org.sbml.jsbml.ext.comp.CompModelPlugin 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.HashMap;
import java.util.List;
import java.util.Map;
import javax.swing.tree.TreeNode;
import org.apache.log4j.Logger;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.SBase;
import org.sbml.jsbml.util.IdManager;
import org.sbml.jsbml.util.filters.NameFilter;
/**
* Adds two lists, one for holding {@link Submodel}s and the other for holding {@link Port}s.
*
* @author Nicolas Rodriguez
* @since 1.0
*/
public class CompModelPlugin extends CompSBasePlugin implements IdManager {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = 7104644706063096211L;
/**
* A {@link Logger} for this class.
*/
private static final transient Logger logger = Logger.getLogger(CompModelPlugin.class);
/**
*
*/
private ListOf listOfPorts;
/**
*
*/
private ListOf listOfSubmodels;
/**
* Maps between the {@link Port} identifiers and themselves.
*/
private Map mapOfPorts;
/**
* Creates a new {@link CompModelPlugin} instance that is a copy of the current {@link CompModelPlugin}.
*
* @param obj the {@link CompModelPlugin} to clone.
*/
public CompModelPlugin(CompModelPlugin obj) {
super(obj);
if (obj.isSetListOfSubmodels()) {
setListOfSubmodels(obj.getListOfSubmodels().clone());
}
if (obj.isSetListOfPorts()) {
setListOfPorts(obj.getListOfPorts().clone());
}
}
/**
* Creates a new {@link CompModelPlugin} instance, associated with the given {@link Model}
*
* @param model the extended core {@link Model}
*/
public CompModelPlugin(Model model) {
super(model);
}
/**
* Adds a new {@link Port} to the listOfPorts.
* The listOfPorts is initialized if necessary.
*
* @param port the element to add to the list
* @return {@code true} (as specified by {@link java.util.Collection#add})
*/
public boolean addPort(Port port) {
return getListOfPorts().add(port);
}
/**
* Adds a new {@link Submodel} to the listOfSubmodels.
*
The listOfSubmodels is initialized if necessary.
*
* @param submodel the element to add to the list
* @return {@code true} (as specified by {@link java.util.Collection#add})
*/
public boolean addSubmodel(Submodel submodel) {
return getListOfSubmodels().add(submodel);
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.comp.CompSBasePlugin#clone()
*/
@Override
public CompModelPlugin clone() {
return new CompModelPlugin(this);
}
/* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
final int prime = 3371;
int result = super.hashCode();
result = prime * result
+ ((listOfPorts == null) ? 0 : listOfPorts.hashCode());
result = prime * result
+ ((listOfSubmodels == null) ? 0 : listOfSubmodels.hashCode());
result = prime * result
+ ((mapOfPorts == null) ? 0 : mapOfPorts.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;
}
CompModelPlugin other = (CompModelPlugin) obj;
if (listOfPorts == null) {
if (other.listOfPorts != null) {
return false;
}
} else if (!listOfPorts.equals(other.listOfPorts)) {
return false;
}
if (listOfSubmodels == null) {
if (other.listOfSubmodels != null) {
return false;
}
} else if (!listOfSubmodels.equals(other.listOfSubmodels)) {
return false;
}
if (mapOfPorts == null) {
if (other.mapOfPorts != null) {
return false;
}
} else if (!mapOfPorts.equals(other.mapOfPorts)) {
return false;
}
return true;
}
/**
* Creates a new {@link Port} element and adds it to the ListOfPorts list
*
* @return a new {@link Port} instance.
*/
public Port createPort() {
return createPort(null);
}
/**
* Creates a new {@link Port} element and adds it to the ListOfPorts list
*
* @param id the id
* @return a new {@link Port} element
*/
public Port createPort(String id) {
Port port = new Port(id);
addPort(port);
return port;
}
/**
* Creates a new {@link Submodel} element and adds it to the ListOfSubmodels list
*
* @return a new {@link Submodel} element
*/
public Submodel createSubmodel() {
return createSubmodel(null);
}
/**
* Creates a new {@link Submodel} element and adds it to the ListOfSubmodels
* list
*
* @param id the id
* @return a new {@link Submodel} element
*/
public Submodel createSubmodel(String id) {
Submodel submodel = new Submodel(id);
addSubmodel(submodel);
return submodel;
}
/**
* Returns a {@link Port} element that has the given 'id' within
* this {@link Model} or {@code null} if no such element can be found.
*
* @param id
* an id indicating a {@link Port} element of the
* {@link Model}.
* @return a {@link Port} element of the {@link Model} that has
* the given 'id' as id or {@code null} if no element with this
* 'id' can be found.
*/
public Port findPort(String id) {
return mapOfPorts == null ? null : mapOfPorts.get(id);
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.comp.CompSBasePlugin#getAllowsChildren()
*/
@Override
public boolean getAllowsChildren() {
return true;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.comp.CompSBasePlugin#getChildAt(int)
*/
@Override
public TreeNode getChildAt(int childIndex) {
if (childIndex < 0) {
throw new IndexOutOfBoundsException(MessageFormat.format(resourceBundle.getString("IndexSurpassesBoundsException"), childIndex, 0));
}
int pos = 0;
if (isSetListOfSubmodels()) {
if (pos == childIndex) {
return getListOfSubmodels();
}
pos++;
}
if (isSetListOfPorts()) {
if (pos == childIndex) {
return getListOfPorts();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"),
childIndex, Math.min(pos, 0)));
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.comp.CompSBasePlugin#getChildCount()
*/
@Override
public int getChildCount()
{
int count = 0;
if (isSetListOfSubmodels()) {
count++;
}
if (isSetListOfPorts()) {
count++;
}
return count;
}
/**
* Returns the listOfPorts. Creates it if it is not already existing.
*
* @return the listOfPorts
*/
public ListOf getListOfPorts() {
if (!isSetListOfPorts()) {
if (extendedSBase != null) {
listOfPorts = new ListOf(extendedSBase.getLevel(),
extendedSBase.getVersion());
} else {
listOfPorts = new ListOf();
}
listOfPorts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfPorts.setPackageName(null);
listOfPorts.setPackageName(CompConstants.shortLabel);
listOfPorts.setSBaseListType(ListOf.Type.other);
listOfPorts.setOtherListName(CompConstants.listOfPorts);
if (extendedSBase != null) {
extendedSBase.registerChild(listOfPorts);
}
}
return listOfPorts;
}
/**
* Returns the listOfSubmodels. Creates it if it is not already existing.
*
* @return the listOfSubmodels
*/
public ListOf getListOfSubmodels() {
if (!isSetListOfSubmodels()) {
if (extendedSBase != null) {
listOfSubmodels = new ListOf(extendedSBase.getLevel(),
extendedSBase.getVersion());
} else {
listOfSubmodels = new ListOf();
}
listOfSubmodels.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfSubmodels.setPackageName(null);
listOfSubmodels.setPackageName(CompConstants.shortLabel);
listOfSubmodels.setSBaseListType(ListOf.Type.other);
listOfSubmodels.setOtherListName(CompConstants.listOfSubmodels);
if (extendedSBase != null) {
extendedSBase.registerChild(listOfSubmodels);
}
}
return listOfSubmodels;
}
/**
* Returns the number of {@link Port} of this {@link CompModelPlugin}.
*
* @return the number of {@link Port} of this {@link CompModelPlugin}.
* @libsbml.deprecated use {@link #getPortCount()}
*/
public int getNumPorts() {
return getPortCount();
}
/**
* Returns the number of {@link Submodel} of this {@link CompModelPlugin}.
*
* @return the number of {@link Submodel} of this {@link CompModelPlugin}.
* @libsbml.deprecated use {@link #getSubmodelCount()}
*/
public int getNumSubmodels() {
return getSubmodelCount();
}
/**
* Returns the n-th {@link Port} object in this {@link CompModelPlugin}.
*
* @param index an index
* @return the {@link Port} with the given index if it exists.
* @throws IndexOutOfBoundsException if the index is out of range: {@code (index < 0 || index >= size())}
*/
public Port getPort(int index) {
return getListOfPorts().get(index);
}
/**
* Returns a {@link Port} element that has the given 'id' within
* this {@link CompModelPlugin} or {@code null} if no such element can be found.
*
* @param id
* an id indicating a {@link Port} element of the
* {@link CompModelPlugin}.
* @return a {@link Port} element of the {@link CompModelPlugin} that has
* the given 'id' as id or {@code null} if no element with this
* 'id' can be found.
*/
public Port getPort(String id) {
// not using the mapsOfPorts as it can be null when using a cloned instance
return getListOfPorts().get(id);
}
/**
* Returns the number of {@link Port} objects in this {@link CompModelPlugin}.
*
* @return the number of {@link Port} objects in this {@link CompModelPlugin}.
*/
public int getPortCount() {
if (!isSetListOfPorts()) {
return 0;
}
return getListOfPorts().size();
}
/**
* Returns the n-th {@link Submodel} object in this {@link CompModelPlugin}.
*
* @param index an index
* @return the {@link Submodel} with the given index if it exists.
* @throws IndexOutOfBoundsException if the index is out of range: {@code (index < 0 || index >= size())}
*/
public Submodel getSubmodel(int index) {
return getListOfSubmodels().get(index);
}
/**
* Returns a {@link Submodel} element that has the given 'id' within
* this {@link CompModelPlugin} or {@code null} if no such element can be found.
*
* @param id
* an id indicating a {@link Submodel} element of the
* {@link CompModelPlugin}.
* @return a {@link Submodel} element of the {@link CompModelPlugin} that has
* the given 'id' as id or {@code null} if no element with this
* 'id' can be found.
*/
public Submodel getSubmodel(String id) {
return getListOfSubmodels().get(id);
}
/**
* Returns the number of {@link Submodel} objects in this {@link CompModelPlugin}.
*
* @return the number of {@link Submodel} objects in this {@link CompModelPlugin}.
*/
public int getSubmodelCount() {
if (!isSetListOfSubmodels()) {
return 0;
}
return getListOfSubmodels().size();
}
/**
* Returns {@code true}, if listOfPorts contains at least one element.
*
* @return {@code true}, if listOfPorts contains at least one element,
* otherwise {@code false}
*/
public boolean isSetListOfPorts() {
if ((listOfPorts == null) || listOfPorts.isEmpty()) {
return false;
}
return true;
}
/**
* Returns {@code true}, if listOfSubmodels contains at least one element.
*
* @return {@code true}, if listOfSubmodels contains at least one element,
* otherwise {@code false}
*/
public boolean isSetListOfSubmodels() {
if ((listOfSubmodels == null) || listOfSubmodels.isEmpty()) {
return false;
}
return true;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.comp.CompSBasePlugin#readAttribute(java.lang.String, java.lang.String, java.lang.String)
*/
@Override
public boolean readAttribute(String attributeName, String prefix, String value) {
return false;
}
/**
* Removes an element from the listOfPorts at the given index.
*
* @param i the index where to remove the {@link Port}
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size)
*/
public void removePort(int i) {
if (!isSetListOfPorts()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
getListOfPorts().remove(i);
}
/**
* Removes an element from the listOfPorts.
*
* @param port 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 removePort(Port port) {
if (isSetListOfPorts()) {
return getListOfPorts().remove(port);
}
return false;
}
/**
* Removes an element from the listOfSubmodels at the given index.
*
* @param i the index where to remove the {@link Submodel}
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size)
*/
public void removeSubmodel(int i) {
if (!isSetListOfSubmodels()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
getListOfSubmodels().remove(i);
}
/**
* Removes an element from the listOfSubmodels.
*
* @param id the id of 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 removeSubmodel(String id) {
Submodel removedSM = getListOfSubmodels().removeFirst(new NameFilter(id));
if (removedSM != null) {
return true;
}
return false;
}
/**
* Removes an element from the listOfSubmodels.
*
* @param submodel 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 removeSubmodel(Submodel submodel) {
if (isSetListOfSubmodels()) {
return getListOfSubmodels().remove(submodel);
}
return false;
}
/**
* Sets the optional {@code ListOf}. If listOfPorts
* was defined before and contains some elements, they are all unset.
*
* @param listOfPorts the list of {@link Port}s.
*/
public void setListOfPorts(ListOf listOfPorts) {
unsetListOfPorts();
this.listOfPorts = listOfPorts;
if ((this.listOfPorts != null)) {
listOfPorts.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfPorts.setPackageName(null);
listOfPorts.setPackageName(CompConstants.shortLabel);
listOfPorts.setSBaseListType(ListOf.Type.other);
listOfPorts.setOtherListName(CompConstants.listOfPorts);
}
if (extendedSBase != null) {
extendedSBase.registerChild(this.listOfPorts);
}
}
/**
* Sets the optional {@code ListOf}. If listOfSubmodels
* was defined before and contains some elements, they are all unset.
*
* @param listOfSubmodels the list of {@link Submodel}s.
*/
public void setListOfSubmodels(ListOf listOfSubmodels) {
unsetListOfSubmodels();
this.listOfSubmodels = listOfSubmodels;
if ((this.listOfSubmodels != null)) {
listOfSubmodels.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfSubmodels.setPackageName(null);
listOfSubmodels.setPackageName(CompConstants.shortLabel);
listOfSubmodels.setSBaseListType(ListOf.Type.other);
listOfSubmodels.setOtherListName(CompConstants.listOfSubmodels);
}
if (extendedSBase != null) {
extendedSBase.registerChild(this.listOfSubmodels);
}
}
/**
* Returns {@code true}, if listOfPorts contain at least one element,
* otherwise {@code false}
*
* @return {@code true}, if listOfPorts contain at least one element,
* otherwise {@code false}
*/
public boolean unsetListOfPorts() {
if (isSetListOfPorts()) {
ListOf oldPorts = listOfPorts;
listOfPorts = null;
oldPorts.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Returns {@code true}, if listOfSubmodels contain at least one element,
* otherwise {@code false}
*
* @return {@code true}, if listOfSubmodels contain at least one element,
* otherwise {@code false}
*/
public boolean unsetListOfSubmodels() {
if (isSetListOfSubmodels()) {
ListOf oldSubmodels = listOfSubmodels;
listOfSubmodels = null;
oldSubmodels.fireNodeRemovedEvent();
return true;
}
return false;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.ext.comp.CompSBasePlugin#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
return null;
}
@Override
public boolean accept(SBase sbase) {
// System.out.println("DEBUG : CompModelPlugin accept method called !!");
return sbase instanceof Port;
}
@Override
public boolean register(SBase sbase) {
boolean success = true;
if (sbase instanceof Port) {
Port port = (Port) sbase;
if (port.isSetId()) {
String portId = port.getId();
if (mapOfPorts == null) {
mapOfPorts = new HashMap();
}
if (mapOfPorts.containsKey(portId) && mapOfPorts.get(portId) != sbase) {
logger.error(MessageFormat.format(
"A Port with the id \"{0}\" is already present in this model {1}. The new element will not be added to the model.",
portId, (isSetExtendedSBase() ? ((Model) getExtendedSBase()).getId() : "")));
success = false;
} else {
mapOfPorts.put(portId, port);
if (logger.isDebugEnabled()) {
logger.debug(MessageFormat.format("registered port id={0} in model {1}",
portId, (isSetExtendedSBase() ? ((Model) getExtendedSBase()).getId() : "")));
}
}
}
} else {
logger.error(MessageFormat.format(
"Trying to register something that is not a Port: \"{0}\".", sbase));
}
// TODO : register all the Port children if any !!
return success;
}
@Override
public boolean unregister(SBase sbase) {
// Always returning true at the moment to avoid exception when unregistering element
boolean success = true;
if (sbase instanceof Port) {
Port port = (Port) sbase;
if (port.isSetId()) {
String portId = port.getId();
if (mapOfPorts == null) {
logger.warn(MessageFormat.format(
"No Port have been registered in this model {0}. Nothing to be done.",
(isSetExtendedSBase() ? ((Model) getExtendedSBase()).getId() : "")));
return success;
}
if (mapOfPorts.containsKey(portId)) {
mapOfPorts.remove(portId);
if (logger.isDebugEnabled()) {
logger.debug(MessageFormat.format("unregistered port id={0} in model {1}",
portId, (isSetExtendedSBase() ? ((Model) getExtendedSBase()).getId() : "")));
}
} else {
logger.warn(MessageFormat.format(
"A Port with the id \"{0}\" is not present in this model {1}. Nothing to be done.",
portId, (isSetExtendedSBase() ? ((Model) getExtendedSBase()).getId() : "")));
}
}
} else {
logger.error(MessageFormat.format(
"Trying to unregister something that is not a Port: \"{0}\".", sbase));
}
// TODO : unregister all the Port children if any !!
return success;
}
}