org.sbml.jsbml.ext.comp.SBaseRef 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 static java.text.MessageFormat.format;
import java.text.MessageFormat;
import java.util.Map;
import javax.swing.tree.TreeNode;
import org.sbml.jsbml.AbstractSBase;
import org.sbml.jsbml.UnitDefinition;
import org.sbml.jsbml.validator.SyntaxChecker;
/**
* Contains the machinery for constructing references to specific components
* within enclosed models or even within external models located in other files.
*
* The four different attributes on SBaseRef are mutually exclusive: only one of
* the attributes can have a value at any given time, and exactly one must have
* a value in a given SBaseRef object instance.
*
* @author Nicolas Rodriguez
* @since 1.0
*/
public class SBaseRef extends AbstractSBase {
/**
* Generated serial version identifier.
*/
private static final long serialVersionUID = -4434500961448381830L;
/**
* This attribute is used to refer
* to a port identifier, in the case when the reference being constructed with the SBaseRef is intended to refer to a
* port on a submodel. The namespace of the PortSIdRef value is the set of identifiers of type PortSId defined in the
* submodel, not the parent model.
*/
private String portRef;
/**
* This attribute is used to refer to
* a regular identifier (i.e., the value of an id attribute on some other object), in the case when the reference being
* constructed with the SBaseRef is intended to refer to an object that does not have a port identifier. The namespace
* of the SIdRef value is the set of identifiers of type SId defined in the submodel, not the parent model.
*/
private String idRef;
/**
* This attribute is used to refer to the identifier of a
* UnitDefinition object. The namespace of the UnitSIdRef value is the set of unit identifiers defined in the submodel,
* not the parent model.
*/
private String unitRef;
/**
* This attribute is used to refer to a metaid attribute
* value on some other object, in the case when the reference being constructed with the SBaseRef is intended to refer
* to an object that does not have a port identifier. The namespace of the metaIdRef value is the entire document in
* which the referenced model resides
*/
private String metaIdRef;
/**
* An SBaseRef object may have up to one subcomponent named sBaseRef.
* This permits recursive structures to be constructed so that objects inside submodels can be referenced.
*/
private SBaseRef sBaseRef;
/**
* Creates a {@link SBaseRef} instance.
*/
public SBaseRef() {
super();
initDefaults();
}
/**
* Creates a SBaseRef instance with a level and version.
*
* @param level the SBML level
* @param version the SBML version
*/
public SBaseRef(int level, int version) {
super(level, version);
initDefaults();
}
/**
* Clone constructor
*
* @param obj the instance to clone
*/
public SBaseRef(SBaseRef obj) {
super(obj);
if (obj.isSetPortRef()) {
setPortRef(obj.getPortRef());
}
if (obj.isSetIdRef()) {
setIdRef(obj.getIdRef());
}
if (obj.isSetUnitRef()) {
setUnitRef(obj.getUnitRef());
}
if (obj.isSetMetaIdRef()) {
setMetaIdRef(obj.getMetaIdRef());
}
if (obj.isSetSBaseRef()) {
setSBaseRef(obj.getSBaseRef().clone());
}
}
@Override
public SBaseRef clone() {
return new SBaseRef(this);
}
/**
* Initializes the default values.
*/
public void initDefaults() {
setPackageVersion(-1);
packageName = CompConstants.shortLabel;
}
/**
* Returns the value of portRef
*
* @return the value of portRef
*/
public String getPortRef() {
if (isSetPortRef()) {
return portRef;
}
return "";
}
/**
* Returns whether portRef is set
*
* @return whether portRef is set
*/
public boolean isSetPortRef() {
return portRef != null;
}
/**
* Sets the value of the optional portRef attribute.
*
*
As its name implies, this attribute is used to refer
* to a port identifier, in the case when the reference
* being constructed with the {@link SBaseRef} is
* intended to refer to a port on a submodel.
*
* @param portRef the value of portRef
*
*/
public void setPortRef(String portRef) {
if (portRef != null && portRef.trim().length() == 0) {
portRef = null;
}
if (!isReadingInProgress() && portRef != null) {
// This method will throw IllegalArgumentException if the given id does not respect the SId syntax
checkIdentifier(portRef);
}
String oldPortRef = this.portRef;
this.portRef = portRef;
firePropertyChange(CompConstants.portRef, oldPortRef, this.portRef);
}
/**
* Unsets the variable portRef
*
* @return {@code true}, if portRef was set before,
* otherwise {@code false}
*/
public boolean unsetPortRef() {
if (isSetPortRef()) {
String oldPortRef = portRef;
portRef = null;
firePropertyChange(CompConstants.portRef, oldPortRef, portRef);
return true;
}
return false;
}
/**
* Returns the value of idRef
*
* @return the value of idRef
*/
public String getIdRef() {
if (isSetIdRef()) {
return idRef;
}
return "";
}
/**
* Returns whether idRef is set
*
* @return whether idRef is set
*/
public boolean isSetIdRef() {
return idRef != null;
}
/**
* Sets the value of the optional idRef attribute.
*
* As its name implies, this attribute is used to
* refer to a regular identifier (i.e., the value of
* an id attribute on some other object), in the case
* when the reference being constructed with the
* {@link SBaseRef} is intended to refer to an object
* that does not have a port identifier.
*
* @param idRef the value of idRef
*
*/
public void setIdRef(String idRef) {
if (idRef != null && idRef.trim().length() == 0) {
idRef = null;
}
if (!isReadingInProgress() && idRef != null) {
// This method will throw IllegalArgumentException if the given id does not respect the SId syntax
checkIdentifier(idRef);
}
String oldIdRef = this.idRef;
this.idRef = idRef;
firePropertyChange(CompConstants.idRef, oldIdRef, this.idRef);
}
/**
* Unsets the variable idRef
*
* @return {@code true}, if idRef was set before,
* otherwise {@code false}
*/
public boolean unsetIdRef() {
if (isSetIdRef()) {
String oldIdRef = idRef;
idRef = null;
firePropertyChange(CompConstants.idRef, oldIdRef, idRef);
return true;
}
return false;
}
/**
* Returns the value of unitRef
*
* @return the value of unitRef
*/
public String getUnitRef() {
if (isSetUnitRef()) {
return unitRef;
}
return "";
}
/**
* Returns whether unitRef is set
*
* @return whether unitRef is set
*/
public boolean isSetUnitRef() {
return unitRef != null;
}
/**
* Sets the value of the optional unitRef attribute
*
* This attribute is used to refer to the identifier of a
* {@link UnitDefinition} object. The namespace of the
* UnitSIdRef value is the set of unit identifiers defined
* in the submodel, not the parent model.
*
* Note that even though this attribute is of type UnitSIdRef,
* the reserved unit identifiers that are defined by SBML Level 3
* are not permitted as values of unitRef. Reserved unit
* identifiers may not be replaced or deleted.
*
* @param unitRef the value of unitRef
*
*/
public void setUnitRef(String unitRef) {
String oldUnitRef = this.unitRef;
this.unitRef = unitRef;
firePropertyChange(CompConstants.unitRef, oldUnitRef, this.unitRef);
}
/**
* Unsets the variable unitRef
*
* @return {@code true}, if unitRef was set before,
* otherwise {@code false}
*/
public boolean unsetUnitRef() {
if (isSetUnitRef()) {
String oldUnitRef = unitRef;
unitRef = null;
firePropertyChange(CompConstants.unitRef, oldUnitRef, unitRef);
return true;
}
return false;
}
/**
* Returns the value of metaIdRef
*
* @return the value of metaIdRef
*/
public String getMetaIdRef() {
if (isSetMetaIdRef()) {
return metaIdRef;
}
return "";
}
/**
* Returns whether metaIdRef is set
*
* @return whether metaIdRef is set
*/
public boolean isSetMetaIdRef() {
return metaIdRef != null;
}
/**
* Sets the value of the optional metaIdRef attribute.
*
* This attribute is used to refer to a metaid attribute value on some
* other object, in the case when the reference being constructed with
* the {@link SBaseRef} is intended to refer to an object that does not
* have a port identifier. The namespace of the metaIdRef value is the
* entire document in which the referenced model resides, but must refer
* to a sub-element of the referenced model. Since meta identifiers are
* optional attributes of SBase, all SBML objects have the potential to
* have a meta identifier value.
*
* @param metaIdRef the value of metaIdRef
*/
public void setMetaIdRef(String metaIdRef) {
if (metaIdRef != null && metaIdRef.trim().length() == 0) {
metaIdRef = null;
}
if (!isReadingInProgress() && metaIdRef != null) {
// This method will throw IllegalArgumentException if the given id does not respect the SId syntax
// checkIdentifier(idRef);
boolean isValid = SyntaxChecker.isValidMetaId(metaIdRef);
if (!isValid) {
throw new IllegalArgumentException(format(
resourceBundle.getString("AbstractSBase.setMetaId"),
metaIdRef, getElementName()));
}
}
String oldIdRef = this.metaIdRef;
this.metaIdRef = metaIdRef;
firePropertyChange(CompConstants.metaIdRef, oldIdRef, this.metaIdRef);
}
/**
* Unsets the variable metaIdRef
* @return {@code true}, if metaIdRef was set before,
* otherwise {@code false}
*/
public boolean unsetMetaIdRef() {
if (isSetMetaIdRef()) {
String oldIdRef = metaIdRef;
metaIdRef = null;
firePropertyChange(CompConstants.metaIdRef, oldIdRef, metaIdRef);
return true;
}
return false;
}
/**
* Creates a new {@link SBaseRef} instance and add it to this {@link SBaseRef}
*
* @return a new {@link SBaseRef} instance (added to this {@link SBaseRef})
*/
public SBaseRef createSBaseRef()
{
setSBaseRef(new SBaseRef());
return sBaseRef;
}
/**
* Returns the value of sBaseRef
*
* @return the value of sBaseRef
*/
public SBaseRef getSBaseRef() {
if (isSetSBaseRef()) {
return sBaseRef;
}
return null;
}
/**
* Returns whether sBaseRef is set
*
* @return whether sBaseRef is set
*/
public boolean isSetSBaseRef() {
return sBaseRef != null;
}
/**
* Sets the value of the optional sBaseRef element.
*
* An {@link SBaseRef} object may have up to one subcomponent named
* sBaseRef, of type {@link SBaseRef}. This permits recursive structures
* to be constructed so that objects inside submodels can be referenced.
*
* @param sBaseRef the value of sBaseRef
*
*/
public void setSBaseRef(SBaseRef sBaseRef) {
SBaseRef oldSBaseRef = this.sBaseRef;
this.sBaseRef = sBaseRef;
firePropertyChange(CompConstants.sBaseRef, oldSBaseRef, this.sBaseRef);
// registering the new sBaseRef in the model/document // Could be done in org.sbml.jsbml.AbstractSBase.firePropertyChange(String, Object, Object)
registerChild(sBaseRef);
}
/**
* Unsets the variable sBaseRef
*
* @return {@code true}, if sBaseRef was set before,
* otherwise {@code false}
*/
public boolean unsetSBaseRef() {
if (isSetSBaseRef()) {
SBaseRef oldSBaseRef = sBaseRef;
sBaseRef = null;
firePropertyChange(CompConstants.sBaseRef, oldSBaseRef, sBaseRef);
return true;
}
return false;
}
@Override
public boolean getAllowsChildren() {
return true;
}
@Override
public int getChildCount() {
int count = super.getChildCount();
if (isSetSBaseRef()) {
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 (isSetSBaseRef()) {
if (pos == index) {
return getSBaseRef();
}
pos++;
}
throw new IndexOutOfBoundsException(MessageFormat.format(
resourceBundle.getString("IndexExceedsBoundsException"), index,
Math.min(pos, 0)));
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#writeXMLAttributes()
*/
@Override
public Map writeXMLAttributes() {
Map attributes = super.writeXMLAttributes();
if (getPackageName().equals(CompConstants.shortLabel) && isSetId()) {
attributes.remove("id");
attributes.put(CompConstants.shortLabel + ":id", getId());
}
if (getPackageName().equals(CompConstants.shortLabel) && isSetName()) {
attributes.remove("name");
attributes.put(CompConstants.shortLabel + ":name", getName());
}
if (isSetPortRef()) {
attributes.put(CompConstants.shortLabel + ':' + CompConstants.portRef, getPortRef());
}
if (isSetIdRef()) {
attributes.put(CompConstants.shortLabel + ':' + CompConstants.idRef, getIdRef());
}
if (isSetUnitRef()) {
attributes.put(CompConstants.shortLabel + ':' + CompConstants.unitRef, getUnitRef());
}
if (isSetMetaIdRef()) {
attributes.put(CompConstants.shortLabel + ':' + CompConstants.metaIdRef, getMetaIdRef());
}
return attributes;
}
/* (non-Javadoc)
* @see org.sbml.jsbml.AbstractSBase#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.portRef)) {
setPortRef(value);
}
else if (attributeName.equals(CompConstants.idRef)) {
setIdRef(value);
} else if (attributeName.equals(CompConstants.unitRef)) {
setUnitRef(value);
} else if (attributeName.equals(CompConstants.metaIdRef)) {
setMetaIdRef(value);
}
else {
isAttributeRead = false;
}
}
return isAttributeRead;
}
/* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
final int prime = 31;
int result = super.hashCode();
result = prime * result + ((idRef == null) ? 0 : idRef.hashCode());
result = prime * result
+ ((metaIdRef == null) ? 0 : metaIdRef.hashCode());
result = prime * result + ((portRef == null) ? 0 : portRef.hashCode());
result = prime * result
+ ((sBaseRef == null) ? 0 : sBaseRef.hashCode());
result = prime * result + ((unitRef == null) ? 0 : unitRef.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;
}
SBaseRef other = (SBaseRef) obj;
if (idRef == null) {
if (other.idRef != null) {
return false;
}
} else if (!idRef.equals(other.idRef)) {
return false;
}
if (metaIdRef == null) {
if (other.metaIdRef != null) {
return false;
}
} else if (!metaIdRef.equals(other.metaIdRef)) {
return false;
}
if (portRef == null) {
if (other.portRef != null) {
return false;
}
} else if (!portRef.equals(other.portRef)) {
return false;
}
if (sBaseRef == null) {
if (other.sBaseRef != null) {
return false;
}
} else if (!sBaseRef.equals(other.sBaseRef)) {
return false;
}
if (unitRef == null) {
if (other.unitRef != null) {
return false;
}
} else if (!unitRef.equals(other.unitRef)) {
return false;
}
return true;
}
}