org.sbml.jsbml.ext.spatial.AnalyticGeometry 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.spatial;
import java.text.MessageFormat;
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.util.filters.NameFilter;
/**
* @author Alex Thomas
* @author Andreas Dräger
* @author Piero Dalle Pezze
* @since 1.0
*/
public class AnalyticGeometry extends GeometryDefinition {
/**
*
*/
private ListOf listOfAnalyticVolumes;
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -6680739495215471035L;
/**
*
*/
public AnalyticGeometry() {
super();
}
/**
* @param analyticGeometry
*/
public AnalyticGeometry(AnalyticGeometry analyticGeometry) {
super(analyticGeometry);
if (analyticGeometry.isSetListOfAnalyticVolumes()) {
setListOfAnalyticVolumes(analyticGeometry.getListOfAnalyticVolumes().clone());
}
}
/**
* @param id
* @param level
* @param version
*/
public AnalyticGeometry(String id, int level, int version) {
super(id,level,version);
}
/*
* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#clone()
*/
@Override
public AnalyticGeometry clone() {
return new AnalyticGeometry(this);
}
/**
* Returns {@code true}, if listOfAnalyticVolumes contains at least one element.
*
* @return {@code true}, if listOfAnalyticVolumes contains at least one element,
* otherwise {@code false}
*/
public boolean isSetListOfAnalyticVolumes() {
if (listOfAnalyticVolumes == null) {
return false;
}
return true;
}
/**
* Returns the listOfAnalyticVolumes. Creates it if it is not already existing.
*
* @return the listOfAnalyticVolumes
*/
public ListOf getListOfAnalyticVolumes() {
if (!isSetListOfAnalyticVolumes()) {
listOfAnalyticVolumes = new ListOf();
listOfAnalyticVolumes.setNamespace(SpatialConstants.namespaceURI);
listOfAnalyticVolumes.setSBaseListType(ListOf.Type.other);
registerChild(listOfAnalyticVolumes);
}
return listOfAnalyticVolumes;
}
/**
* Sets the given {@code ListOf}. If listOfAnalyticVolumes
* was defined before and contains some elements, they are all unset.
*
* @param listOfAnalyticVolumes
*/
public void setListOfAnalyticVolumes(ListOf listOfAnalyticVolumes) {
unsetListOfAnalyticVolumes();
this.listOfAnalyticVolumes = listOfAnalyticVolumes;
registerChild(this.listOfAnalyticVolumes);
}
/**
* Returns {@code true}, if listOfAnalyticVolumes contain at least one element,
* otherwise {@code false}
*
* @return {@code true}, if listOfAnalyticVolumes contain at least one element,
* otherwise {@code false}
*/
public boolean unsetListOfAnalyticVolumes() {
if (isSetListOfAnalyticVolumes()) {
ListOf oldAnalyticVolumes = listOfAnalyticVolumes;
listOfAnalyticVolumes = null;
oldAnalyticVolumes.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Adds a new {@link AnalyticVolume} to the listOfAnalyticVolumes.
* The listOfAnalyticVolumes is initialized if necessary.
*
* @param analyticVolume the element to add to the list
* @return {@code true} (as specified by {@link java.util.Collection#add})
*/
public boolean addAnalyticVolume(AnalyticVolume analyticVolume) {
return getListOfAnalyticVolumes().add(analyticVolume);
}
/**
* Removes an element from the listOfAnalyticVolumes.
*
* @param analyticVolume the element to be removed from the list
* @return {@code true} if the list contained the specified element
* @see java.util.List#remove(Object)
*/
public boolean removeAnalyticVolume(AnalyticVolume analyticVolume) {
if (isSetListOfAnalyticVolumes()) {
if (getListOfAnalyticVolumes().size()<=1) {
return false; //There must be at least one AnalyticVolume defined for this list
} else {
return getListOfAnalyticVolumes().remove(analyticVolume);
}
}
return false;
}
/**
* Removes an element from the listOfAnalyticVolumes at the given index.
*
* @param i the index where to remove the {@link AnalyticVolume}
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size).
*/
public void removeAnalyticVolume(int i) {
if (!isSetListOfAnalyticVolumes()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
if (getListOfAnalyticVolumes().size()<=1) {
throw new SBMLException("There must be at least one AnalyticVolume defined for this list");
}
getListOfAnalyticVolumes().remove(i);
}
/**
*
* @param id
*/
public void removeAnalyticVolume(String id) {
getListOfAnalyticVolumes().removeFirst(new NameFilter(id));
}
/**
* Creates a new AnalyticVolume element and adds it to the ListOfAnalyticVolumes list
* @return
*/
public AnalyticVolume createAnalyticVolume() {
return createAnalyticVolume(null);
}
/**
* Creates a new {@link AnalyticVolume} element and adds it to the ListOfAnalyticVolumes list
*
* @param id
* @return a new {@link AnalyticVolume} element
*/
public AnalyticVolume createAnalyticVolume(String id) {
AnalyticVolume analyticVolume = new AnalyticVolume(id, getLevel(), getVersion());
addAnalyticVolume(analyticVolume);
return analyticVolume;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#getAllowsChildren()
*/
@Override
public boolean getAllowsChildren() {
return true;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#getChildCount()
*/
@Override
public int getChildCount() {
int count = super.getChildCount();
if (isSetListOfAnalyticVolumes()) {
count++;
}
return count;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#getChildAt(int)
*/
@Override
public TreeNode getChildAt(int index) {
if (index < 0) {
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexSurpassesBoundsException"), index, 0));
}
int count = super.getChildCount(), pos = 0;
if (index < count) {
return super.getChildAt(index);
} else {
index -= count;
}
if (isSetListOfAnalyticVolumes()) {
if (pos == index) {
return getListOfAnalyticVolumes();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.GeometryDefinition#equals(java.lang.Object)
*/
@Override
public boolean equals(Object object) {
boolean equal = super.equals(object);
if (equal) {
AnalyticGeometry gm = (AnalyticGeometry) object;
equal &= gm.isSetListOfAnalyticVolumes() == isSetListOfAnalyticVolumes();
if (equal && isSetListOfAnalyticVolumes()) {
equal &= gm.getListOfAnalyticVolumes().equals(getListOfAnalyticVolumes());
}
}
return equal;
}
@Override
public int hashCode() {
final int prime = 1039;//Change this prime number
int hashCode = super.hashCode();
if (isSetListOfAnalyticVolumes()) {
hashCode += prime * getListOfAnalyticVolumes().hashCode();
}
return hashCode;
}
}