org.sbml.jsbml.ext.multi

Class SpeciesFeature

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.multi.SpeciesFeature

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, ListOfSpeciesFeatureContent, NamedSBase, SBase, TreeNodeWithChangeSupport

public class SpeciesFeature
extends AbstractNamedSBase
implements ListOfSpeciesFeatureContent

Defines the state of a component in a species by selecting values from the listOfPossibleSpeciesFeatureValues of the referenced SpeciesFeatureType.

Since:

1.1

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

Method Summary

Modifier and Type	Method and Description
boolean	addSpeciesFeatureValue(SpeciesFeatureValue speciesFeatureValue) Adds a new SpeciesFeatureValue to the listOfSpeciesFeatureValues.
SpeciesFeature	clone() clones this class
SpeciesFeatureValue	createSpeciesFeatureValue() Creates a new SpeciesFeatureValue element and adds it to the listOfSpeciesFeatureValues list.
boolean	equals(Object obj)
boolean	getAllowsChildren()
TreeNode	getChildAt(int index)
int	getChildCount()
String	getComponent() Returns the value of component.
ListOf<SpeciesFeatureValue>	getListOfSpeciesFeatureValues() Returns the listOfSpeciesFeatureValues.
int	getNumSpeciesFeatureValues() Returns the number of SpeciesFeatureValues in this SpeciesFeature.
int	getOccur() Returns the value of occur.
String	getSpeciesFeatureType() Returns the value of speciesFeatureType.
SpeciesFeatureValue	getSpeciesFeatureValue(int i) Gets an element from the listOfSpeciesFeatureValues at the given index.
int	getSpeciesFeatureValueCount() Returns the number of SpeciesFeatureValues in this SpeciesFeature.
int	hashCode()
void	initDefaults() Initializes the default values using the namespace.
boolean	isIdMandatory()
boolean	isSetComponent() Returns whether component is set.
boolean	isSetListOfSpeciesFeatureValues() Returns true if listOfSpeciesFeatureValues contains at least one element.
boolean	isSetOccur() Returns whether occur is set.
boolean	isSetSpeciesFeatureType() Returns whether speciesFeatureType is set.
boolean	readAttribute(String attributeName, String prefix, String value)
SpeciesFeatureValue	removeSpeciesFeatureValue(int i) Removes an element from the listOfSpeciesFeatureValues at the given index.
boolean	removeSpeciesFeatureValue(SpeciesFeatureValue speciesFeatureValue) Removes an element from the listOfSpeciesFeatureValues.
void	setComponent(String component) Sets the value of component
void	setListOfSpeciesFeatureValues(ListOf<SpeciesFeatureValue> listOfSpeciesFeatureValues) Sets the given ListOf<SpeciesFeatureValue>.
void	setOccur(int occur) Sets the value of occur
void	setSpeciesFeatureType(String speciesFeatureType) Sets the value of speciesFeatureType
boolean	unsetComponent() Unsets the variable component.
boolean	unsetListOfSpeciesFeatureValues() Returns true if listOfSpeciesFeatureValues contains at least one element, otherwise false.
boolean	unsetOccur() Unsets the variable occur.
boolean	unsetSpeciesFeatureType() Unsets the variable speciesFeatureType.
Map<String,String>	writeXMLAttributes()

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, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAnnotation, getAnnotationString, 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, 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 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, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, 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, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, 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, getIndex, getParent, isLeaf

Methods inherited from interface org.sbml.jsbml.NamedSBase

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

Constructor Detail

SpeciesFeature

public SpeciesFeature()

Creates an SpeciesFeature instance

SpeciesFeature

public SpeciesFeature(String id)

Creates a SpeciesFeature instance with an id.

Parameters:

id - the identifier for the new element.

SpeciesFeature

public SpeciesFeature(int level,
                      int version)

Creates a SpeciesFeature instance with a level and version.

Parameters:

level - SBML Level

version - SBML Version

SpeciesFeature

public SpeciesFeature(String id,
                      int level,
                      int version)

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

Parameters:

id - the identifier for this element.

level - the SBML Level

version - the SBML Version

SpeciesFeature

public SpeciesFeature(String id,
                      String name,
                      int level,
                      int version)

Creates a SpeciesFeature 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

SpeciesFeature

public SpeciesFeature(SpeciesFeature obj)

Clone constructor

Method Detail

clone

public SpeciesFeature clone()

clones this class

Specified by:

clone in interface SBase

Overrides:

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(Object obj)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

isSetListOfSpeciesFeatureValues

public boolean isSetListOfSpeciesFeatureValues()

Returns true if listOfSpeciesFeatureValues contains at least one element.

Returns:

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

getListOfSpeciesFeatureValues

public ListOf<SpeciesFeatureValue> getListOfSpeciesFeatureValues()

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

Returns:

the listOfSpeciesFeatureValues.

setListOfSpeciesFeatureValues

public void setListOfSpeciesFeatureValues(ListOf<SpeciesFeatureValue> listOfSpeciesFeatureValues)

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

Parameters:

listOfSpeciesFeatureValues - the list of SpeciesFeatureValues to set

unsetListOfSpeciesFeatureValues

public boolean unsetListOfSpeciesFeatureValues()

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

Returns:

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

addSpeciesFeatureValue

public boolean addSpeciesFeatureValue(SpeciesFeatureValue speciesFeatureValue)

Adds a new SpeciesFeatureValue to the listOfSpeciesFeatureValues.

The listOfSpeciesFeatureValues is initialized if necessary.

Parameters:

speciesFeatureValue - the element to add to the list

Returns:

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

See Also:

Collection.add(Object)

removeSpeciesFeatureValue

public boolean removeSpeciesFeatureValue(SpeciesFeatureValue speciesFeatureValue)

Removes an element from the listOfSpeciesFeatureValues.

Parameters:

speciesFeatureValue - 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)

removeSpeciesFeatureValue

public SpeciesFeatureValue removeSpeciesFeatureValue(int i)

Removes an element from the listOfSpeciesFeatureValues at the given index.

Parameters:

i - the index where to remove the SpeciesFeatureValue.

Returns:

the specified element if it was successfully found and removed.

Throws:

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

createSpeciesFeatureValue

public SpeciesFeatureValue createSpeciesFeatureValue()

Creates a new SpeciesFeatureValue element and adds it to the listOfSpeciesFeatureValues list.

Returns:

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

getSpeciesFeatureValue

public SpeciesFeatureValue getSpeciesFeatureValue(int i)

Gets an element from the listOfSpeciesFeatureValues at the given index.

Parameters:

i - the index of the SpeciesFeatureValue element to get.

Returns:

an element from the listOfSpeciesFeatureValues at the given index.

Throws:

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

getSpeciesFeatureValueCount

public int getSpeciesFeatureValueCount()

Returns the number of SpeciesFeatureValues in this SpeciesFeature.

Returns:

the number of SpeciesFeatureValues in this SpeciesFeature.

getNumSpeciesFeatureValues

public int getNumSpeciesFeatureValues()

Returns the number of SpeciesFeatureValues in this SpeciesFeature.

Returns:

the number of SpeciesFeatureValues in this SpeciesFeature.

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

same as getSpeciesFeatureValueCount()

getSpeciesFeatureType

public String getSpeciesFeatureType()

Returns the value of speciesFeatureType.

Returns:

the value of speciesFeatureType.

isSetSpeciesFeatureType

public boolean isSetSpeciesFeatureType()

Returns whether speciesFeatureType is set.

Returns:

whether speciesFeatureType is set.

setSpeciesFeatureType

public void setSpeciesFeatureType(String speciesFeatureType)

Sets the value of speciesFeatureType

Parameters:

speciesFeatureType - the value of speciesFeatureType to be set.

unsetSpeciesFeatureType

public boolean unsetSpeciesFeatureType()

Unsets the variable speciesFeatureType.

Returns:

true if speciesFeatureType was set before, otherwise false.

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.

getComponent

public String getComponent()

Returns the value of component.

Returns:

the value of component.

isSetComponent

public boolean isSetComponent()

Returns whether component is set.

Returns:

whether component is set.

setComponent

public void setComponent(String component)

Sets the value of component

Parameters:

component - the value of component to be set.

unsetComponent

public boolean unsetComponent()

Unsets the variable component.

Returns:

true if component 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

getAllowsChildren

public boolean getAllowsChildren()

Specified by:

getAllowsChildren in interface TreeNode

Overrides:

getAllowsChildren in class AbstractSBase

getChildCount

public int getChildCount()

Specified by:

getChildCount in interface TreeNode

Overrides:

getChildCount in class AbstractSBase

getChildAt

public TreeNode getChildAt(int index)

Specified by:

getChildAt in interface TreeNode

Overrides:

getChildAt in class AbstractSBase

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase