Package org.sbml.jsbml.ext.multi

Class SpeciesFeatureType

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.multi.SpeciesFeatureType

All Implemented Interfaces:

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

public class SpeciesFeatureType
extends AbstractNamedSBase
implements UniqueNamedSBase

A species type (MultiSpeciesType) can carry any number of features (SpeciesFeatureType), which are characteristic properties specific for this type of species (Species). The element SpeciesFeatureType of SBML Level 3 Version 1 multi Version 1 corresponds to the "state variable" of the SBGN Entity Relationship language. A SpeciesFeatureType is identified by an id and an optional name. A SpeciesFeatureType is linked to a list of possible values.

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

Method Summary

Modifier and Type	Method	Description
boolean	addPossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue possibleSpeciesFeatureValue)	Adds a new PossibleSpeciesFeatureValue to the listOfPossibleSpeciesFeatureValues.
SpeciesFeatureType	clone()	clones this class
PossibleSpeciesFeatureValue	createPossibleSpeciesFeatureValue()	Creates a new PossibleSpeciesFeatureValue element and adds it to the listOfPossibleSpeciesFeatureValues list.
PossibleSpeciesFeatureValue	createPossibleSpeciesFeatureValue(java.lang.String id)	Creates a new PossibleSpeciesFeatureValue element and adds it to the listOfPossibleSpeciesFeatureValues list.
boolean	equals(java.lang.Object obj)
javax.swing.tree.TreeNode	getChildAt(int index)
int	getChildCount()
ListOf<PossibleSpeciesFeatureValue>	getListOfPossibleSpeciesFeatureValues()	Returns the listOfPossibleSpeciesFeatureValues.
int	getNumPossibleSpeciesFeatureValues()	Returns the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.
int	getOccur()	Returns the value of occur.
PossibleSpeciesFeatureValue	getPossibleSpeciesFeatureValue(int i)	Gets an element from the listOfPossibleSpeciesFeatureValues at the given index.
PossibleSpeciesFeatureValue	getPossibleSpeciesFeatureValue(java.lang.String possibleSpeciesFeatureValueId)	Gets an element from the listOfPossibleSpeciesFeatureValues, with the given id.
int	getPossibleSpeciesFeatureValueCount()	Returns the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.
int	hashCode()
void	initDefaults()	Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetListOfPossibleSpeciesFeatureValues()	Returns true if listOfPossibleSpeciesFeatureValues contains at least one element.
boolean	isSetOccur()	Returns whether occur is set.
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
PossibleSpeciesFeatureValue	removePossibleSpeciesFeatureValue(int i)	Removes an element from the listOfPossibleSpeciesFeatureValues at the given index.
PossibleSpeciesFeatureValue	removePossibleSpeciesFeatureValue(java.lang.String possibleSpeciesFeatureValueId)	Removes an element from the listOfPossibleSpeciesFeatureValues.
boolean	removePossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue possibleSpeciesFeatureValue)	Removes an element from the listOfPossibleSpeciesFeatureValues.
void	setListOfPossibleSpeciesFeatureValues(ListOf<PossibleSpeciesFeatureValue> listOfPossibleSpeciesFeatureValues)	Sets the given ListOf<PossibleSpeciesFeatureValue>.
void	setOccur(int occur)	Sets the value of occur
boolean	unsetListOfPossibleSpeciesFeatureValues()	Returns true if listOfPossibleSpeciesFeatureValues contains at least one element, otherwise false.
boolean	unsetOccur()	Unsets the variable occur.
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, 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, 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

SpeciesFeatureType

public SpeciesFeatureType()

Creates an SpeciesFeatureType instance

SpeciesFeatureType

public SpeciesFeatureType(java.lang.String id)

Creates a SpeciesFeatureType instance with an id.

Parameters:

id - the identifier for the new element.

SpeciesFeatureType

public SpeciesFeatureType(int level,
                          int version)

Creates a SpeciesFeatureType instance with a level and version.

Parameters:

level - SBML Level

version - SBML Version

SpeciesFeatureType

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

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

Parameters:

id - the identifier for this element.

level - the SBML Level

version - the SBML Version

SpeciesFeatureType

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

Creates a SpeciesFeatureType 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

SpeciesFeatureType

public SpeciesFeatureType(SpeciesFeatureType obj)

Clone constructor

Method Detail

clone

public SpeciesFeatureType 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.

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

isSetListOfPossibleSpeciesFeatureValues

public boolean isSetListOfPossibleSpeciesFeatureValues()

Returns true if listOfPossibleSpeciesFeatureValues contains at least one element.

Returns:

true if listOfPossibleSpeciesFeatureValues contains at least one element, otherwise false.

getListOfPossibleSpeciesFeatureValues

public ListOf<PossibleSpeciesFeatureValue> getListOfPossibleSpeciesFeatureValues()

Returns the listOfPossibleSpeciesFeatureValues. Creates it if it does not already exist.

Returns:

the listOfPossibleSpeciesFeatureValues.

setListOfPossibleSpeciesFeatureValues

public void setListOfPossibleSpeciesFeatureValues(ListOf<PossibleSpeciesFeatureValue> listOfPossibleSpeciesFeatureValues)

Sets the given ListOf<PossibleSpeciesFeatureValue>. If listOfPossibleSpeciesFeatureValues was defined before and contains some elements, they are all unset.

Parameters:

listOfPossibleSpeciesFeatureValues - the list of PossibleSpeciesFeatureValue

unsetListOfPossibleSpeciesFeatureValues

public boolean unsetListOfPossibleSpeciesFeatureValues()

Returns true if listOfPossibleSpeciesFeatureValues contains at least one element, otherwise false.

Returns:

true if listOfPossibleSpeciesFeatureValues contains at least one element, otherwise false.

addPossibleSpeciesFeatureValue

public boolean addPossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue possibleSpeciesFeatureValue)

Adds a new PossibleSpeciesFeatureValue to the listOfPossibleSpeciesFeatureValues.

The listOfPossibleSpeciesFeatureValues is initialized if necessary.

Parameters:

possibleSpeciesFeatureValue - the element to add to the list

Returns:

true (as specified by Collection.add(E))

See Also:

Collection.add(Object)

removePossibleSpeciesFeatureValue

public boolean removePossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue possibleSpeciesFeatureValue)

Removes an element from the listOfPossibleSpeciesFeatureValues.

Parameters:

possibleSpeciesFeatureValue - the element to be removed from the list.

Returns:

true if the list contained the specified element and it was removed.

See Also:

List.remove(Object)

removePossibleSpeciesFeatureValue

public PossibleSpeciesFeatureValue removePossibleSpeciesFeatureValue(java.lang.String possibleSpeciesFeatureValueId)

Removes an element from the listOfPossibleSpeciesFeatureValues.

Parameters:

possibleSpeciesFeatureValueId - the id of the element to be removed from the list.

Returns:

the removed element, if it was successfully found and removed or null.

removePossibleSpeciesFeatureValue

public PossibleSpeciesFeatureValue removePossibleSpeciesFeatureValue(int i)

Removes an element from the listOfPossibleSpeciesFeatureValues at the given index.

Parameters:

i - the index where to remove the PossibleSpeciesFeatureValue.

Returns:

the specified element if it was successfully found and removed.

Throws:

java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound ((i < 0) || (i > listOfPossibleSpeciesFeatureValues)).

createPossibleSpeciesFeatureValue

public PossibleSpeciesFeatureValue createPossibleSpeciesFeatureValue()

Creates a new PossibleSpeciesFeatureValue element and adds it to the listOfPossibleSpeciesFeatureValues list.

Returns:

the newly created element, i.e., the last item in the listOfPossibleSpeciesFeatureValues

createPossibleSpeciesFeatureValue

public PossibleSpeciesFeatureValue createPossibleSpeciesFeatureValue(java.lang.String id)

Creates a new PossibleSpeciesFeatureValue element and adds it to the listOfPossibleSpeciesFeatureValues list.

Parameters:

id - the identifier that is to be applied to the new element.

Returns:

the newly created PossibleSpeciesFeatureValue element, which is the last element in the listOfPossibleSpeciesFeatureValues.

getPossibleSpeciesFeatureValue

public PossibleSpeciesFeatureValue getPossibleSpeciesFeatureValue(int i)

Gets an element from the listOfPossibleSpeciesFeatureValues at the given index.

Parameters:

i - the index of the PossibleSpeciesFeatureValue element to get.

Returns:

an element from the listOfPossibleSpeciesFeatureValues at the given index.

Throws:

java.lang.IndexOutOfBoundsException - if the listOf is not set or if the index is out of bound (index < 0 || index > list.size).

getPossibleSpeciesFeatureValue

public PossibleSpeciesFeatureValue getPossibleSpeciesFeatureValue(java.lang.String possibleSpeciesFeatureValueId)

Gets an element from the listOfPossibleSpeciesFeatureValues, with the given id.

Parameters:

possibleSpeciesFeatureValueId - the id of the PossibleSpeciesFeatureValue element to get.

Returns:

an element from the listOfPossibleSpeciesFeatureValues with the given id or null.

getPossibleSpeciesFeatureValueCount

public int getPossibleSpeciesFeatureValueCount()

Returns the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.

Returns:

the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.

getNumPossibleSpeciesFeatureValues

public int getNumPossibleSpeciesFeatureValues()

Returns the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.

Returns:

the number of PossibleSpeciesFeatureValues in this SpeciesFeatureType.

Note: this method is kept here as it exist in libSBML.

same as getPossibleSpeciesFeatureValueCount()

getOccur

public int getOccur()

Returns the value of occur.

Returns:

the value of occur.

isSetOccur

public boolean isSetOccur()

Returns whether occur is set.

Returns:

whether occur is set.

setOccur

public void setOccur(int occur)

Sets the value of occur

Parameters:

occur - the value of occur to be set.

unsetOccur

public boolean unsetOccur()

Unsets the variable occur.

Returns:

true if occur was set before, otherwise false.

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

getChildAt

public javax.swing.tree.TreeNode getChildAt(int index)

Specified by:

getChildAt in interface javax.swing.tree.TreeNode

Overrides:

getChildAt in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface javax.swing.tree.TreeNode

Overrides:

getChildCount 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