java.io.Serializable
, java.lang.Cloneable
, javax.swing.tree.TreeNode
, CallableSBase
, NamedSBase
, NamedSBaseWithDerivedUnit
, SBase
, SBaseWithDerivedUnit
, UniqueNamedSBase
, UniqueSId
, TreeNodeWithChangeSupport
public class Output extends AbstractNamedSBase implements UniqueNamedSBase, CallableSBase
Output
refers to a QualitativeSpecies
that participates
in (is affected by) the corresponding Transition
. In Petri net models
these are the output places of the transition. In a logical model, a
QualitativeSpecies
should be referenced in at most one listOfOutputs,
(that of the Transition
defining the evolution of this species). When
a Transition
has several outputs, it is because the referenced
species share the same regulators and the same logical rules.JSBML_WRONG_SBO_TERM
Constructor | Description |
---|---|
Output() |
Creates a new
Output instance. |
Output(int level,
int version) |
Creates a new
Output instance. |
Output(java.lang.String id) |
Creates a new
Output instance. |
Output(java.lang.String id,
int level,
int version) |
Creates a new
Output instance. |
Output(java.lang.String id,
java.lang.String name,
int level,
int version) |
Creates a new
Output instance. |
Output(java.lang.String id,
QualitativeSpecies qualitativeSpecies,
OutputTransitionEffect transitionEffect) |
Creates a new
Output instance. |
Output(Output out) |
Creates a new
Output instance. |
Output(QualitativeSpecies qualitativeSpecies,
OutputTransitionEffect transitionEffect) |
Creates a new
Output instance. |
Modifier and Type | Method | Description |
---|---|---|
Output |
clone() |
Creates a deep copy of this object, i.e., a new
SBase with the same
properties
like this one. |
boolean |
containsUndeclaredUnits() |
Returns
true or false depending on whether this
SBaseWithDerivedUnit refers to elements such as parameters or
numbers with undeclared units. |
boolean |
equals(java.lang.Object object) |
|
UnitDefinition |
getDerivedUnitDefinition() |
Derives the unit of this quantity and tries to identify an
equivalent
UnitDefinition within the corresponding Model . |
java.lang.String |
getDerivedUnits() |
Derives the unit of this quantity.
|
int |
getOutputLevel() |
Returns the outputLevel.
|
java.lang.String |
getQualitativeSpecies() |
Returns the qualitativeSpecies
|
QualitativeSpecies |
getQualitativeSpeciesInstance() |
|
OutputTransitionEffect |
getTransitionEffect() |
Returns the transitionEffect
|
int |
hashCode() |
Returns a hash code value for this
SBase instance. |
void |
initDefaults() |
|
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 |
isOutputLevelMandatory() |
|
boolean |
isQualitativeSpeciesMandatory() |
|
boolean |
isSetOutputLevel() |
|
boolean |
isSetQualitativeSpecies() |
|
boolean |
isSetTransitionEffect() |
|
boolean |
isTransitionEffectMandatory() |
|
boolean |
readAttribute(java.lang.String attributeName,
java.lang.String prefix,
java.lang.String value) |
Sets the given attribute in this
SBase . |
void |
setOutputLevel(int level) |
The outputLevel is a non-negative integer used along with the transitionEffect to specify
the effect of the
Transition on the corresponding QualitativeSpecies . |
void |
setQualitativeSpecies(java.lang.String qualitativeSpecies) |
The required attribute qualitativeSpecies is used to identify the
QualitativeSpecies
that is the output of this Transition . |
void |
setTransitionEffect(OutputTransitionEffect transitionEffect) |
Each
Output has a required attribute transitionEffect of type OutputTransitionEffect
which describes how the QualitativeSpecies referenced by the Output is affected by
the Transition . |
boolean |
unsetOutputLevel() |
|
boolean |
unsetQualitativeSpecies() |
|
boolean |
unsetTransitionEffect() |
|
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 Output()
Output
instance.public Output(java.lang.String id)
Output
instance.id
- the idpublic Output(QualitativeSpecies qualitativeSpecies, OutputTransitionEffect transitionEffect)
Output
instance.qualitativeSpecies
- the QualitativeSpecies
linked to this Output
.transitionEffect
- the transition effectpublic Output(java.lang.String id, QualitativeSpecies qualitativeSpecies, OutputTransitionEffect transitionEffect)
Output
instance.id
- the idqualitativeSpecies
- the QualitativeSpecies
linked to this Output
.transitionEffect
- the transition effectpublic Output(int level, int version)
Output
instance.level
- the SBML levelversion
- the SBML versionpublic Output(java.lang.String id, int level, int version)
Output
instance.id
- the idlevel
- the SBML levelversion
- the SBML versionpublic Output(java.lang.String id, java.lang.String name, int level, int version)
Output
instance.id
- the idname
- the namelevel
- the SBML levelversion
- the SBML versionpublic void initDefaults()
public Output clone()
SBase
SBase
with the same
properties
like this one.clone
in interface SBase
clone
in class AbstractSBase
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 isQualitativeSpeciesMandatory()
public boolean isSetQualitativeSpecies()
public java.lang.String getQualitativeSpecies()
PropertyUndefinedError
- if isSetQualitativeSpecies()
return false
.public QualitativeSpecies getQualitativeSpeciesInstance()
public void setQualitativeSpecies(java.lang.String qualitativeSpecies)
QualitativeSpecies
that is the output of this Transition
. The attribute's value must be the identifier
of an existing QualitativeSpecies
object in the Model
. This attribute is
comparable with the species attribute on the SpeciesReference
element.qualitativeSpecies
- the qualitativeSpecies to setpublic boolean unsetQualitativeSpecies()
public boolean isTransitionEffectMandatory()
public boolean isSetTransitionEffect()
public OutputTransitionEffect getTransitionEffect()
PropertyUndefinedError
- if isSetTransitionEffect()
return false
.public void setTransitionEffect(OutputTransitionEffect transitionEffect)
Output
has a required attribute transitionEffect of type OutputTransitionEffect
which describes how the QualitativeSpecies
referenced by the Output
is affected by
the Transition
.
In logical models the transitionEffect is set to "assignmentLevel" whilst in standard Petri nets it
is set to "production". It is envisioned that to encode High Level Petri nets it will be necessary
to allow the use of "assignmentLevel" as an OutputTransitionEffect
; however considering the
implications of this is left to future versions of the specification.transitionEffect
- the transitionEffect to setpublic boolean unsetTransitionEffect()
public boolean isOutputLevelMandatory()
public boolean isSetOutputLevel()
public int getOutputLevel()
PropertyUndefinedError
- if isSetOutputLevel()
return false
.public void setOutputLevel(int level)
Transition
on the corresponding QualitativeSpecies
. It
does not specify the result of a Transition
; this is done by using the resultLevel
attribute on a FunctionTerm
. However, in Petri nets, it relates to the weight of the
arc connecting the Transition
to the output place and may be multiplied by the
resultLevel in a "production" situation. In logical models there is no interpretation of the
outputLevel attribute as the outcome of a Transition
is always an assignment to
the resultLevel defined by the FunctionTerm
.
The outputLevel attribute is optional since if the transitionEffect is set to "assignmentLevel"
(as in logical models), it has no meaning. However, where the transitionEffect of the
Output
is set to "production" (as in Petri net models) the resulting level of the
QualitativeSpecies
is the resultLevel from the appropriate FunctionTerm
multiplied
by the outputLevel. Since there are no default values in SBML Level 3, when the transitionEffect
is set to "production" the outputLevel attribute must have a value.level
- the level to setpublic boolean unsetOutputLevel()
public boolean equals(java.lang.Object object)
SBase
public int hashCode()
SBase
SBase
instance.hashCode
in interface SBase
hashCode
in class AbstractSBase
SBase
instance.Object.hashCode()
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 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 containsUndeclaredUnits()
SBaseWithDerivedUnit
true
or false
depending on whether this
SBaseWithDerivedUnit
refers to elements such as parameters or
numbers with undeclared units.
A return value of true indicates that the UnitDefinition
returned by SBaseWithDerivedUnit.getDerivedUnitDefinition()
may not accurately
represent the units of the expression.containsUndeclaredUnits
in interface SBaseWithDerivedUnit
true
if the math expression of this SBaseWithDerivedUnit
includes parameters/numbers with undeclared units,
false
otherwise.public UnitDefinition getDerivedUnitDefinition()
SBaseWithDerivedUnit
UnitDefinition
within the corresponding Model
.
If no equivalent unit definition can be found, a new unit definition will
be created that is not part of the model but represents the unit of this
quantity. If it is not possible to derive a unit for this quantity, null
will be returned.getDerivedUnitDefinition
in interface SBaseWithDerivedUnit
UnitDefinition
that represent the derived unit of this quantity, or null
if it is not possible to derive a unit.public java.lang.String getDerivedUnits()
SBaseWithDerivedUnit
Unit.Kind
this
method will return the String
representation of this
Unit.Kind
.getDerivedUnits
in interface SBaseWithDerivedUnit
String
that represent the id of a UnitDefinition
. This UnitDefinition
represent the derived unit of this quantity. If it is not possible to derive a unit for this quantity
or if no equivalent UnitDefinition
can be found in the Model
, null is returned.