org.sbml.jsbml.ext.spatial.Domain 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 java.util.Map;
import javax.swing.tree.TreeNode;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.SBMLException;
/**
* @author Alex Thomas
* @author Andreas Dräger
* @since 1.0
*/
public class Domain extends AbstractSpatialNamedSBase {
/**
* A {@link Logger} for this class.
*/
private static final transient Logger logger = Logger.getLogger(Domain.class);
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 7959434109047369076L;
/**
*
*/
private String domainType;
/**
*
*/
private ListOf listOfInteriorPoints;
/**
*
*/
public Domain() {
super();
}
/**
* @param level
* @param version
*/
public Domain(int level, int version) {
super(level, version);
}
/**
* @param id
* @param level
* @param version
*/
public Domain(String id, int level, int version) {
super(id,level,version);
}
/**
* @param dm
*/
public Domain(Domain dm) {
super(dm);
if (dm.isSetListOfInteriorPoints()) {
setListOfInteriorPoints(dm.getListOfInteriorPoints().clone());
}
if (dm.isSetDomainType()) {
setDomainType(dm.getDomainType());
}
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#clone()
*/
@Override
public Domain clone() {
return new Domain(this);
}
/**
* Returns the value of domainType
*
* @return the value of domainType
*/
public String getDomainType() {
if (isSetDomainType()) {
return domainType;
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(SpatialConstants.domainType, this);
}
/**
* Returns whether domainType is set
*
* @return whether domainType is set
*/
public boolean isSetDomainType() {
return domainType != null;
}
/**
* Sets the value of domainType
* @param domainType
*/
public void setDomainType(String domainType) {
String oldDomainType = this.domainType;
this.domainType = domainType;
firePropertyChange(SpatialConstants.domainType, oldDomainType, this.domainType);
}
/**
* Unsets the variable domainType
*
* @return {@code true}, if domainType was set before,
* otherwise {@code false}
*/
public boolean unsetDomainType() {
if (isSetDomainType()) {
String oldDomainType = domainType;
domainType = null;
firePropertyChange(SpatialConstants.domainType, oldDomainType, domainType);
return true;
}
return false;
}
/**
* Returns {@code true}, if listOfInteriorPoints contains at least one element.
*
* @return {@code true}, if listOfInteriorPoints contains at least one element,
* otherwise {@code false}
*/
public boolean isSetListOfInteriorPoints() {
if (listOfInteriorPoints == null) {
return false;
}
return true;
}
/**
* Returns the listOfInteriorPoints. Creates it if it is not already existing.
*
* @return the listOfInteriorPoints
*/
public ListOf getListOfInteriorPoints() {
if (!isSetListOfInteriorPoints()) {
listOfInteriorPoints = new ListOf();
listOfInteriorPoints.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfInteriorPoints.setPackageName(null);
listOfInteriorPoints.setPackageName(SpatialConstants.shortLabel);
listOfInteriorPoints.setSBaseListType(ListOf.Type.other);
registerChild(listOfInteriorPoints);
}
return listOfInteriorPoints;
}
/**
* Sets the given {@code ListOf}. If listOfInteriorPoints
* was defined before and contains some elements, they are all unset.
*
* @param listOfInteriorPoints
*/
public void setListOfInteriorPoints(ListOf listOfInteriorPoints) {
unsetListOfInteriorPoints();
this.listOfInteriorPoints = listOfInteriorPoints;
if (listOfInteriorPoints != null) {
listOfInteriorPoints.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'spatial'
listOfInteriorPoints.setPackageName(null);
listOfInteriorPoints.setPackageName(SpatialConstants.shortLabel);
listOfInteriorPoints.setSBaseListType(ListOf.Type.other);
registerChild(this.listOfInteriorPoints);
}
}
/**
* Returns {@code true}, if listOfInteriorPoints contain at least one element,
* otherwise {@code false}
*
* @return {@code true}, if listOfInteriorPoints contain at least one element,
* otherwise {@code false}
*/
public boolean unsetListOfInteriorPoints() {
if (isSetListOfInteriorPoints()) {
ListOf oldInteriorPoints = listOfInteriorPoints;
listOfInteriorPoints = null;
oldInteriorPoints.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Adds a new {@link InteriorPoint} to the listOfInteriorPoints.
* The listOfInteriorPoints is initialized if necessary.
*
* @param interiorPoint the element to add to the list
* @return {@code true} (as specified by {@link java.util.Collection#add})
*/
public boolean addInteriorPoint(InteriorPoint interiorPoint) {
return getListOfInteriorPoints().add(interiorPoint);
}
/**
* Removes an element from the listOfInteriorPoints.
*
* @param interiorPoint 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 removeInteriorPoint(InteriorPoint interiorPoint) {
if (isSetListOfInteriorPoints()) {
if (getListOfInteriorPoints().size()<=1) {
return false; // There must be at least one InteriorPoint defined in this list
}
else {
return getListOfInteriorPoints().remove(interiorPoint);
}
}
return false;
}
/**
* Removes an element from the listOfInteriorPoints at the given index.
*
* @param i the index where to remove the {@link InteriorPoint}
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size).
*/
public void removeInteriorPoint(int i) {
if (!isSetListOfInteriorPoints()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
if (getListOfInteriorPoints().size()<=1) {
throw new SBMLException("There must be at least one InteriorPoint defined for this list");
}
getListOfInteriorPoints().remove(i);
}
/**
* Creates a new {@link InteriorPoint} element and adds it to the ListOfInteriorPoints list
*
* @return a new {@link InteriorPoint} element
*/
public InteriorPoint createInteriorPoint() {
InteriorPoint interiorPoint = new InteriorPoint(getLevel(), getVersion());
addInteriorPoint(interiorPoint);
return interiorPoint;
}
/*
* (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 (isSetListOfInteriorPoints()) {
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 (isSetListOfInteriorPoints()) {
if (pos == index) {
return getListOfInteriorPoints();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
/*
* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#hashCode()
*/
@Override
public int hashCode() {
final int prime = 1571;
int hashCode = super.hashCode();
if (isSetDomainType()) {
hashCode += prime * getDomainType().hashCode();
}
if (isSetListOfInteriorPoints()) {
hashCode += prime * getListOfInteriorPoints().hashCode();
}
return hashCode;
}
/*
* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetDomainType()) {
attributes.remove("domainType");
attributes.put(SpatialConstants.shortLabel + ":domainType", getDomainType());
}
return attributes;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.spatial.AbstractSpatialNamedSBase#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(SpatialConstants.domainType)) {
try {
setDomainType(value);
} catch (Exception e) {
logger.warn(MessageFormat.format(
SpatialConstants.bundle.getString("COULD_NOT_READ_ATTRIBUTE"), value, SpatialConstants.domainType, getElementName()));
}
}
else {
isAttributeRead = false;
}
}
return isAttributeRead;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#equals(java.lang.Object)
*/
@Override
public boolean equals(Object object) {
boolean equal = super.equals(object);
if (equal) {
Domain dm = (Domain) object;
equal &= dm.isSetDomainType() == isSetDomainType();
if (equal && isSetDomainType()) {
equal &= dm.getDomainType().equals(getDomainType());
}
equal &= dm.isSetListOfInteriorPoints() == isSetListOfInteriorPoints();
if (equal && isSetListOfInteriorPoints()) {
equal &= dm.getListOfInteriorPoints().equals(getListOfInteriorPoints());
}
}
return equal;
}
}