org.sbml.jsbml.ext.spatial.SpatialModelPlugin Maven / Gradle / Ivy
The newest version!
/*
* ----------------------------------------------------------------------------
* 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.HashMap;
import java.util.Map;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.SBase;
import org.sbml.jsbml.util.IdManager;
/**
* @author Alex Thomas
* @since 1.0
*/
public class SpatialModelPlugin extends AbstractSpatialSBasePlugin implements IdManager {
/**
* Generated serial version ID
*/
private static final long serialVersionUID = 8449591192464040411L;
/**
*
*/
private Geometry geometry;
/**
*
*/
private Map spatialIdMap;
/**
* A logger for this class.
*/
private static final transient Logger logger = Logger.getLogger(SpatialModelPlugin.class);
/**
* Returns the value of geometry
*
* @return the value of geometry
*/
public Geometry getGeometry() {
if (isSetGeometry()) {
return geometry;
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(SpatialConstants.geometry, this);
}
/**
* Creates a new {@link Geometry}, adds it to this object
* and returns a pointer to it.
*
* @return a new {@link Geometry} object.
*
*/
public Geometry createGeometry() {
Geometry geometry = new Geometry();
setGeometry(geometry);
return geometry;
}
/**
* Returns whether geometry is set
*
* @return whether geometry is set
*/
public boolean isSetGeometry() {
return geometry != null;
}
/**
* Sets the value of geometry
* @param geometry
*/
public void setGeometry(Geometry geometry) {
Geometry oldGeometry = this.geometry;
this.geometry = geometry;
if (isSetExtendedSBase()) {
getExtendedSBase().registerChild(geometry);
}
firePropertyChange(SpatialConstants.geometry, oldGeometry, this.geometry);
}
/**
* Unsets the variable geometry
*
* @return {@code true}, if geometry was set before,
* otherwise {@code false}
*/
public boolean unsetGeometry() {
if (isSetGeometry()) {
Geometry oldGeometry = geometry;
geometry = null;
firePropertyChange(SpatialConstants.geometry, oldGeometry, geometry);
return true;
}
return false;
}
/**
*
*/
public SpatialModelPlugin() {
super();
}
/**
* @param model
*/
public SpatialModelPlugin(Model model) {
super(model);
}
/**
* @param spatialModelPlugin
*/
public SpatialModelPlugin(SpatialModelPlugin spatialModelPlugin) {
super(spatialModelPlugin);
if (spatialModelPlugin.isSetGeometry()) {
setGeometry(spatialModelPlugin.getGeometry().clone());
}
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.AbstractSBasePlugin#getExtendedSBase()
*/
@Override
public Model getExtendedSBase() {
if (isSetExtendedSBase()) {
return (Model) super.getExtendedSBase();
}
return null;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.AbstractSBasePlugin#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
return null;
}
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getAllowsChildren()
*/
@Override
public boolean getAllowsChildren() {
return true;
}
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getChildAt(int)
*/
@Override
public Geometry getChildAt(int index) {
if (index < 0) {
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexSurpassesBoundsException"), index, 0));
}
int pos = 0;
if (isSetGeometry()) {
if (pos == index) {
return getGeometry();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"),
index, pos));
}
/* (non-Javadoc)
* @see javax.swing.tree.TreeNode#getChildCount()
*/
@Override
public int getChildCount() {
return isSetGeometry() ? 1 : 0;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.AbstractSBasePlugin#clone()
*/
@Override
public SpatialModelPlugin clone() {
return new SpatialModelPlugin(this);
}
/* (non-Javadoc)
* @see org.sbml.jsbml.util.IdManager#accept(org.sbml.jsbml.SBase)
*/
@Override
public boolean accept(SBase sbase) {
if (logger.isDebugEnabled()) {
logger.debug(MessageFormat.format("accept called on {0}", sbase.getElementName()));
}
if (sbase instanceof SpatialNamedSBase) {
return true;
}
if (sbase instanceof ListOf) {
ListOf listOf = (ListOf) sbase;
if ((listOf.size() > 0) && (listOf.get(0) instanceof SpatialNamedSBase)) {
return true;
}
}
return false;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.util.IdManager#register(org.sbml.jsbml.SBase)
*/
@Override
public boolean register(SBase sbase) {
boolean success = true;
if (sbase instanceof SpatialNamedSBase) {
SpatialNamedSBase spatialSBase = (SpatialNamedSBase) sbase;
if (spatialSBase.isSetSpatialId()) {
String id = spatialSBase.getSpatialId();
if (spatialIdMap == null) {
spatialIdMap = new HashMap();
}
if (spatialIdMap.containsKey(id)) {
logger.error(MessageFormat.format(
"The spatial id \"{0}\" is already present in the spatial model assigned to the model {1}. The new element will not be added to the model.",
id, (isSetExtendedSBase() ? getExtendedSBase().getId() : "")));
success = false;
} else {
spatialIdMap.put(id, spatialSBase);
if (logger.isDebugEnabled()) {
logger.debug(MessageFormat.format("registered spatial id={0} in {1}",
id, (isSetExtendedSBase() ? getExtendedSBase().getElementName() : "")));
}
}
}
} else {
logger.error(MessageFormat.format(
"Trying to register something that does not have a spatialId: \"{0}\".", sbase));
}
// Register all spatial model children if any
return success;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.util.IdManager#unregister(org.sbml.jsbml.SBase)
*/
@Override
public boolean unregister(SBase sbase) {
// Always returning true at the moment to avoid exception when unregistering element
boolean success = true;
if (sbase instanceof SpatialNamedSBase) {
SpatialNamedSBase spatialSbase = (SpatialNamedSBase) sbase;
if (spatialSbase.isSetSpatialId()) {
String id = spatialSbase.getSpatialId();
if (spatialIdMap == null) {
logger.warn(MessageFormat.format(
"No elements with spatial ids have been registered in this {0}. Nothing to be done.",
(isSetExtendedSBase() ? getExtendedSBase().getElementName() : "")));
return success;
}
if (spatialIdMap.containsKey(id)) {
spatialIdMap.remove(id);
if (logger.isDebugEnabled()) {
logger.debug(MessageFormat.format("unregistered spatial id={0} in {1}",
id, (isSetExtendedSBase() ? getExtendedSBase().getElementName() : "")));
}
} else {
logger.warn(MessageFormat.format(
"The spatial id \"{0}\" is not present in this model {1}. Nothing to be done.",
id, (isSetExtendedSBase() ? getExtendedSBase().getId() : "")));
}
}
} else {
logger.error(MessageFormat.format(
"Trying to unregister something that does not have a spatial id: \"{0}\".", sbase));
}
// Unregister all spatial model children if any
return success;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.AbstractSBasePlugin#hashCode()
*/
@Override
public int hashCode() {
final int prime = 2039;
int hashCode = super.hashCode();
if (isSetGeometry()) {
hashCode += prime * getGeometry().hashCode();
}
return hashCode;
}
}