java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, CompartmentalizedSBase
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
BindingSiteSpeciesType
public class MultiSpeciesType extends SpeciesType implements CompartmentalizedSBase, UniqueNamedSBase
The element MultiSpeciesType, which is part of SBML Level 2 Version 4 specification, is not part of SBML Level 3 Version 1 Core any more. Instead, it will be defined in the multi package. The MultiSpeciesType element carries not only the basic attributes which it had in SBML Level 2 Version 4 (metaid, id, name), but is also extended for the needs of describing multi-component entities with the attribute bindingSite and for the needs of multistate entities by linking it to a list of StateFeatures
A species type can be used to describe a component of a supra-macromolecular assembly, but also a domain of a macromolecule. Such a domain can be a portion of the macromolecule, a non-connex set of atoms forming a functional domain, or just a conceptual construct suiting the needs of the modeler. The type of component can be specified by referring terms from the subbranch functional entity of the Systems Biology Ontology through the optional sboTerm attribute. The following table provides typical examples of component or domains (the list is absolutely not complete).
SBO identifier | Definition |
---|---|
SBO:0000242 | channel |
SBO:0000244 | receptor |
SBO:0000284 | transporter |
SBO:0000280 | ligand |
SBO:0000493 | functional domain |
SBO:0000494 | binding site |
SBO:0000495 | catalytic site |
SBO:0000496 | transmembrane domain |
JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
MultiSpeciesType() |
Creates an MultiSpeciesType instance
|
MultiSpeciesType(int level,
int version) |
Creates a MultiSpeciesType instance with a level and version.
|
MultiSpeciesType(java.lang.String id) |
Creates a MultiSpeciesType instance with an id.
|
MultiSpeciesType(java.lang.String id,
int level,
int version) |
Creates a MultiSpeciesType instance with an id, level, and version.
|
MultiSpeciesType(java.lang.String id,
java.lang.String name,
int level,
int version) |
Creates a MultiSpeciesType instance with an id, name, level, and version.
|
MultiSpeciesType(MultiSpeciesType obj) |
Creates a new
MultiSpeciesType instance cloned from the given MultiSpeciesType . |
Modifier and Type | Method | Description |
---|---|---|
boolean |
addInSpeciesTypeBond(InSpeciesTypeBond inSpeciesTypeBond) |
Adds a new
InSpeciesTypeBond to the listOfInSpeciesTypeBonds . |
boolean |
addSpeciesFeatureType(SpeciesFeatureType speciesFeatureType) |
Adds a new
SpeciesFeatureType to the listOfSpeciesFeatureTypes . |
boolean |
addSpeciesTypeComponentIndex(SpeciesTypeComponentIndex speciesTypeComponentIndex) |
Adds a new
SpeciesTypeComponentIndex to the listOfSpeciesTypeComponentIndexes . |
boolean |
addSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance) |
Adds a new
SpeciesTypeInstance to the listOfSpeciesTypeInstances . |
MultiSpeciesType |
clone() |
clones this class
|
InSpeciesTypeBond |
createInSpeciesTypeBond() |
Creates a new InSpeciesTypeBond element and adds it to the
listOfInSpeciesTypeBonds list. |
InSpeciesTypeBond |
createInSpeciesTypeBond(java.lang.String id) |
Creates a new
InSpeciesTypeBond element and adds it to the
listOfInSpeciesTypeBonds list. |
SpeciesFeatureType |
createSpeciesFeatureType() |
Creates a new SpeciesFeatureType element and adds it to the
listOfSpeciesFeatureTypes list. |
SpeciesFeatureType |
createSpeciesFeatureType(java.lang.String id) |
Creates a new
SpeciesFeatureType element and adds it to the
listOfSpeciesFeatureTypes list. |
SpeciesTypeComponentIndex |
createSpeciesTypeComponentIndex() |
Creates a new SpeciesTypeComponentIndex element and adds it to the
listOfSpeciesTypeComponentIndexes list. |
SpeciesTypeComponentIndex |
createSpeciesTypeComponentIndex(java.lang.String id) |
Creates a new
SpeciesTypeComponentIndex element and adds it to the
listOfSpeciesTypeComponentIndexes list. |
SpeciesTypeInstance |
createSpeciesTypeInstance() |
Creates a new SpeciesTypeInstance element and adds it to the
listOfSpeciesTypeInstances list. |
SpeciesTypeInstance |
createSpeciesTypeInstance(java.lang.String id) |
Creates a new
SpeciesTypeInstance element and adds it to the
listOfSpeciesTypeInstances list. |
boolean |
equals(java.lang.Object obj) |
|
javax.swing.tree.TreeNode |
getChildAt(int index) |
|
int |
getChildCount() |
|
java.lang.String |
getCompartment() |
Returns the value of the referenced compartment.
|
Compartment |
getCompartmentInstance() |
Returns the
Compartment that is referenced by this SBase . |
java.lang.String |
getElementName() |
Returns the XML element name of this object.
|
InSpeciesTypeBond |
getInSpeciesTypeBond(int i) |
Gets an element from the
listOfInSpeciesTypeBonds at the given index. |
InSpeciesTypeBond |
getInSpeciesTypeBond(java.lang.String inSpeciesTypeBondId) |
Gets an element from the listOfInSpeciesTypeBonds, with the given id.
|
int |
getInSpeciesTypeBondCount() |
Returns the number of
InSpeciesTypeBond s in this
MultiSpeciesType . |
ListOf<InSpeciesTypeBond> |
getListOfInSpeciesTypeBonds() |
Returns the
listOfInSpeciesTypeBonds . |
ListOf<SpeciesFeatureType> |
getListOfSpeciesFeatureTypes() |
Returns the
listOfSpeciesFeatureTypes . |
ListOf<SpeciesTypeComponentIndex> |
getListOfSpeciesTypeComponentIndexes() |
Returns the
listOfSpeciesTypeComponentIndexes . |
ListOf<SpeciesTypeInstance> |
getListOfSpeciesTypeInstances() |
Returns the
listOfSpeciesTypeInstances . |
int |
getNumInSpeciesTypeBonds() |
Returns the number of
InSpeciesTypeBond s in this
MultiSpeciesType . |
int |
getNumSpeciesFeatureTypes() |
Returns the number of
SpeciesFeatureType s in this
MultiSpeciesType . |
int |
getNumSpeciesTypeComponentIndexes() |
Returns the number of
SpeciesTypeComponentIndex s in this
MultiSpeciesType . |
int |
getNumSpeciesTypeInstances() |
Returns the number of
SpeciesTypeInstance s in this
MultiSpeciesType . |
SpeciesFeatureType |
getSpeciesFeatureType(int i) |
Gets an element from the
listOfSpeciesFeatureTypes at the given index. |
SpeciesFeatureType |
getSpeciesFeatureType(java.lang.String speciesFeatureTypeId) |
Gets an element from the listOfSpeciesFeatureTypes, with the given id.
|
int |
getSpeciesFeatureTypeCount() |
Returns the number of
SpeciesFeatureType s in this
MultiSpeciesType . |
SpeciesTypeComponentIndex |
getSpeciesTypeComponentIndex(int i) |
Gets an element from the
listOfSpeciesTypeComponentIndexes at the given index. |
SpeciesTypeComponentIndex |
getSpeciesTypeComponentIndex(java.lang.String speciesTypeComponentIndexId) |
Gets an element from the listOfSpeciesTypeComponentIndexes, with the given id.
|
int |
getSpeciesTypeComponentIndexCount() |
Returns the number of
SpeciesTypeComponentIndex s in this
MultiSpeciesType . |
SpeciesTypeInstance |
getSpeciesTypeInstance(int i) |
Gets an element from the
listOfSpeciesTypeInstances at the given index. |
SpeciesTypeInstance |
getSpeciesTypeInstance(java.lang.String speciesTypeInstanceId) |
Gets an element from the listOfSpeciesTypeInstances, with the given id.
|
int |
getSpeciesTypeInstanceCount() |
Returns the number of
SpeciesTypeInstance s in this
MultiSpeciesType . |
int |
hashCode() |
Returns a hash code value for this
SBase instance. |
void |
initDefaults() |
Initializes the default values.
|
boolean |
isCompartmentMandatory() |
|
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 |
isSetCompartment() |
|
boolean |
isSetCompartmentInstance() |
|
boolean |
isSetListOfInSpeciesTypeBonds() |
Returns
true if listOfInSpeciesTypeBonds contains at least
one element. |
boolean |
isSetListOfSpeciesFeatureTypes() |
Returns
true if listOfSpeciesFeatureTypes contains at least
one element. |
boolean |
isSetListOfSpeciesTypeComponentIndexes() |
Returns
true if listOfSpeciesTypeComponentIndexes contains at least
one element. |
boolean |
isSetListOfSpeciesTypeInstances() |
Returns
true if listOfSpeciesTypeInstances contains at least
one element. |
boolean |
readAttribute(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value) |
Sets the given attribute in this
SBase . |
InSpeciesTypeBond |
removeInSpeciesTypeBond(int i) |
Removes an element from the
listOfInSpeciesTypeBonds at the given index. |
InSpeciesTypeBond |
removeInSpeciesTypeBond(java.lang.String inSpeciesTypeBondId) |
Removes an element from the
listOfInSpeciesTypeBonds . |
boolean |
removeInSpeciesTypeBond(InSpeciesTypeBond inSpeciesTypeBond) |
Removes an element from the
listOfInSpeciesTypeBonds . |
SpeciesFeatureType |
removeSpeciesFeatureType(int i) |
Removes an element from the
listOfSpeciesFeatureTypes at the given index. |
SpeciesFeatureType |
removeSpeciesFeatureType(java.lang.String speciesFeatureTypeId) |
Removes an element from the
listOfSpeciesFeatureTypes . |
boolean |
removeSpeciesFeatureType(SpeciesFeatureType speciesFeatureType) |
Removes an element from the
listOfSpeciesFeatureTypes . |
SpeciesTypeComponentIndex |
removeSpeciesTypeComponentIndex(int i) |
Removes an element from the
listOfSpeciesTypeComponentIndexes at the given index. |
SpeciesTypeComponentIndex |
removeSpeciesTypeComponentIndex(java.lang.String speciesTypeComponentIndexId) |
Removes an element from the
listOfSpeciesTypeComponentIndexes . |
boolean |
removeSpeciesTypeComponentIndex(SpeciesTypeComponentIndex speciesTypeComponentIndex) |
Removes an element from the
listOfSpeciesTypeComponentIndexes . |
SpeciesTypeInstance |
removeSpeciesTypeInstance(int i) |
Removes an element from the
listOfSpeciesTypeInstances at the given index. |
SpeciesTypeInstance |
removeSpeciesTypeInstance(java.lang.String speciesTypeInstanceId) |
Removes an element from the
listOfSpeciesTypeInstances . |
boolean |
removeSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance) |
Removes an element from the
listOfSpeciesTypeInstances . |
boolean |
setCompartment(java.lang.String compartment) |
Sets the compartment attribute.
|
boolean |
setCompartment(Compartment compartment) |
Sets the compartment identifiers of this
CompartmentalizedSBase to
the id of the Compartment 'compartment'. |
void |
setListOfInSpeciesTypeBonds(ListOf<InSpeciesTypeBond> listOfInSpeciesTypeBonds) |
Sets the given
ListOf<InSpeciesTypeBond> . |
void |
setListOfSpeciesFeatureTypes(ListOf<SpeciesFeatureType> listOfSpeciesFeatureTypes) |
Sets the given
ListOf<SpeciesFeatureType> . |
void |
setListOfSpeciesTypeComponentIndexes(ListOf<SpeciesTypeComponentIndex> listOfSpeciesTypeComponentIndexes) |
Sets the given
ListOf<SpeciesTypeComponentIndex> . |
void |
setListOfSpeciesTypeInstances(ListOf<SpeciesTypeInstance> listOfSpeciesTypeInstances) |
Sets the given
ListOf<SpeciesTypeInstance> . |
boolean |
unsetCompartment() |
Remove the reference to a compartment, i.e., unset the value of the
variable 'compartment'.
|
boolean |
unsetListOfInSpeciesTypeBonds() |
|
boolean |
unsetListOfSpeciesFeatureTypes() |
|
boolean |
unsetListOfSpeciesTypeComponentIndexes() |
|
boolean |
unsetListOfSpeciesTypeInstances() |
|
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, getExtension, getExtensionCount, getExtensionPackages, getFirstElementIndex, 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, 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, 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
getParent
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 MultiSpeciesType()
public MultiSpeciesType(int level, int version)
level
- SBML Levelversion
- SBML Versionpublic MultiSpeciesType(MultiSpeciesType obj)
MultiSpeciesType
instance cloned from the given MultiSpeciesType
.obj
- the MultiSpeciesType
to clonepublic MultiSpeciesType(java.lang.String id)
id
- the identifier for the new element.public MultiSpeciesType(java.lang.String id, int level, int version)
id
- the identifier for this element.level
- the SBML Levelversion
- the SBML Versionpublic MultiSpeciesType(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 boolean addInSpeciesTypeBond(InSpeciesTypeBond inSpeciesTypeBond)
InSpeciesTypeBond
to the listOfInSpeciesTypeBonds
.
The listOfInSpeciesTypeBonds is initialized if necessary.
inSpeciesTypeBond
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public boolean addSpeciesFeatureType(SpeciesFeatureType speciesFeatureType)
SpeciesFeatureType
to the listOfSpeciesFeatureTypes
.
The listOfSpeciesFeatureTypes is initialized if necessary.
speciesFeatureType
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public boolean addSpeciesTypeComponentIndex(SpeciesTypeComponentIndex speciesTypeComponentIndex)
SpeciesTypeComponentIndex
to the listOfSpeciesTypeComponentIndexes
.
The listOfSpeciesTypeComponentIndexes is initialized if necessary.
speciesTypeComponentIndex
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public boolean addSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance)
SpeciesTypeInstance
to the listOfSpeciesTypeInstances
.
The listOfSpeciesTypeInstances is initialized if necessary.
speciesTypeInstance
- the element to add to the listtrue
(as specified by Collection.add(E)
)Collection.add(Object)
public MultiSpeciesType clone()
clone
in interface SBase
clone
in class SpeciesType
public InSpeciesTypeBond createInSpeciesTypeBond()
listOfInSpeciesTypeBonds
list.listOfInSpeciesTypeBonds
public InSpeciesTypeBond createInSpeciesTypeBond(java.lang.String id)
InSpeciesTypeBond
element and adds it to the
listOfInSpeciesTypeBonds
list.id
- the identifier that is to be applied to the new element.InSpeciesTypeBond
element, which is the last
element in the listOfInSpeciesTypeBonds
.public SpeciesFeatureType createSpeciesFeatureType()
listOfSpeciesFeatureTypes
list.listOfSpeciesFeatureTypes
public SpeciesFeatureType createSpeciesFeatureType(java.lang.String id)
SpeciesFeatureType
element and adds it to the
listOfSpeciesFeatureTypes
list.id
- the identifier that is to be applied to the new element.SpeciesFeatureType
element, which is the last
element in the listOfSpeciesFeatureTypes
.public SpeciesTypeComponentIndex createSpeciesTypeComponentIndex()
listOfSpeciesTypeComponentIndexes
list.listOfSpeciesTypeComponentIndexes
public SpeciesTypeComponentIndex createSpeciesTypeComponentIndex(java.lang.String id)
SpeciesTypeComponentIndex
element and adds it to the
listOfSpeciesTypeComponentIndexes
list.id
- the identifier that is to be applied to the new element.SpeciesTypeComponentIndex
element, which is the last
element in the listOfSpeciesTypeComponentIndexes
.public SpeciesTypeInstance createSpeciesTypeInstance()
listOfSpeciesTypeInstances
list.listOfSpeciesTypeInstances
public SpeciesTypeInstance createSpeciesTypeInstance(java.lang.String id)
SpeciesTypeInstance
element and adds it to the
listOfSpeciesTypeInstances
list.id
- the identifier that is to be applied to the new element.SpeciesTypeInstance
element, which is the last
element in the listOfSpeciesTypeInstances
.public boolean equals(java.lang.Object obj)
SBase
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.lang.String getCompartment()
CompartmentalizedSBase
getCompartment
in interface CompartmentalizedSBase
String
if it is not set.public Compartment getCompartmentInstance()
CompartmentalizedSBase
Compartment
that is referenced by this SBase
.
Note that the return type of this method is NamedSBase
because it
could be possible that some subclasses link other elements than
Compartment
.getCompartmentInstance
in interface CompartmentalizedSBase
Model
that represents the linked
Compartment
or null
if it does not exist or cannot
be retrieved (e.g., if this component has not yet been linked to a
Model
).public java.lang.String getElementName()
SBase
getElementName
in interface SBase
getElementName
in class AbstractSBase
public InSpeciesTypeBond getInSpeciesTypeBond(int i)
listOfInSpeciesTypeBonds
at the given index.i
- the index of the InSpeciesTypeBond
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 InSpeciesTypeBond getInSpeciesTypeBond(java.lang.String inSpeciesTypeBondId)
inSpeciesTypeBondId
- the id of the InSpeciesTypeBond
element to get.null
.public int getInSpeciesTypeBondCount()
InSpeciesTypeBond
s in this
MultiSpeciesType
.InSpeciesTypeBond
s in this
MultiSpeciesType
.public ListOf<InSpeciesTypeBond> getListOfInSpeciesTypeBonds()
listOfInSpeciesTypeBonds
.
Creates it if it does not already exist.listOfInSpeciesTypeBonds
.public ListOf<SpeciesFeatureType> getListOfSpeciesFeatureTypes()
listOfSpeciesFeatureTypes
.
Creates it if it does not already exist.listOfSpeciesFeatureTypes
.public ListOf<SpeciesTypeComponentIndex> getListOfSpeciesTypeComponentIndexes()
listOfSpeciesTypeComponentIndexes
.
Creates it if it does not already exist.listOfSpeciesTypeComponentIndexes
.public ListOf<SpeciesTypeInstance> getListOfSpeciesTypeInstances()
listOfSpeciesTypeInstances
.
Creates it if it does not already exist.listOfSpeciesTypeInstances
.public int getNumInSpeciesTypeBonds()
InSpeciesTypeBond
s in this
MultiSpeciesType
.InSpeciesTypeBond
s in this
MultiSpeciesType
.getInSpeciesTypeBondCount()
public int getNumSpeciesFeatureTypes()
SpeciesFeatureType
s in this
MultiSpeciesType
.SpeciesFeatureType
s in this
MultiSpeciesType
.getSpeciesFeatureTypeCount()
public int getNumSpeciesTypeComponentIndexes()
SpeciesTypeComponentIndex
s in this
MultiSpeciesType
.SpeciesTypeComponentIndex
s in this
MultiSpeciesType
.getSpeciesTypeComponentIndexCount()
public int getNumSpeciesTypeInstances()
SpeciesTypeInstance
s in this
MultiSpeciesType
.SpeciesTypeInstance
s in this
MultiSpeciesType
.getSpeciesTypeInstanceCount()
public SpeciesFeatureType getSpeciesFeatureType(int i)
listOfSpeciesFeatureTypes
at the given index.i
- the index of the SpeciesFeatureType
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 SpeciesFeatureType getSpeciesFeatureType(java.lang.String speciesFeatureTypeId)
speciesFeatureTypeId
- the id of the SpeciesFeatureType
element to get.null
.public int getSpeciesFeatureTypeCount()
SpeciesFeatureType
s in this
MultiSpeciesType
.SpeciesFeatureType
s in this
MultiSpeciesType
.public SpeciesTypeComponentIndex getSpeciesTypeComponentIndex(int i)
listOfSpeciesTypeComponentIndexes
at the given index.i
- the index of the SpeciesTypeComponentIndex
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 SpeciesTypeComponentIndex getSpeciesTypeComponentIndex(java.lang.String speciesTypeComponentIndexId)
speciesTypeComponentIndexId
- the id of the SpeciesTypeComponentIndex
element to get.null
.public int getSpeciesTypeComponentIndexCount()
SpeciesTypeComponentIndex
s in this
MultiSpeciesType
.SpeciesTypeComponentIndex
s in this
MultiSpeciesType
.public SpeciesTypeInstance getSpeciesTypeInstance(int i)
listOfSpeciesTypeInstances
at the given index.i
- the index of the SpeciesTypeInstance
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 SpeciesTypeInstance getSpeciesTypeInstance(java.lang.String speciesTypeInstanceId)
speciesTypeInstanceId
- the id of the SpeciesTypeInstance
element to get.null
.public int getSpeciesTypeInstanceCount()
SpeciesTypeInstance
s in this
MultiSpeciesType
.SpeciesTypeInstance
s in this
MultiSpeciesType
.public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractSBase
SBase
instance.Object.hashCode()
public void initDefaults()
public boolean isCompartmentMandatory()
isCompartmentMandatory
in interface CompartmentalizedSBase
true
if for this object the compartment attribute is
mandatory, false
otherwise.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 SpeciesType
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 isSetCompartment()
isSetCompartment
in interface CompartmentalizedSBase
true
if compartment attribute is set, i.e., not
null
, false
otherwise.public boolean isSetCompartmentInstance()
isSetCompartmentInstance
in interface CompartmentalizedSBase
true
if the Compartment
which has the compartment
identifier stored in this CompartmentalizedSBase
as id is
not null
and this Compartment
can be retrieved from
the Model
that contains this CompartmentalizedSBase
.
In other words, this method also returns false
if the
this object is not linked to any model.public boolean isSetListOfInSpeciesTypeBonds()
true
if listOfInSpeciesTypeBonds
contains at least
one element.true
if listOfInSpeciesTypeBonds
contains at least
one element, otherwise false
.public boolean isSetListOfSpeciesFeatureTypes()
true
if listOfSpeciesFeatureTypes
contains at least
one element.true
if listOfSpeciesFeatureTypes
contains at least
one element, otherwise false
.public boolean isSetListOfSpeciesTypeComponentIndexes()
true
if listOfSpeciesTypeComponentIndexes
contains at least
one element.true
if listOfSpeciesTypeComponentIndexes
contains at least
one element, otherwise false
.public boolean isSetListOfSpeciesTypeInstances()
true
if listOfSpeciesTypeInstances
contains at least
one element.true
if listOfSpeciesTypeInstances
contains at least
one element, otherwise false
.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.public boolean removeInSpeciesTypeBond(InSpeciesTypeBond inSpeciesTypeBond)
listOfInSpeciesTypeBonds
.inSpeciesTypeBond
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public InSpeciesTypeBond removeInSpeciesTypeBond(int i)
listOfInSpeciesTypeBonds
at the given index.i
- the index where to remove the InSpeciesTypeBond
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfInSpeciesTypeBonds)
).public InSpeciesTypeBond removeInSpeciesTypeBond(java.lang.String inSpeciesTypeBondId)
listOfInSpeciesTypeBonds
.inSpeciesTypeBondId
- the id of the element to be removed from the list.null
.public SpeciesFeatureType removeSpeciesFeatureType(int i)
listOfSpeciesFeatureTypes
at the given index.i
- the index where to remove the SpeciesFeatureType
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfSpeciesFeatureTypes)
).public boolean removeSpeciesFeatureType(SpeciesFeatureType speciesFeatureType)
listOfSpeciesFeatureTypes
.speciesFeatureType
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public SpeciesFeatureType removeSpeciesFeatureType(java.lang.String speciesFeatureTypeId)
listOfSpeciesFeatureTypes
.speciesFeatureTypeId
- the id of the element to be removed from the list.null
.public SpeciesTypeComponentIndex removeSpeciesTypeComponentIndex(int i)
listOfSpeciesTypeComponentIndexes
at the given index.i
- the index where to remove the SpeciesTypeComponentIndex
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfSpeciesTypeComponentIndexes)
).public boolean removeSpeciesTypeComponentIndex(SpeciesTypeComponentIndex speciesTypeComponentIndex)
listOfSpeciesTypeComponentIndexes
.speciesTypeComponentIndex
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public SpeciesTypeComponentIndex removeSpeciesTypeComponentIndex(java.lang.String speciesTypeComponentIndexId)
listOfSpeciesTypeComponentIndexes
.speciesTypeComponentIndexId
- the id of the element to be removed from the list.null
.public SpeciesTypeInstance removeSpeciesTypeInstance(int i)
listOfSpeciesTypeInstances
at the given index.i
- the index where to remove the SpeciesTypeInstance
.java.lang.IndexOutOfBoundsException
- if the listOf is not set or if the index is
out of bound ((i < 0) || (i > listOfSpeciesTypeInstances)
).public boolean removeSpeciesTypeInstance(SpeciesTypeInstance speciesTypeInstance)
listOfSpeciesTypeInstances
.speciesTypeInstance
- the element to be removed from the list.true
if the list contained the specified element and it was
removed.List.remove(Object)
public SpeciesTypeInstance removeSpeciesTypeInstance(java.lang.String speciesTypeInstanceId)
listOfSpeciesTypeInstances
.speciesTypeInstanceId
- the id of the element to be removed from the list.null
.public boolean setCompartment(Compartment compartment)
CompartmentalizedSBase
CompartmentalizedSBase
to
the id of the Compartment
'compartment'.
The compartment attribute is used to add a reference to the id of
the corresponding Compartment
in the Model
.
In some situations, the compartment might be optional, so that the user can
even specify Compartment
s that are not part of the Model
.
setCompartment
in interface CompartmentalizedSBase
compartment
- the Compartment
whose identifier should be referenced.true
if this operation caused any change.CompartmentalizedSBase.setCompartment(String)
,
CompartmentalizedSBase.isCompartmentMandatory()
public boolean setCompartment(java.lang.String compartment)
CompartmentalizedSBase
The required attribute compartment is used to identify the
Compartment
in which the CompartmentalizedSBase
is located.
The attribute's value should be the identifier of an existing
Compartment
object in the model.
setCompartment
in interface CompartmentalizedSBase
compartment
- the identifier of the compartment to be set.true
if this operation caused any change.CompartmentalizedSBase.setCompartment(Compartment)
,
CompartmentalizedSBase.isCompartmentMandatory()
public void setListOfInSpeciesTypeBonds(ListOf<InSpeciesTypeBond> listOfInSpeciesTypeBonds)
ListOf<InSpeciesTypeBond>
.
If listOfInSpeciesTypeBonds
was defined before and contains some
elements, they are all unset.listOfInSpeciesTypeBonds
- the list of InSpeciesTypeBond
public void setListOfSpeciesFeatureTypes(ListOf<SpeciesFeatureType> listOfSpeciesFeatureTypes)
ListOf<SpeciesFeatureType>
.
If listOfSpeciesFeatureTypes
was defined before and contains some
elements, they are all unset.listOfSpeciesFeatureTypes
- the list of SpeciesFeatureType
public void setListOfSpeciesTypeComponentIndexes(ListOf<SpeciesTypeComponentIndex> listOfSpeciesTypeComponentIndexes)
ListOf<SpeciesTypeComponentIndex>
.
If listOfSpeciesTypeComponentIndexes
was defined before and contains some
elements, they are all unset.listOfSpeciesTypeComponentIndexes
- the list of SpeciesTypeComponentIndex
public void setListOfSpeciesTypeInstances(ListOf<SpeciesTypeInstance> listOfSpeciesTypeInstances)
ListOf<SpeciesTypeInstance>
.
If listOfSpeciesTypeInstances
was defined before and contains some
elements, they are all unset.listOfSpeciesTypeInstances
- the list of SpeciesTypeInstance
public boolean unsetCompartment()
CompartmentalizedSBase
unsetCompartment
in interface CompartmentalizedSBase
true
if compartment was set before, otherwise false
.public boolean unsetListOfInSpeciesTypeBonds()
true
if listOfInSpeciesTypeBonds
contains at least
one element, otherwise false
.public boolean unsetListOfSpeciesFeatureTypes()
true
if listOfSpeciesFeatureTypes
contains at least
one element, otherwise false
.public boolean unsetListOfSpeciesTypeComponentIndexes()
true
if listOfSpeciesTypeComponentIndexes
contains at least
one element, otherwise false
.public boolean unsetListOfSpeciesTypeInstances()
true
if listOfSpeciesTypeInstances
contains at least
one element, otherwise false
.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.