/**
* Unsets the variable compartmentType.
*
* @return {@code true} if compartmentType was set before, otherwise {@code false}.
*/
public boolean unsetCompartmentType() {
if (isSetCompartmentType()) {
String oldCompartmentType = compartmentType;
compartmentType = null;
firePropertyChange(MultiConstants.compartmentType, oldCompartmentType, compartmentType);
return true;
}
return false;
}
/**
* Returns the value of {@link #isType}.
*
* @return the value of {@link #isType}.
*/
public boolean getIsType() {
if (isSetIsType()) {
return isType;
}
// This is necessary if we cannot return null here. For variables of type String return an empty String if no value is defined.
throw new PropertyUndefinedError(MultiConstants.isType, this);
}
/**
* Returns the value of {@link #isType}, return false if isType is not defined.
*
* @return the value of {@link #isType}, return false if isType is not defined.
*/
public boolean isType() {
if (isSetIsType()) {
return isType;
}
return false;
}
/**
* Returns whether {@link #isType} is set.
*
* @return whether {@link #isType} is set.
*/
public boolean isSetIsType() {
return isType != null;
}
/**
* Sets the value of isType
*
* @param isType the value of isType to be set.
*/
public void setIsType(boolean isType) {
Boolean oldIsType = this.isType;
this.isType = isType;
firePropertyChange(MultiConstants.isType, oldIsType, this.isType);
}
/**
* Unsets the variable isType.
*
* @return {@code true} if isType was set before, otherwise {@code false}.
*/
public boolean unsetIsType() {
if (isSetIsType()) {
Boolean oldIsType = isType;
isType = null;
firePropertyChange(MultiConstants.isType, oldIsType, isType);
return true;
}
return false;
}
@Override
public boolean getAllowsChildren() {
return true;
}
@Override
public int getChildCount() {
int count = 0;
if (isSetListOfCompartmentReferences()) {
count++;
}
return count;
}
@Override
public TreeNode getChildAt(int index) {
if (index < 0) {
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexSurpassesBoundsException"), index, 0));
}
int pos = 0;
if (isSetListOfCompartmentReferences()) {
if (pos == index) {
return getListOfCompartmentReferences();
}
pos++;
}
throw new IndexOutOfBoundsException(
MessageFormat.format(resourceBundle.getString("IndexExceedsBoundsException"),
index, Math.min(pos, 0)));
}
/* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
final int prime = 6217;
int result = super.hashCode();
result = prime * result
+ ((compartmentType == null) ? 0 : compartmentType.hashCode());
result = prime * result + ((isType == null) ? 0 : isType.hashCode());
result = prime * result + ((listOfCompartmentReferences == null) ? 0
: listOfCompartmentReferences.hashCode());
return result;
}
/* (non-Javadoc)
* @see java.lang.Object#equals(java.lang.Object)
*/
@Override
public boolean equals(Object obj) {
if (this == obj) {
return true;
}
if (!super.equals(obj)) {
return false;
}
if (getClass() != obj.getClass()) {
return false;
}
MultiCompartmentPlugin other = (MultiCompartmentPlugin) obj;
if (compartmentType == null) {
if (other.compartmentType != null) {
return false;
}
} else if (!compartmentType.equals(other.compartmentType)) {
return false;
}
if (isType == null) {
if (other.isType != null) {
return false;
}
} else if (!isType.equals(other.isType)) {
return false;
}
if (listOfCompartmentReferences == null) {
if (other.listOfCompartmentReferences != null) {
return false;
}
} else if (!listOfCompartmentReferences
.equals(other.listOfCompartmentReferences)) {
return false;
}
return true;
}
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetCompartmentType()) {
attributes.put(MultiConstants.shortLabel + ":" + MultiConstants.compartmentType, getCompartmentType());
}
if (isSetIsType()) {
attributes.put(MultiConstants.shortLabel + ":" + MultiConstants.isType, isType.toString());
}
return attributes;
}
@Override
public boolean readAttribute(String attributeName, String prefix, String value) {
boolean isAttributeRead = true;
if (attributeName.equals(MultiConstants.compartmentType)) {
setCompartmentType(value);
}
else if (attributeName.equals(MultiConstants.isType)) {
setIsType(StringTools.parseSBMLBoolean(value));
}
else {
isAttributeRead = false;
}
return isAttributeRead;
}
}