java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, NamedSBase
, SBase
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
public class SpeciesTypeInstance extends AbstractNamedSBase implements UniqueNamedSBase
MultiSpeciesType
s and Species
with multiple components.
A speciesType can contain a list of instances of other speciesTypes which can also have their own speciesTypeInstances, so the complete structure of a speciesType can be like a tree. A speciesType can not contain an instance of any other speciesType that already contains the instance of it. In other words, circular references are not allowed when constructing speciesTypes. For example, if a speciesType 'A' contains the instance of another speciesType 'B', 'B' must not contain the instance of 'A' anywhere in the complete structure of 'B'.
JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
SpeciesTypeInstance() |
Creates an SpeciesTypeInstance instance
|
SpeciesTypeInstance(int level,
int version) |
Creates a SpeciesTypeInstance instance with a level and version.
|
SpeciesTypeInstance(java.lang.String id) |
Creates a SpeciesTypeInstance instance with an id.
|
SpeciesTypeInstance(java.lang.String id,
int level,
int version) |
Creates a SpeciesTypeInstance instance with an id, level, and version.
|
SpeciesTypeInstance(java.lang.String id,
java.lang.String name,
int level,
int version) |
Creates a SpeciesTypeInstance instance with an id, name, level, and version.
|
SpeciesTypeInstance(SpeciesTypeInstance obj) |
Clone constructor
|
Modifier and Type | Method | Description |
---|---|---|
SpeciesTypeInstance |
clone() |
clones this class
|
boolean |
equals(java.lang.Object obj) |
|
java.lang.String |
getCompartmentReference() |
Returns the value of
compartmentReference . |
java.lang.String |
getSpeciesType() |
Returns the value of
speciesType . |
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 |
isSetCompartmentReference() |
Returns whether
compartmentReference is set. |
boolean |
isSetSpeciesType() |
Returns whether
speciesType is set. |
boolean |
readAttribute(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value) |
Sets the given attribute in this
SBase . |
void |
setCompartmentReference(java.lang.String compartmentReference) |
Sets the value of compartmentReference
|
void |
setSpeciesType(java.lang.String speciesType) |
Sets the value of speciesType
|
boolean |
unsetCompartmentReference() |
Unsets the variable compartmentReference.
|
boolean |
unsetSpeciesType() |
Unsets the variable speciesType.
|
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, getChildAt, getChildCount, 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, getChildAt, getChildCount, 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 SpeciesTypeInstance()
public SpeciesTypeInstance(java.lang.String id)
id
- the identifier for the new element.public SpeciesTypeInstance(int level, int version)
level
- SBML Levelversion
- SBML Versionpublic SpeciesTypeInstance(java.lang.String id, int level, int version)
id
- the identifier for this element.level
- the SBML Levelversion
- the SBML Versionpublic SpeciesTypeInstance(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 SpeciesTypeInstance(SpeciesTypeInstance obj)
public SpeciesTypeInstance clone()
clone
in interface SBase
clone
in class AbstractSBase
public void initDefaults()
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 java.lang.String getSpeciesType()
speciesType
.speciesType
.public boolean isSetSpeciesType()
speciesType
is set.speciesType
is set.public void setSpeciesType(java.lang.String speciesType)
speciesType
- the value of speciesType to be set.public boolean unsetSpeciesType()
true
if speciesType was set before, otherwise false
.public java.lang.String getCompartmentReference()
compartmentReference
.compartmentReference
.public boolean isSetCompartmentReference()
compartmentReference
is set.compartmentReference
is set.public void setCompartmentReference(java.lang.String compartmentReference)
compartmentReference
- the value of compartmentReference to be set.public boolean unsetCompartmentReference()
true
if compartmentReference was set before, otherwise false
.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 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.