org.sbml.jsbml.ext.qual

Class Output

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.qual.Output

All Implemented Interfaces:

Serializable, Cloneable, TreeNode, CallableSBase, NamedSBase, NamedSBaseWithDerivedUnit, SBase, SBaseWithDerivedUnit, UniqueNamedSBase, UniqueSId, TreeNodeWithChangeSupport

public class Output
extends AbstractNamedSBase
implements UniqueNamedSBase, CallableSBase

Each 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.

Since:

1.0

Author:

Nicolas Rodriguez, Finja Büchel, Florian Mittag

See Also:

Serialized Form

Field Summary

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements, JSBML_WRONG_SBO_TERM, packageName

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, resourceBundle

Constructor Summary

Constructors

Constructor and Description
Output() Creates a new Output instance.
Output(int level, int version) Creates a new Output instance.
Output(Output out) Creates a new Output instance.
Output(QualitativeSpecies qualitativeSpecies, OutputTransitionEffect transitionEffect) Creates a new Output instance.
Output(String id) Creates a new Output instance.
Output(String id, int level, int version) Creates a new Output instance.
Output(String id, QualitativeSpecies qualitativeSpecies, OutputTransitionEffect transitionEffect) Creates a new Output instance.
Output(String id, String name, int level, int version) Creates a new Output instance.

Method Summary

Modifier and Type	Method and Description
Output	clone()
boolean	containsUndeclaredUnits()
boolean	equals(Object object)
UnitDefinition	getDerivedUnitDefinition()
String	getDerivedUnits()
int	getOutputLevel() Returns the outputLevel.
String	getQualitativeSpecies() Returns the qualitativeSpecies
QualitativeSpecies	getQualitativeSpeciesInstance()
OutputTransitionEffect	getTransitionEffect() Returns the transitionEffect
int	hashCode()
void	initDefaults()
boolean	isIdMandatory()
boolean	isOutputLevelMandatory()
boolean	isQualitativeSpeciesMandatory()
boolean	isSetOutputLevel()
boolean	isSetQualitativeSpecies()
boolean	isSetTransitionEffect()
boolean	isTransitionEffectMandatory()
boolean	readAttribute(String attributeName, String prefix, String value)
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(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()
Map<String,String>	writeXMLAttributes()

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendAnnotation, appendAnnotation, appendNotes, appendNotes, checkAndSetPackageNamespaceAndVersion, checkAndSetPackageNamespaceAndVersion, checkAttribute, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementByMetaId, getElementBySId, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getId, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getName, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getPackageName, getPackageVersion, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getURI, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetId, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetName, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setAnnotation, setAnnotation, setHistory, setId, setLevel, setMetaId, setName, setNamespace, setNotes, setNotes, setPackageVersion, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, toString, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetId, unsetMetaId, unsetName, unsetNamespace, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from class org.sbml.jsbml.AbstractTreeNode

addAllChangeListeners, addAllChangeListeners, addTreeNodeChangeListener, addTreeNodeChangeListener, children, clearUserObjects, containsUserObjectKey, filter, filter, filter, fireNodeAddedEvent, getIndex, getListOfTreeNodeChangeListeners, getNumChildren, getRoot, getTreeNodeChangeListenerCount, getUserObject, indexOf, isCloningInProgress, isInvalidSBMLAllowed, isLeaf, isReadingInProgress, isRoot, isSetParent, isSetUserObjects, putUserObject, removeAllTreeNodeChangeListeners, removeAllTreeNodeChangeListeners, removeFromParent, removeTreeNodeChangeListener, removeTreeNodeChangeListener, removeUserObject, setParent, userObjectKeySet

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.sbml.jsbml.NamedSBase

getId, getName, isSetId, isSetName, setId, setName, unsetId, unsetName

Methods inherited from interface org.sbml.jsbml.SBase

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, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetPackageVErsion, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setAnnotation, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, setPackageVersion, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, unsetNotes, unsetPlugin, unsetSBOTerm

Methods inherited from interface org.sbml.jsbml.util.TreeNodeWithChangeSupport

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

Methods inherited from interface javax.swing.tree.TreeNode

children, getAllowsChildren, getChildAt, getChildCount, getIndex, getParent, isLeaf

Constructor Detail

Output

public Output()

Creates a new Output instance.

Output

public Output(String id)

Creates a new Output instance.

Parameters:

id - the id

Output

public Output(QualitativeSpecies qualitativeSpecies,
              OutputTransitionEffect transitionEffect)

Creates a new Output instance.

Parameters:

qualitativeSpecies - the QualitativeSpecies linked to this Output.

transitionEffect - the transition effect

Output

public Output(String id,
              QualitativeSpecies qualitativeSpecies,
              OutputTransitionEffect transitionEffect)

Creates a new Output instance.

Parameters:

id - the id

qualitativeSpecies - the QualitativeSpecies linked to this Output.

transitionEffect - the transition effect

Output

public Output(int level,
              int version)

Creates a new Output instance.

Parameters:

level - the SBML level

version - the SBML version

Output

public Output(String id,
              int level,
              int version)

Creates a new Output instance.

Parameters:

id - the id

level - the SBML level

version - the SBML version

Output

public Output(String id,
              String name,
              int level,
              int version)

Creates a new Output instance.

Parameters:

id - the id

name - the name

level - the SBML level

version - the SBML version

Output

public Output(Output out)

Creates a new Output instance.

Parameters:

out - the Output instance to be cloned

Method Detail

initDefaults

public void initDefaults()

clone

public Output clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

isIdMandatory

public boolean isIdMandatory()

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

isQualitativeSpeciesMandatory

public boolean isQualitativeSpeciesMandatory()

Returns:

true

isSetQualitativeSpecies

public boolean isSetQualitativeSpecies()

Returns:

getQualitativeSpecies

public String getQualitativeSpecies()

Returns the qualitativeSpecies

Returns:

the qualitativeSpecies

Throws:

PropertyUndefinedError - if isSetQualitativeSpecies() return false.

getQualitativeSpeciesInstance

public QualitativeSpecies getQualitativeSpeciesInstance()

setQualitativeSpecies

public void setQualitativeSpecies(String qualitativeSpecies)

The required attribute qualitativeSpecies is used to identify the 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.

Parameters:

qualitativeSpecies - the qualitativeSpecies to set

unsetQualitativeSpecies

public boolean unsetQualitativeSpecies()

Returns:

isTransitionEffectMandatory

public boolean isTransitionEffectMandatory()

Returns:

false

isSetTransitionEffect

public boolean isSetTransitionEffect()

Returns:

getTransitionEffect

public OutputTransitionEffect getTransitionEffect()

Returns the transitionEffect

Returns:

the transitionEffect

Throws:

PropertyUndefinedError - if isSetTransitionEffect() return false.

setTransitionEffect

public 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. 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.

Parameters:

transitionEffect - the transitionEffect to set

unsetTransitionEffect

public boolean unsetTransitionEffect()

Returns:

isOutputLevelMandatory

public boolean isOutputLevelMandatory()

Returns:

false

isSetOutputLevel

public boolean isSetOutputLevel()

Returns:

getOutputLevel

public int getOutputLevel()

Returns the outputLevel.

Returns:

the outputLevel

Throws:

PropertyUndefinedError - if isSetOutputLevel() return false.

setOutputLevel

public 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. 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.

Parameters:

level - the level to set

unsetOutputLevel

public boolean unsetOutputLevel()

Returns:

equals

public boolean equals(Object object)

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractSBase

hashCode

public int hashCode()

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractSBase

readAttribute

public boolean readAttribute(String attributeName,
                             String prefix,
                             String value)

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractSBase

writeXMLAttributes

public Map<String,String> writeXMLAttributes()

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractSBase

containsUndeclaredUnits

public boolean containsUndeclaredUnits()

Specified by:

containsUndeclaredUnits in interface SBaseWithDerivedUnit

getDerivedUnitDefinition

public UnitDefinition getDerivedUnitDefinition()

Specified by:

getDerivedUnitDefinition in interface SBaseWithDerivedUnit

getDerivedUnits

public String getDerivedUnits()

Specified by:

getDerivedUnits in interface SBaseWithDerivedUnit