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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.TreeNode, CallableSBase, NamedSBase, NamedSBaseWithDerivedUnit, SBase, SBaseWithDerivedUnit, UniqueNamedSBase, 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

Version:

$Rev: 1725 $

Author:

Nicolas Rodriguez, Finja Büchel, Florian Mittag

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
private java.lang.Integer	outputLevel
private java.lang.String	qualitativeSpecies
private static long	serialVersionUID Generated serial version identifier.
private OutputTransitionEffect	transitionEffect

Fields inherited from class org.sbml.jsbml.AbstractSBase

ignoredExtensions, ignoredXMLElements

Fields inherited from class org.sbml.jsbml.AbstractTreeNode

listOfListeners, parent, UNKNOWN_ATTRIBUTES, UNKNOWN_ELEMENTS

Constructor Summary

Constructors

Constructor and Description
Output()
Output(int level, int version)
Output(Output out)
Output(QualitativeSpecies qualitativeSpecies, OutputTransitionEffect transitionEffect)
Output(java.lang.String id)
Output(java.lang.String id, int level, int version)
Output(java.lang.String id, QualitativeSpecies qualitativeSpecies, OutputTransitionEffect transitionEffect)
Output(java.lang.String id, java.lang.String name, int level, int version)

Method Summary

Methods

Modifier and Type	Method and 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) Returns true if and only if the given SBase has exactly the same properties like this SBase instance.
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
OutputTransitionEffect	getTransitionEffect() Returns the transitionEffect
int	hashCode() Returns a hash code value for this SBase instance.
void	initDefaults()
boolean	isIdMandatory() This method can be used to query if the identifier of this NamedSBase 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.

Methods inherited from class org.sbml.jsbml.AbstractNamedSBase

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

Methods inherited from class org.sbml.jsbml.AbstractSBase

addCVTerm, addDeclaredNamespace, addExtension, addPlugin, appendNotes, appendNotes, checkLevelAndVersionCompatibility, createHistory, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, fireNodeRemovedEvent, firePropertyChange, getAllowsChildren, getAnnotation, getAnnotationString, getChildAt, getChildCount, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getIdManager, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParent, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, isValidLevelAndVersionCombination, isValidMetaId, notifyChildChange, registerChild, removeCVTerm, removeCVTerm, setAnnotation, setHistory, setLevel, setMetaId, setNamespace, setNotes, setNotes, setParentSBML, setParentSBMLObject, setSBOTerm, setSBOTerm, setThisAsParentSBMLObject, setVersion, unregisterChild, unsetAnnotation, unsetCVTerms, unsetExtension, unsetHistory, unsetMetaId, 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, isLeaf, 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, appendNotes, appendNotes, createPlugin, disablePackage, enablePackage, enablePackage, filterCVTerms, filterCVTerms, filterCVTerms, filterCVTerms, getAnnotation, getAnnotationString, getCVTerm, getCVTermCount, getCVTerms, getDeclaredNamespaces, getElementName, getExtension, getExtensionCount, getExtensionPackages, getHistory, getLevel, getLevelAndVersion, getMetaId, getModel, getNamespace, getNotes, getNotesString, getNumCVTerms, getNumPlugins, getParentSBMLObject, getPlugin, getSBMLDocument, getSBOTerm, getSBOTermID, getVersion, hasValidAnnotation, hasValidLevelVersionNamespaceCombination, isExtendedByOtherPackages, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetHistory, isSetLevel, isSetLevelAndVersion, isSetMetaId, isSetNotes, isSetParentSBMLObject, isSetPlugin, isSetSBOTerm, isSetVersion, registerChild, removeCVTerm, removeCVTerm, removeTreeNodeChangeListener, setAnnotation, setHistory, setLevel, setMetaId, setNotes, setNotes, 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

Field Detail

serialVersionUID

private static final long serialVersionUID

Generated serial version identifier.

See Also:

Constant Field Values

qualitativeSpecies

private java.lang.String qualitativeSpecies

transitionEffect

private OutputTransitionEffect transitionEffect

outputLevel

private java.lang.Integer outputLevel

Constructor Detail

Output

public Output()

Output

public Output(java.lang.String id)

Parameters:

id -

Output

public Output(QualitativeSpecies qualitativeSpecies,
      OutputTransitionEffect transitionEffect)

Parameters:

qualitativeSpecies -

Output

public Output(java.lang.String id,
      QualitativeSpecies qualitativeSpecies,
      OutputTransitionEffect transitionEffect)

Parameters:

id -

qualitativeSpecies -

transitionEffect -

Output

public Output(int level,
      int version)

Parameters:

level -

version -

Output

public Output(java.lang.String id,
      int level,
      int version)

Parameters:

id -

level -

version -

Output

public Output(java.lang.String id,
      java.lang.String name,
      int level,
      int version)

Parameters:

id -

name -

level -

version -

Output

public Output(Output out)

Method Detail

initDefaults

public void initDefaults()

clone

public Output clone()

Description copied from interface: SBase

Creates a deep copy of this object, i.e., a new SBase with the same properties like this one.

Specified by:

clone in interface SBase

Specified by:

clone in class AbstractSBase

Returns:

a copy of this object

isIdMandatory

public boolean isIdMandatory()

Description copied from interface: NamedSBase

This method can be used to query if the identifier of this NamedSBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Returns:

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.

isQualitativeSpeciesMandatory

public boolean isQualitativeSpeciesMandatory()

Returns:

true

isSetQualitativeSpecies

public boolean isSetQualitativeSpecies()

Returns:

getQualitativeSpecies

public java.lang.String getQualitativeSpecies()

Returns the qualitativeSpecies

Returns:

the qualitativeSpecies

Throws:

PropertyUndefinedError - if isSetQualitativeSpecies() return false.

setQualitativeSpecies

public void setQualitativeSpecies(java.lang.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(java.lang.Object object)

Description copied from interface: SBase

Returns true if and only if the given SBase has exactly the same properties like this SBase instance.

Specified by:

equals in interface SBase

Overrides:

equals in class AbstractNamedSBase

Parameters:

object - the SBase to be compared to.

Returns:

true if and only if the given Object is an instance of SBase that has exactly the same properties like this SBase instance.

hashCode

public int hashCode()

Description copied from interface: SBase

Returns a hash code value for this SBase instance.

Specified by:

hashCode in interface SBase

Overrides:

hashCode in class AbstractNamedSBase

Returns:

a hash code value for this SBase instance.

See Also:

Object.hashCode()

readAttribute

public boolean readAttribute(java.lang.String attributeName,
                    java.lang.String prefix,
                    java.lang.String value)

Description copied from interface: SBase

Sets the given attribute in this SBase.

If the given attribute name is not recognized, nothing is done and false is returned.

Specified by:

readAttribute in interface SBase

Overrides:

readAttribute in class AbstractNamedSBase

Parameters:

attributeName - localName of the XML attribute

prefix - prefix of the XML attribute

value - value of the XML attribute

Returns:

true if the attribute has been successfully read.

writeXMLAttributes

public java.util.Map<java.lang.String,java.lang.String> writeXMLAttributes()

Description copied from interface: SBase

Returns a map with all the attributes of this 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.

Specified by:

writeXMLAttributes in interface SBase

Overrides:

writeXMLAttributes in class AbstractNamedSBase

Returns:

a Map containing the XML attributes of this object.

containsUndeclaredUnits

public boolean containsUndeclaredUnits()

Description copied from interface: SBaseWithDerivedUnit

Returns 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.

Specified by:

containsUndeclaredUnits in interface SBaseWithDerivedUnit

Returns:

true if the math expression of this SBaseWithDerivedUnit includes parameters/numbers with undeclared units, false otherwise.

getDerivedUnitDefinition

public UnitDefinition getDerivedUnitDefinition()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity and tries to identify an equivalent 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.

Specified by:

getDerivedUnitDefinition in interface SBaseWithDerivedUnit

Returns:

a UnitDefinition that represent the derived unit of this quantity, or null if it is not possible to derive a unit.

getDerivedUnits

public java.lang.String getDerivedUnits()

Description copied from interface: SBaseWithDerivedUnit

Derives the unit of this quantity. If the model that contains this quantity already contains a unit that is equivalent to the derived unit, the corresponding identifier will be returned. In case that the unit cannot be derived or that no equivalent unit exists within the model, or if the model has not been defined yet, null will be returned. In case that this quantity represents a basic Unit.Kind this method will return the String representation of this Unit.Kind.

Specified by:

getDerivedUnits in interface SBaseWithDerivedUnit

Returns:

a 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.