java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
public class SpeciesFeatureType extends AbstractNamedSBase implements UniqueNamedSBase
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.JSBML_WRONG_SBO_TERM
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
|
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
PossibleSpeciesFeatureValue s 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
PossibleSpeciesFeatureValue s in this
SpeciesFeatureType . |
int |
hashCode() |
Returns a hash code value for this
SBase instance. |
void |
initDefaults() |
Initializes the default values using the namespace.
|
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 |
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) |
Sets the given attribute in this
SBase . |
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() |
|
boolean |
unsetOccur() |
Unsets the variable occur.
|
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. |
isValidId
addCVTerm, addDeclaredNamespace, addExtension, addPlugin, addResources, appendAnnotation, appendAnnotation, appendNotes, appendNotes, 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, 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, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm
addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isLeaf, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet
getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName
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
children, getAllowsChildren, getIndex, getParent, isLeaf
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
public SpeciesFeatureType()
public SpeciesFeatureType(java.lang.String id)
id
- the identifier for the new element.public SpeciesFeatureType(int level, int version)
level
- SBML Levelversion
- SBML Versionpublic SpeciesFeatureType(java.lang.String id, int level, int version)
id
- the identifier for this element.level
- the SBML Levelversion
- the SBML Versionpublic SpeciesFeatureType(java.lang.String id, java.lang.String name, int level, int version)
id
- the identifier for this element.name
- a human-readable name for this element that can be used for display purposes.level
- the SBML Levelversion
- the SBML Versionpublic SpeciesFeatureType(SpeciesFeatureType obj)
public SpeciesFeatureType clone()
clone
in interface SBase
clone
in class AbstractSBase
public void initDefaults()
public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractSBase
SBase
instance.Object.hashCode()
public boolean equals(java.lang.Object obj)
SBase
public boolean isSetListOfPossibleSpeciesFeatureValues()
true
if listOfPossibleSpeciesFeatureValues
contains at least
one element.true
if listOfPossibleSpeciesFeatureValues
contains at least
one element, otherwise false
.public ListOf<PossibleSpeciesFeatureValue> getListOfPossibleSpeciesFeatureValues()
listOfPossibleSpeciesFeatureValues
.
Creates it if it does not already exist.listOfPossibleSpeciesFeatureValues
.public void setListOfPossibleSpeciesFeatureValues(ListOf<PossibleSpeciesFeatureValue> listOfPossibleSpeciesFeatureValues)
ListOf<PossibleSpeciesFeatureValue>
.
If listOfPossibleSpeciesFeatureValues
was defined before and contains some
elements, they are all unset.listOfPossibleSpeciesFeatureValues
- the list of PossibleSpeciesFeatureValue
public boolean unsetListOfPossibleSpeciesFeatureValues()
true
if listOfPossibleSpeciesFeatureValues
contains at least
one element, otherwise false
.public boolean addPossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue possibleSpeciesFeatureValue)
PossibleSpeciesFeatureValue
to the listOfPossibleSpeciesFeatureValues
.
The listOfPossibleSpeciesFeatureValues is initialized if necessary.
possibleSpeciesFeatureValue
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public boolean removePossibleSpeciesFeatureValue(PossibleSpeciesFeatureValue possibleSpeciesFeatureValue)
listOfPossibleSpeciesFeatureValues
.possibleSpeciesFeatureValue
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public PossibleSpeciesFeatureValue removePossibleSpeciesFeatureValue(java.lang.String possibleSpeciesFeatureValueId)
listOfPossibleSpeciesFeatureValues
.possibleSpeciesFeatureValueId
- the id of the element to be removed from the list.null
.public PossibleSpeciesFeatureValue removePossibleSpeciesFeatureValue(int i)
listOfPossibleSpeciesFeatureValues
at the given index.i
- the index where to remove the PossibleSpeciesFeatureValue
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfPossibleSpeciesFeatureValues)
).public PossibleSpeciesFeatureValue createPossibleSpeciesFeatureValue()
listOfPossibleSpeciesFeatureValues
list.listOfPossibleSpeciesFeatureValues
public PossibleSpeciesFeatureValue createPossibleSpeciesFeatureValue(java.lang.String id)
PossibleSpeciesFeatureValue
element and adds it to the
listOfPossibleSpeciesFeatureValues
list.id
- the identifier that is to be applied to the new element.PossibleSpeciesFeatureValue
element, which is the last
element in the listOfPossibleSpeciesFeatureValues
.public PossibleSpeciesFeatureValue getPossibleSpeciesFeatureValue(int i)
listOfPossibleSpeciesFeatureValues
at the given index.i
- the index of the PossibleSpeciesFeatureValue
element to get.java.lang.IndexOutOfBoundsException
- if the listOf is not set or
if the index is out of bound (index < 0 || index > list.size).public PossibleSpeciesFeatureValue getPossibleSpeciesFeatureValue(java.lang.String possibleSpeciesFeatureValueId)
possibleSpeciesFeatureValueId
- the id of the PossibleSpeciesFeatureValue
element to get.null
.public int getPossibleSpeciesFeatureValueCount()
PossibleSpeciesFeatureValue
s in this
SpeciesFeatureType
.PossibleSpeciesFeatureValue
s in this
SpeciesFeatureType
.public int getNumPossibleSpeciesFeatureValues()
PossibleSpeciesFeatureValue
s in this
SpeciesFeatureType
.PossibleSpeciesFeatureValue
s in this
SpeciesFeatureType
.getPossibleSpeciesFeatureValueCount()
public boolean isSetOccur()
occur
is set.occur
is set.public void setOccur(int occur)
occur
- the value of occur to be set.public boolean unsetOccur()
true
if occur was set before, otherwise false
.public boolean isIdMandatory()
SBase
true
if the identifier of this
SBase
is required to be defined (i.e., not null
)
in the definition of SBML.isIdMandatory
in interface NamedSBase
isIdMandatory
in interface SBase
isIdMandatory
in class AbstractSBase
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.public javax.swing.tree.TreeNode getChildAt(int index)
getChildAt
in interface javax.swing.tree.TreeNode
getChildAt
in class AbstractSBase
public int getChildCount()
getChildCount
in interface javax.swing.tree.TreeNode
getChildCount
in class AbstractSBase
public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()
SBase
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.
writeXMLAttributes
in interface SBase
writeXMLAttributes
in class AbstractSBase
Map
containing the XML attributes of this object.public boolean readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)
SBase
SBase
.
If the given attribute name is not recognized, nothing is done and
false
is returned.
readAttribute
in interface SBase
readAttribute
in class AbstractSBase
attributeName
- localName of the XML attributeprefix
- prefix of the XML attributevalue
- value of the XML attributetrue
if the attribute has been successfully read.