java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, ListOfSpeciesFeatureContent
, NamedSBase
, SBase
, TreeNodeWithChangeSupport
public class SpeciesFeature extends AbstractNamedSBase implements ListOfSpeciesFeatureContent
SpeciesFeatureType
.JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
SpeciesFeature() |
Creates an SpeciesFeature instance
|
SpeciesFeature(int level,
int version) |
Creates a SpeciesFeature instance with a level and version.
|
SpeciesFeature(java.lang.String id) |
Creates a SpeciesFeature instance with an id.
|
SpeciesFeature(java.lang.String id,
int level,
int version) |
Creates a SpeciesFeature instance with an id, level, and version.
|
SpeciesFeature(java.lang.String id,
java.lang.String name,
int level,
int version) |
Creates a SpeciesFeature instance with an id, name, level, and version.
|
SpeciesFeature(SpeciesFeature obj) |
Clone constructor
|
Modifier and Type | Method | 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(java.lang.Object obj) |
|
boolean |
getAllowsChildren() |
|
javax.swing.tree.TreeNode |
getChildAt(int index) |
|
int |
getChildCount() |
|
java.lang.String |
getComponent() |
Returns the value of
component . |
ListOf<SpeciesFeatureValue> |
getListOfSpeciesFeatureValues() |
Returns the
listOfSpeciesFeatureValues . |
int |
getNumSpeciesFeatureValues() |
Returns the number of
SpeciesFeatureValue s in this
SpeciesFeature . |
int |
getOccur() |
Returns the value of
occur . |
java.lang.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
SpeciesFeatureValue s in this
SpeciesFeature . |
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 |
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(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value) |
Sets the given attribute in this
SBase . |
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(java.lang.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(java.lang.String speciesFeatureType) |
Sets the value of speciesFeatureType
|
boolean |
unsetComponent() |
Unsets the variable component.
|
boolean |
unsetListOfSpeciesFeatureValues() |
|
boolean |
unsetOccur() |
Unsets the variable occur.
|
boolean |
unsetSpeciesFeatureType() |
Unsets the variable speciesFeatureType.
|
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, 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, getId, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, 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, registerChild, removeCVTerm, removeCVTerm, removeDeclaredNamespaceByNamespace, removeDeclaredNamespaceByPrefix, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTreeNodeChangeListener, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, 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
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 SpeciesFeature()
public SpeciesFeature(java.lang.String id)
id
- the identifier for the new element.public SpeciesFeature(int level, int version)
level
- SBML Levelversion
- SBML Versionpublic SpeciesFeature(java.lang.String id, int level, int version)
id
- the identifier for this element.level
- the SBML Levelversion
- the SBML Versionpublic SpeciesFeature(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 SpeciesFeature(SpeciesFeature obj)
public SpeciesFeature 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 isSetListOfSpeciesFeatureValues()
true
if listOfSpeciesFeatureValues
contains at least
one element.true
if listOfSpeciesFeatureValues
contains at least
one element, otherwise false
.public ListOf<SpeciesFeatureValue> getListOfSpeciesFeatureValues()
listOfSpeciesFeatureValues
.
Creates it if it does not already exist.listOfSpeciesFeatureValues
.public void setListOfSpeciesFeatureValues(ListOf<SpeciesFeatureValue> listOfSpeciesFeatureValues)
ListOf<SpeciesFeatureValue>
.
If listOfSpeciesFeatureValues
was defined before and contains some
elements, they are all unset.listOfSpeciesFeatureValues
- the list of SpeciesFeatureValue
s to setpublic boolean unsetListOfSpeciesFeatureValues()
true
if listOfSpeciesFeatureValues
contains at least
one element, otherwise false
.public boolean addSpeciesFeatureValue(SpeciesFeatureValue speciesFeatureValue)
SpeciesFeatureValue
to the listOfSpeciesFeatureValues
.
The listOfSpeciesFeatureValues is initialized if necessary.
speciesFeatureValue
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public boolean removeSpeciesFeatureValue(SpeciesFeatureValue speciesFeatureValue)
listOfSpeciesFeatureValues
.speciesFeatureValue
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public SpeciesFeatureValue removeSpeciesFeatureValue(int i)
listOfSpeciesFeatureValues
at the given index.i
- the index where to remove the SpeciesFeatureValue
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfSpeciesFeatureValues)
).public SpeciesFeatureValue createSpeciesFeatureValue()
listOfSpeciesFeatureValues
list.listOfSpeciesFeatureValues
public SpeciesFeatureValue getSpeciesFeatureValue(int i)
listOfSpeciesFeatureValues
at the given index.i
- the index of the SpeciesFeatureValue
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 int getSpeciesFeatureValueCount()
SpeciesFeatureValue
s in this
SpeciesFeature
.SpeciesFeatureValue
s in this
SpeciesFeature
.public int getNumSpeciesFeatureValues()
SpeciesFeatureValue
s in this
SpeciesFeature
.SpeciesFeatureValue
s in this
SpeciesFeature
.getSpeciesFeatureValueCount()
public java.lang.String getSpeciesFeatureType()
speciesFeatureType
.speciesFeatureType
.public boolean isSetSpeciesFeatureType()
speciesFeatureType
is set.speciesFeatureType
is set.public void setSpeciesFeatureType(java.lang.String speciesFeatureType)
speciesFeatureType
- the value of speciesFeatureType to be set.public boolean unsetSpeciesFeatureType()
true
if speciesFeatureType was set before, otherwise false
.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 java.lang.String getComponent()
component
.component
.public boolean isSetComponent()
component
is set.component
is set.public void setComponent(java.lang.String component)
component
- the value of component to be set.public boolean unsetComponent()
true
if component 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 boolean getAllowsChildren()
getAllowsChildren
in interface javax.swing.tree.TreeNode
getAllowsChildren
in class AbstractSBase
public int getChildCount()
getChildCount
in interface javax.swing.tree.TreeNode
getChildCount
in class AbstractSBase
public javax.swing.tree.TreeNode getChildAt(int index)
getChildAt
in interface javax.swing.tree.TreeNode
getChildAt
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.