org.sbml.jsbml.ext.comp.CompSBasePlugin Maven / Gradle / Ivy
/*
* ----------------------------------------------------------------------------
* This file is part of JSBML. Please visit
* for the latest version of JSBML and more information about SBML.
*
* Copyright (C) 2009-2022 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.comp;
import java.text.MessageFormat;
import java.util.Collection;
import java.util.List;
import java.util.Map;
import java.util.TreeMap;
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.SBase;
import org.sbml.jsbml.ext.AbstractSBasePlugin;
/**
* Extends the {@link SBase} class by adding an optional ListOf{@link ReplacedElement}s child and a single optional {@link ReplacedBy} child.
*
* The {@link CompSBasePlugin} class codifies the extensions to the {@link SBase} class defined in the 'Hierarchical Model Composition' package (comp).
* These extensions allows the modeler to define one or more {@link Submodel} elements which the parent {@link SBase} object replaces,
* and/or a single {@link Submodel} element which replaces the parent {@link SBase} object.
*
*
This is accomplished through the addition of an optional ListOf{@link ReplacedElement}s child, which may contain one or more {@link ReplacedElement}
* objects, each of which references a {@link Submodel} element to be replaced by the containing {@link SBase} object, and through the addition of a single
* optional {@link ReplacedBy} child, which references a {@link Submodel} element which is to replace the containing {@link SBase} object.
*
*
If a single {@link SBase} element both contains a ListOf{@link ReplacedElement}s and has a {@link ReplacedBy} child, it and all the referenced
* {@link ReplacedElement} objects are to be replaced by the object referenced by the {@link ReplacedBy} element.
*
*
* @author Nicolas Rodriguez
* @since 1.0
* @see ReplacedElement
* @see ReplacedBy
*/
public class CompSBasePlugin extends AbstractSBasePlugin {
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.SBasePlugin#getPackageName()
*/
@Override
public String getPackageName() {
return CompConstants.shortLabel;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.SBasePlugin#getPrefix()
*/
@Override
public String getPrefix() {
return CompConstants.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 SBase getParent() {
if (isSetExtendedSBase()) {
return (SBase) getExtendedSBase().getParent();
}
return null;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.AbstractSBasePlugin#getParentSBMLObject()
*/
@Override
public SBase getParentSBMLObject() {
return getParent();
}
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 3364911411091523856L;
/**
*
*/
ListOf listOfReplacedElements;
/**
*
*/
ReplacedBy replacedBy;
/**
* Creates an CompSBasePlugin instance
*/
public CompSBasePlugin() {
super();
initDefaults();
}
/**
* Creates a CompSBasePlugin instance with a level and version.
*
* @param extendedSBase the core {@link SBase} that is extended.
*/
public CompSBasePlugin(SBase extendedSBase) {
super(extendedSBase);
initDefaults();
}
/**
* Clone constructor
*
* @param obj the instance to clone
*/
public CompSBasePlugin(CompSBasePlugin obj) {
super(obj);
if (obj.isSetListOfReplacedElements()) {
setListOfReplacedElements(obj.getListOfReplacedElements().clone());
}
if (obj.isSetReplacedBy()) {
setReplacedBy(obj.getReplacedBy().clone());
}
}
/**
* clones this class
*/
@Override
public CompSBasePlugin clone() {
return new CompSBasePlugin(this);
}
/**
* Initializes the default values using the namespace.
*/
public void initDefaults() {}
/* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
final int prime = 3359;
int result = super.hashCode();
result = prime
* result
+ ((listOfReplacedElements == null) ? 0
: listOfReplacedElements.hashCode());
result = prime * result
+ ((replacedBy == null) ? 0 : replacedBy.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;
}
CompSBasePlugin other = (CompSBasePlugin) obj;
if (listOfReplacedElements == null) {
if (other.listOfReplacedElements != null) {
return false;
}
} else if (!listOfReplacedElements.equals(other.listOfReplacedElements)) {
return false;
}
if (replacedBy == null) {
if (other.replacedBy != null) {
return false;
}
} else if (!replacedBy.equals(other.replacedBy)) {
return false;
}
return true;
}
/**
* Returns the value of replacedBy
*
* @return the value of replacedBy
*/
public ReplacedBy getReplacedBy() {
if (isSetReplacedBy()) {
return replacedBy;
}
return null;
}
/**
* Returns whether replacedBy is set
*
* @return whether replacedBy is set
*/
public boolean isSetReplacedBy() {
return replacedBy != null;
}
/**
* Sets the value of the optional replacedBy element.
*
* @param replacedBy the value of replacedBy
*
*/
public void setReplacedBy(ReplacedBy replacedBy) {
ReplacedBy oldReplacedBy = this.replacedBy;
this.replacedBy = replacedBy;
if (extendedSBase != null) {
extendedSBase.registerChild(replacedBy);
}
firePropertyChange(CompConstants.replacedBy, oldReplacedBy, this.replacedBy);
}
/**
* Creates a new {@link ReplacedBy} element and sets it in this {@link CompSBasePlugin}.
*
* @return a new {@link ReplacedBy} element.
*/
public ReplacedBy createReplacedBy() {
ReplacedBy replacedBy = new ReplacedBy();
setReplacedBy(replacedBy);
return replacedBy;
}
/**
* Unsets the variable replacedBy
* @return {@code true}, if replacedBy was set before,
* otherwise {@code false}
*/
public boolean unsetReplacedBy() {
if (isSetReplacedBy()) {
ReplacedBy oldReplacedBy = replacedBy;
replacedBy = null;
firePropertyChange(CompConstants.replacedBy, oldReplacedBy, replacedBy);
return true;
}
return false;
}
/**
* Returns {@code true}, if listOfReplacedElements contains at least one element,
* otherwise {@code false}
*
* @return {@code true}, if listOfReplacedElements contains at least one element,
* otherwise {@code false}
*/
public boolean isSetListOfReplacedElements() {
if ((listOfReplacedElements == null) || listOfReplacedElements.isEmpty()) {
return false;
}
return true;
}
/**
* Returns the n-th {@link ReplacedElement} object in this {@link CompSBasePlugin}.
*
* @param index an index
* @return the {@link ReplacedElement} with the given index if it exists.
* @throws IndexOutOfBoundsException if the index is out of range: {@code (index < 0 || index >= size())}
*/
public ReplacedElement getReplacedElement(int index) {
return getListOfReplacedElements().get(index);
}
/**
* Returns a {@link ReplacedElement} element that has the given 'id' within
* this {@link CompSBasePlugin} or {@code null} if no such element can be found.
*
* @param id
* an id indicating a {@link ReplacedElement} element of the
* {@link CompSBasePlugin}.
* @return a {@link ReplacedElement} element of the {@link CompSBasePlugin} that has
* the given 'id' as id or {@code null} if no element with this
* 'id' can be found.
*/
public ReplacedElement getReplacedElement(String id) {
return getListOfReplacedElements().get(id);
}
/**
* Returns the number of {@link ReplacedElement} objects in this {@link CompSBasePlugin}.
*
* @return the number of {@link ReplacedElement} objects in this {@link CompSBasePlugin}.
*/
public int getReplacedElementCount() {
if (!isSetListOfReplacedElements()) {
return 0;
}
return getListOfReplacedElements().size();
}
/**
* Returns the listOfReplacedElements
*
* @return the listOfReplacedElements
*/
public ListOf getListOfReplacedElements() {
if (!isSetListOfReplacedElements()) {
if (extendedSBase != null) {
listOfReplacedElements = new ListOf(extendedSBase.getLevel(), extendedSBase.getVersion());
} else {
listOfReplacedElements = new ListOf();
}
listOfReplacedElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfReplacedElements.setPackageName(null);
listOfReplacedElements.setPackageName(CompConstants.shortLabel);
listOfReplacedElements.setSBaseListType(ListOf.Type.other);
listOfReplacedElements.setOtherListName(CompConstants.listOfReplacedElements);
if (extendedSBase != null) {
extendedSBase.registerChild(listOfReplacedElements);
}
}
return listOfReplacedElements;
}
/**
* Returns the number of {@link ReplacedElement} of this {@link CompSBasePlugin}.
*
* @return the number of {@link ReplacedElement} of this {@link CompSBasePlugin}.
* @libsbml.deprecated use {@link #getReplacedElementCount()}
*/
public int getNumReplacedElements() {
return getReplacedElementCount();
}
/**
* Sets the listOfReplacedElements. If there was already some elements defined
* on listOfReplacedElements, they will be unset beforehand. If present it must
* contain at least one {@link ReplacedElement} object.
*
* @param listOfReplacedElements the list of {@link ReplacedElement}s.
*/
public void setListOfReplacedElements(ListOf listOfReplacedElements) {
unsetListOfReplacedElements();
this.listOfReplacedElements = listOfReplacedElements;
if (listOfReplacedElements != null) {
listOfReplacedElements.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfReplacedElements.setPackageName(null);
listOfReplacedElements.setPackageName(CompConstants.shortLabel);
listOfReplacedElements.setSBaseListType(ListOf.Type.other);
listOfReplacedElements.setOtherListName(CompConstants.listOfReplacedElements);
}
if (extendedSBase != null) {
extendedSBase.registerChild(this.listOfReplacedElements);
}
}
/**
* Returns {@code true}, if listOfReplacedElements contained at least one element,
* otherwise {@code false}
*
* @return {@code true}, if listOfReplacedElements contained at least one element,
* otherwise {@code false}
*/
public boolean unsetListOfReplacedElements() {
if (isSetListOfReplacedElements()) {
ListOf oldReplacedElements = listOfReplacedElements;
listOfReplacedElements = null;
oldReplacedElements.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Adds a new element to listOfReplacedElements.
* listOfReplacedElements is initialized if necessary.
*
* @param replacedElement the element to be added to the list
* @return {@code true} (as specified by {@link java.util.Collection#add})
*/
public boolean addReplacedElement(ReplacedElement replacedElement) {
return getListOfReplacedElements().add(replacedElement);
}
/**
* Removes an element from listOfReplacedElements.
*
* @param replacedElement the element to be removed from the list
* @return {@code true} if this list contained the specified element
* @see java.util.List#remove(Object)
*/
public boolean removeReplacedElement(ReplacedElement replacedElement) {
if (isSetListOfReplacedElements()) {
return getListOfReplacedElements().remove(replacedElement);
}
return false;
}
/**
* Removes the ith element from the ListOfReplacedElements.
*
* @param i the index of the element to be removed
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size)
*/
public void removeReplacedElement(int i) {
if (!isSetListOfReplacedElements()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
getListOfReplacedElements().remove(i);
}
/**
* Creates a new {@link ReplacedElement} element and adds it to the ListOfReplacedElements list.
*
* @return a new {@link ReplacedElement} element.
*/
public ReplacedElement createReplacedElement() {
ReplacedElement replacedElement = new ReplacedElement();
addReplacedElement(replacedElement);
return replacedElement;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.SBasePlugin#readAttribute(java.lang.String, java.lang.String, java.lang.String)
*/
@Override
public boolean readAttribute(String attributeName, String prefix,
String value)
{
return false; // no new attributes defined
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.SBasePlugin#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes()
{
// no new attributes defined
return new TreeMap();
}
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getAllowsChildren()
*/
@Override
public boolean getAllowsChildren() {
return true;
}
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getChildCount()
*/
@Override
public int getChildCount() {
int count = 0;
if (isSetListOfReplacedElements()) {
count++;
}
if (isSetReplacedBy()) {
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 (isSetListOfReplacedElements()) {
if (pos == index) {
return getListOfReplacedElements();
}
pos++;
}
if (isSetReplacedBy()) {
if (pos == index) {
return getReplacedBy();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
}