org.sbml.jsbml.ext.comp.Submodel 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 javax.swing.tree.TreeNode;
import org.sbml.jsbml.AbstractNamedSBase;
import org.sbml.jsbml.LevelVersionError;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.Parameter;
import org.sbml.jsbml.PropertyUndefinedError;
import org.sbml.jsbml.UniqueNamedSBase;
import org.sbml.jsbml.util.filters.NameFilter;
/**
* {@link Submodel}s are instantiations of models contained within other models.
* Submodel instances represent submodels contained within {@link CompModelPlugin}.
*
* @author Nicolas Rodriguez
* @since 1.0
*/
public class Submodel extends AbstractNamedSBase implements UniqueNamedSBase {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -2588930216065448311L;
/**
*
*/
private String modelRef;
/**
*
*/
private String timeConversionFactor;
/**
*
*/
private String extentConversionFactor;
/**
*
*/
private ListOf listOfDeletions;
/**
* Creates an Submodel instance
*/
public Submodel() {
super();
initDefaults();
}
/**
* Creates a Submodel instance with an id.
*
* @param id the id
*/
public Submodel(String id) {
super(id);
initDefaults();
}
/**
* Creates a Submodel instance with a level and version.
*
* @param level the SBML level
* @param version the SBML version
*/
public Submodel(int level, int version) {
this(null, null, level, version);
}
/**
* Creates a Submodel instance with an id, level, and version.
*
* @param id the id
* @param level the SBML level
* @param version the SBML version
*/
public Submodel(String id, int level, int version) {
this(id, null, level, version);
}
/**
* Creates a Submodel instance with an id, name, level, and version.
*
* @param id the id
* @param name the name
* @param level the SBML level
* @param version the SBML version
*/
public Submodel(String id, String name, int level, int version) {
super(id, name, level, version);
if (getLevelAndVersion().compareTo(
Integer.valueOf(CompConstants.MIN_SBML_LEVEL),
Integer.valueOf(CompConstants.MIN_SBML_VERSION)) < 0) {
throw new LevelVersionError(getElementName(), level, version);
}
initDefaults();
}
/**
* Clone constructor
*
* @param obj the instance to clone
*/
public Submodel(Submodel obj) {
super(obj);
if (obj.isSetListOfDeletions()) {
setListOfDeletions(obj.getListOfDeletions().clone());
}
if (obj.isSetModelRef()) {
setModelRef(new String(obj.getModelRef()));
}
if (obj.isSetTimeConversionFactor()) {
setTimeConversionFactor(new String(obj.getTimeConversionFactor()));
}
if (obj.isSetExtentConversionFactor()) {
setExtentConversionFactor(new String(obj.getExtentConversionFactor()));
}
}
/**
* clones this class
*/
@Override
public Submodel clone() {
return new Submodel(this);
}
/**
* Initializes the default values using the namespace.
*/
public void initDefaults() {
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
/* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
final int prime = 31;
int result = super.hashCode();
result = prime
* result
+ ((extentConversionFactor == null) ? 0
: extentConversionFactor.hashCode());
result = prime * result
+ ((listOfDeletions == null) ? 0 : listOfDeletions.hashCode());
result = prime * result + ((modelRef == null) ? 0 : modelRef.hashCode());
result = prime * result
+ ((timeConversionFactor == null) ? 0 : timeConversionFactor.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;
}
Submodel other = (Submodel) obj;
if (extentConversionFactor == null) {
if (other.extentConversionFactor != null) {
return false;
}
} else if (!extentConversionFactor.equals(other.extentConversionFactor)) {
return false;
}
if (listOfDeletions == null) {
if (other.listOfDeletions != null) {
return false;
}
} else if (!listOfDeletions.equals(other.listOfDeletions)) {
return false;
}
if (modelRef == null) {
if (other.modelRef != null) {
return false;
}
} else if (!modelRef.equals(other.modelRef)) {
return false;
}
if (timeConversionFactor == null) {
if (other.timeConversionFactor != null) {
return false;
}
} else if (!timeConversionFactor.equals(other.timeConversionFactor)) {
return false;
}
return true;
}
@Override
public boolean isIdMandatory() {
return true;
}
/**
* Returns the value of modelRef
*
* @return the value of modelRef
*/
public String getModelRef() {
if (isSetModelRef()) {
return modelRef;
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(CompConstants.modelRef, this);
}
/**
* Returns whether modelRef is set
*
* @return whether modelRef is set
*/
public boolean isSetModelRef() {
return modelRef != null;
}
/**
* Sets the value of the required modelRef
*
* The whole purpose of a {@link Submodel} object
* is to instantiate a model definition, which is
* to say, either a {@link Model} object defined
* in the same enclosing SBML document, or a model
* defined in an external SBML document. The modelRef
* attribute is the means by which that model is
* identified. This required attribute must refer to
* the identifier of a Model or {@link ExternalModelDefinition}
* object within the enclosing SBML document (i.e., in the
* model namespace of the document).
*
* @param modelRef the value of modelRef
*/
public void setModelRef(String modelRef) {
String oldModelRef = this.modelRef;
this.modelRef = modelRef;
firePropertyChange(CompConstants.modelRef, oldModelRef, this.modelRef);
}
/**
* Unsets the variable modelRef
*
* @return {@code true}, if modelRef was set before,
* otherwise {@code false}
*/
public boolean unsetModelRef() {
if (isSetModelRef()) {
String oldModelRef = modelRef;
modelRef = null;
firePropertyChange(CompConstants.modelRef, oldModelRef, modelRef);
return true;
}
return false;
}
/**
* Returns the value of timeConversionFactor
*
* @return the value of timeConversionFactor
*/
public String getTimeConversionFactor() {
if (isSetTimeConversionFactor()) {
return timeConversionFactor;
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(CompConstants.timeConversionFactor, this);
}
/**
* Returns whether timeConversionFactor is set
*
* @return whether timeConversionFactor is set
*/
public boolean isSetTimeConversionFactor() {
return timeConversionFactor != null;
}
/**
* Sets the value of the optional timeConversionFactor
*
* The optional timeConversionFactor attribute is provided to allow
* references and assumptions about the scale of time in the {@link Submodel}
* to be converted to the scale of time in the containing model. If set, it
* must be the identifier of a {@link Parameter} object in the parent {@link Model}
* object. The units of that {@link Parameter} object, if present, should reduce to
* being dimensionless, and the {@link Parameter} must be constant.
*
* @param timeConversionFactor the value of timeConversionFactor
*/
public void setTimeConversionFactor(String timeConversionFactor) {
String oldTimeConversionFactor = this.timeConversionFactor;
this.timeConversionFactor = timeConversionFactor;
firePropertyChange(CompConstants.timeConversionFactor, oldTimeConversionFactor, this.timeConversionFactor);
}
/**
* Unsets the variable timeConversionFactor
*
* @return {@code true}, if timeConversionFactor was set before,
* otherwise {@code false}
*/
public boolean unsetTimeConversionFactor() {
if (isSetTimeConversionFactor()) {
String oldTimeConversionFactor = timeConversionFactor;
timeConversionFactor = null;
firePropertyChange(CompConstants.timeConversionFactor, oldTimeConversionFactor, timeConversionFactor);
return true;
}
return false;
}
/**
* Returns the value of extentConversionFactor
*
* @return the value of extentConversionFactor
*/
public String getExtentConversionFactor() {
if (isSetExtentConversionFactor()) {
return extentConversionFactor;
}
// This is necessary if we cannot return null here.
throw new PropertyUndefinedError(CompConstants.extentConversionFactor, this);
}
/**
* Returns whether extentConversionFactor is set
*
* @return whether extentConversionFactor is set
*/
public boolean isSetExtentConversionFactor() {
return extentConversionFactor != null;
}
/**
* Sets the value of the optional extentConversionFactor
*
* The optional extentConversionFactor attribute is provided to allow
* references and assumptions about the scale of a model's reaction
* extent to be converted to the scale of the containing model. If set,
* it must be the identifier of a {@link Parameter} object in the
* parent {@link Model} object. The units of that {@link Parameter}
* object, if present, should reduce to being dimensionless, and the
* {@link Parameter} must be constant.
*
* @param extentConversionFactor the value of the optional extentConversionFactor
*/
public void setExtentConversionFactor(String extentConversionFactor) {
String oldExtentConversionFactor = this.extentConversionFactor;
this.extentConversionFactor = extentConversionFactor;
firePropertyChange(CompConstants.extentConversionFactor, oldExtentConversionFactor, this.extentConversionFactor);
}
/**
* Unsets the variable extentConversionFactor
*
* @return {@code true}, if extentConversionFactor was set before,
* otherwise {@code false}
*/
public boolean unsetExtentConversionFactor() {
if (isSetExtentConversionFactor()) {
String oldExtentConversionFactor = extentConversionFactor;
extentConversionFactor = null;
firePropertyChange(CompConstants.extentConversionFactor, oldExtentConversionFactor, extentConversionFactor);
return true;
}
return false;
}
/**
* Returns {@code true}, if listOfDeletions contains at least one element.
*
* @return {@code true}, if listOfDeletions contains at least one element,
* otherwise {@code false}
*/
public boolean isSetListOfDeletions() {
if ((listOfDeletions == null) || listOfDeletions.isEmpty()) {
return false;
}
return true;
}
/**
* Returns the number of {@link Deletion} objects in this {@link Submodel}.
*
* @return the number of {@link Deletion} objects in this {@link Submodel}.
*/
public int getDeletionCount() {
if (!isSetListOfDeletions()) {
return 0;
}
return getListOfDeletions().size();
}
/**
* Returns the listOfDeletions. Creates it if it is not already existing.
*
* @return the listOfDeletions
*/
public ListOf getListOfDeletions() {
if (!isSetListOfDeletions()) {
listOfDeletions = new ListOf(getLevel(), getVersion());
listOfDeletions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfDeletions.setPackageName(null);
listOfDeletions.setPackageName(CompConstants.shortLabel);
listOfDeletions.setSBaseListType(ListOf.Type.other);
listOfDeletions.setOtherListName(CompConstants.listOfDeletions);
registerChild(listOfDeletions);
}
return listOfDeletions;
}
/**
* Sets the given {@code ListOf}.
*
* If listOfDeletions
* was defined before and contains some elements, they are all unset.
*
* This list specifies objects to be removed from the submodel when
* composing the overall model. (The "removal" is mathematical and
* conceptual, not physical.)
*
* @param listOfDeletions the list of {@link Deletion}s
*/
public void setListOfDeletions(ListOf listOfDeletions) {
unsetListOfDeletions();
this.listOfDeletions = listOfDeletions;
if ((listOfDeletions != null)) {
listOfDeletions.setSBaseListType(ListOf.Type.other);
listOfDeletions.setPackageVersion(-1);
// changing the ListOf package name from 'core' to 'comp'
listOfDeletions.setPackageName(null);
listOfDeletions.setPackageName(CompConstants.shortLabel);
listOfDeletions.setOtherListName(CompConstants.listOfDeletions);
}
registerChild(this.listOfDeletions);
}
/**
* Returns {@code true}, if listOfDeletions contain at least one element,
* otherwise {@code false}
*
* @return {@code true}, if listOfDeletions contain at least one element,
* otherwise {@code false}
*/
public boolean unsetListOfDeletions() {
if (isSetListOfDeletions()) {
ListOf oldDeletions = listOfDeletions;
listOfDeletions = null;
oldDeletions.fireNodeRemovedEvent();
return true;
}
return false;
}
/**
* Adds a new {@link Deletion} to the listOfDeletions.
* The listOfDeletions is initialized if necessary.
*
* @param deletion the element to add to the list
* @return {@code true} (as specified by {@link java.util.Collection#add})
*/
public boolean addDeletion(Deletion deletion) {
return getListOfDeletions().add(deletion);
}
/**
* Removes an element from the listOfDeletions.
*
* @param deletion 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 removeDeletion(Deletion deletion) {
if (isSetListOfDeletions()) {
return getListOfDeletions().remove(deletion);
}
return false;
}
/**
* Removes an element from the listOfDeletions at the given index.
*
* @param i the index where to remove the {@link Deletion}
* @throws IndexOutOfBoundsException if the listOf is not set or
* if the index is out of bound (index < 0 || index > list.size)
*/
public void removeDeletion(int i) {
if (!isSetListOfDeletions()) {
throw new IndexOutOfBoundsException(Integer.toString(i));
}
getListOfDeletions().remove(i);
}
/**
* Removes an element from the listOfDeletions with the given id.
*
* @param id the id of the {@link Deletion} element to remove.
*/
public void removeDeletion(String id) {
getListOfDeletions().removeFirst(new NameFilter(id));
}
/**
* Creates a new Deletion element and adds it to the ListOfDeletions list
*
* @return a new {@link Deletion} element
*/
public Deletion createDeletion() {
return createDeletion(null);
}
/**
* Creates a new {@link Deletion} element and adds it to the ListOfDeletions list
*
* @param id the id
* @return a new {@link Deletion} element
*/
public Deletion createDeletion(String id) {
Deletion deletion = new Deletion(id, getLevel(), getVersion());
addDeletion(deletion);
return deletion;
}
@Override
public boolean getAllowsChildren() {
return true;
}
@Override
public int getChildCount() {
int count = super.getChildCount();
if (isSetListOfDeletions()) {
count++;
}
return count;
}
@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 (isSetListOfDeletions()) {
if (pos == index) {
return getListOfDeletions();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (isSetId()) {
attributes.remove("id");
attributes.put(CompConstants.shortLabel + ":id", getId());
}
if (isSetName()) {
attributes.remove("name");
attributes.put(CompConstants.shortLabel + ":name", getName());
}
if (isSetModelRef()) {
attributes.put(CompConstants.shortLabel + ":" + CompConstants.modelRef, getModelRef());
}
if (isSetTimeConversionFactor()) {
attributes.put(CompConstants.shortLabel + ":" + CompConstants.timeConversionFactor, getTimeConversionFactor());
}
if (isSetExtentConversionFactor()) {
attributes.put(CompConstants.shortLabel + ":" + CompConstants.extentConversionFactor, getExtentConversionFactor());
}
return attributes;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractNamedSBase#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(CompConstants.modelRef)) {
setModelRef(value);
}
else if (attributeName.equals(CompConstants.timeConversionFactor)) {
setTimeConversionFactor(value);
}
else if (attributeName.equals(CompConstants.extentConversionFactor)) {
setExtentConversionFactor(value);
}
else {
isAttributeRead = false;
}
}
return isAttributeRead;
}
}