Package org.sbml.jsbml.ext.multi

Class SpeciesTypeInstance

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.multi.SpeciesTypeInstance

All Implemented Interfaces:

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

public class SpeciesTypeInstance
extends AbstractNamedSBase
implements UniqueNamedSBase

Provides a way to construct MultiSpeciesTypes and Species with multiple components.

A speciesType can contain a list of instances of other speciesTypes which can also have their own speciesTypeInstances, so the complete structure of a speciesType can be like a tree. A speciesType can not contain an instance of any other speciesType that already contains the instance of it. In other words, circular references are not allowed when constructing speciesTypes. For example, if a speciesType 'A' contains the instance of another speciesType 'B', 'B' must not contain the instance of 'A' anywhere in the complete structure of 'B'.

Since:

1.0

Author:

Nicolas Rodriguez

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor	Description
SpeciesTypeInstance()	Creates an SpeciesTypeInstance instance
SpeciesTypeInstance(int level, int version)	Creates a SpeciesTypeInstance instance with a level and version.
SpeciesTypeInstance(java.lang.String id)	Creates a SpeciesTypeInstance instance with an id.
SpeciesTypeInstance(java.lang.String id, int level, int version)	Creates a SpeciesTypeInstance instance with an id, level, and version.
SpeciesTypeInstance(java.lang.String id, java.lang.String name, int level, int version)	Creates a SpeciesTypeInstance instance with an id, name, level, and version.
SpeciesTypeInstance(SpeciesTypeInstance obj)	Clone constructor

Method Summary

Modifier and Type	Method	Description
SpeciesTypeInstance	clone()	clones this class
boolean	equals(java.lang.Object obj)
java.lang.String	getCompartmentReference()	Returns the value of compartmentReference.
java.lang.String	getSpeciesType()	Returns the value of speciesType.
int	hashCode()
void	initDefaults()	Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetCompartmentReference()	Returns whether compartmentReference is set.
boolean	isSetSpeciesType()	Returns whether speciesType is set.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
void	setCompartmentReference(java.lang.String compartmentReference)	Sets the value of compartmentReference
void	setSpeciesType(java.lang.String speciesType)	Sets the value of speciesType
boolean	unsetCompartmentReference()	Unsets the variable compartmentReference.
boolean	unsetSpeciesType()	Unsets the variable speciesType.
java.util.Map<java.lang.String,java.lang.String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkIdentifier, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllDeclaredNamespaces, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasExtension, 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, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, 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, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.sbml.jsbml.SBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, 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, hasExtension, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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 javax.swing.tree.TreeNode

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

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

Constructor Detail

SpeciesTypeInstance

public SpeciesTypeInstance()

Creates an SpeciesTypeInstance instance

SpeciesTypeInstance

public SpeciesTypeInstance(java.lang.String id)

Creates a SpeciesTypeInstance instance with an id.

Parameters:

id - the identifier for the new element.

SpeciesTypeInstance

public SpeciesTypeInstance(int level,
                           int version)

Creates a SpeciesTypeInstance instance with a level and version.

Parameters:

level - SBML Level

version - SBML Version

SpeciesTypeInstance

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

Creates a SpeciesTypeInstance instance with an id, level, and version.

Parameters:

id - the identifier for this element.

level - the SBML Level

version - the SBML Version

SpeciesTypeInstance

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

Creates a SpeciesTypeInstance instance with an id, name, level, and version.

Parameters:

id - the identifier for this element.

name - a human-readable name for this element that can be used for display purposes.

level - the SBML Level

version - the SBML Version

SpeciesTypeInstance

public SpeciesTypeInstance(SpeciesTypeInstance obj)

Clone constructor

Method Detail

clone

public SpeciesTypeInstance clone()

clones this class

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

initDefaults

public void initDefaults()

Initializes the default values using the namespace.

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

getSpeciesType

public java.lang.String getSpeciesType()

Returns the value of speciesType.

Returns:

the value of speciesType.

isSetSpeciesType

public boolean isSetSpeciesType()

Returns whether speciesType is set.

Returns:

whether speciesType is set.

setSpeciesType

public void setSpeciesType(java.lang.String speciesType)

Sets the value of speciesType

Parameters:

speciesType - the value of speciesType to be set.

unsetSpeciesType

public boolean unsetSpeciesType()

Unsets the variable speciesType.

Returns:

true if speciesType was set before, otherwise false.

getCompartmentReference

public java.lang.String getCompartmentReference()

Returns the value of compartmentReference.

Returns:

the value of compartmentReference.

isSetCompartmentReference

public boolean isSetCompartmentReference()

Returns whether compartmentReference is set.

Returns:

whether compartmentReference is set.

setCompartmentReference

public void setCompartmentReference(java.lang.String compartmentReference)

Sets the value of compartmentReference

Parameters:

compartmentReference - the value of compartmentReference to be set.

unsetCompartmentReference

public boolean unsetCompartmentReference()

Unsets the variable compartmentReference.

Returns:

true if compartmentReference was set before, otherwise false.

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

equals

public boolean equals(java.lang.Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

writeXMLAttributes

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

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

readAttribute

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

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase