org.sbml.jsbml

Class SimpleSpeciesReference

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.SimpleSpeciesReference

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, NamedSBase, SBase, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

Direct Known Subclasses:

ModifierSpeciesReference, SpeciesReference

public abstract class SimpleSpeciesReference
extends AbstractNamedSBase
implements UniqueNamedSBase

The base class of SpeciesReference and ModifierSpeciesReference.

Since:

0.8

Version:

$Rev$

Author:

Simon Schäfer, Marine Dumousseau, Andreas Dräger

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private static long	serialVersionUID Generated serial version identifier.
private java.lang.String	speciesID Represents the 'species' XML attribute.

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, lv, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
SimpleSpeciesReference() Creates a SimpleSpeciesReference instance.
SimpleSpeciesReference(int level, int version) Creates a SimpleSpeciesReference instance.
SimpleSpeciesReference(SimpleSpeciesReference ssr) Creates a SimpleSpeciesReference instance from a given SimpleSpeciesReference.
SimpleSpeciesReference(Species species) Creates a SimpleSpeciesReference instance from a given Species.
SimpleSpeciesReference(java.lang.String id) Creates a SimpleSpeciesReference instance.
SimpleSpeciesReference(java.lang.String id, int level, int version) Creates a SimpleSpeciesReference instance.
SimpleSpeciesReference(java.lang.String id, java.lang.String name, int level, int version) Creates a SimpleSpeciesReference instance.

Method Summary

Modifier and Type	Method and Description
boolean	equals(java.lang.Object object) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
java.lang.String	getSpecies()
Species	getSpeciesInstance()
int	hashCode() Returns a hash code value for this SBase instance.
boolean	isIdMandatory() Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.
boolean	isSetSpecies()
boolean	isSetSpeciesInstance()
java.lang.String	printSpeciesReference() Human-readable representation of this reference.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value) Sets the given attribute in this SBase.
void	setSpecies(Species species) Sets the speciesID to the id of the Species 'species'.
void	setSpecies(java.lang.String species) Sets the speciesID to 'spec'.
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes() Returns a map with all the attributes of this SBase that need to be written out in XML.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, clone, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setLevelAndVersion, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageNamespaceAndVersion, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, clone, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, fireNodeRemovedEvent, firePropertyChange, getListOfTreeNodeChangeListeners, getRoot, getTreeNodeChangeListenerCount, getUserObject, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeUserObject, userObjectKeySet

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

speciesID

private java.lang.String speciesID

Represents the 'species' XML attribute.

Constructor Detail

SimpleSpeciesReference

public SimpleSpeciesReference()

Creates a SimpleSpeciesReference instance. By default, the speciesId is null.

SimpleSpeciesReference

public SimpleSpeciesReference(int level,
                              int version)

Creates a SimpleSpeciesReference instance.

Parameters:

level - the SBML level

version - the SBML version

SimpleSpeciesReference

public SimpleSpeciesReference(SimpleSpeciesReference ssr)

Creates a SimpleSpeciesReference instance from a given SimpleSpeciesReference.

Parameters:

ssr -

SimpleSpeciesReference

public SimpleSpeciesReference(Species species)

Creates a SimpleSpeciesReference instance from a given Species.

Parameters:

species -

SimpleSpeciesReference

public SimpleSpeciesReference(java.lang.String id)

Creates a SimpleSpeciesReference instance.

Parameters:

id -

SimpleSpeciesReference

public SimpleSpeciesReference(java.lang.String id,
                              int level,
                              int version)

Creates a SimpleSpeciesReference instance.

Parameters:

id -

level - the SBML level

version - the SBML version

SimpleSpeciesReference

public SimpleSpeciesReference(java.lang.String id,
                              java.lang.String name,
                              int level,
                              int version)

Creates a SimpleSpeciesReference instance.

Parameters:

id -

name -

level - the SBML level

version - the SBML version

Method Detail

equals

public boolean equals(java.lang.Object object)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

Parameters:

object - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

getSpecies

public java.lang.String getSpecies()

Returns:

the speciesID of this Species. The empty String if it is not set.

getSpeciesInstance

public Species getSpeciesInstance()

Returns:

The Species instance which has the speciesID of this SimpleSpeciesReference as id. Can be null if it doesn't exist.

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: SBase

Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

Returns:

true if the identifier of this element must be set in order to create a valid SBML representation. false otherwise, i.e., if the identifier can be understood as an optional attribute.

isSetSpecies

public boolean isSetSpecies()

Returns:

true if this speciesID of this SimpleSpeciesReference is not null.

isSetSpeciesInstance

public boolean isSetSpeciesInstance()

Returns:

true if the Species instance which has the speciesID of this SimpleSpeciesReference as id is not null.

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                             java.lang.String prefix,
                             java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

setSpecies

public void setSpecies(Species species)

Sets the speciesID to the id of the Species 'species'.

Parameters:

species -

setSpecies

public void setSpecies(java.lang.String species)

Sets the speciesID to 'spec'.

Parameters:

species -

printSpeciesReference

public java.lang.String printSpeciesReference()

Human-readable representation of this reference.

Returns:

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this SBase that need to be written out in XML.

The attribute name is used as a key and the attribute value as value. If a prefix is needed for the attribute name, it need to be set directly in this map.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

Returns:

a Map containing the XML attributes of this object.