org.sbml.jsbml.ext.qual

Class Input

java.lang.Object

org.sbml.jsbml.AbstractTreeNode

org.sbml.jsbml.AbstractSBase

org.sbml.jsbml.AbstractNamedSBase

org.sbml.jsbml.ext.qual.Input

All Implemented Interfaces:

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

public class Input
extends AbstractNamedSBase
implements UniqueNamedSBase, CallableSBase

Each Input refers to a QualitativeSpecies that participates in the corresponding Transition. In Petri nets, these are the input places of the transition. In logical models, they are the regulators of the species whose behavior is defined by the Transition.

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
Input() Creates a new Input instance.
Input(Input in) Creates a new Input instance cloned from the given Input.
Input(int level, int version) Creates a new Input instance.
Input(String id) Creates a new Input instance.
Input(String id, int level, int version) Creates a new Input instance.
Input(String id, QualitativeSpecies qualitativeSpecies, InputTransitionEffect transitionEffect) Creates a new Input instance.
Input(String id, String name, int level, int version) Creates a new Input instance.

Method Summary

Modifier and Type	Method and Description
Input	clone()
boolean	containsUndeclaredUnits()
boolean	equals(Object object)
UnitDefinition	getDerivedUnitDefinition()
String	getDerivedUnits()
String	getQualitativeSpecies()
QualitativeSpecies	getQualitativeSpeciesInstance()
Sign	getSign()
int	getThresholdLevel()
InputTransitionEffect	getTransitionEffect()
int	hashCode()
void	initDefaults()
boolean	isIdMandatory()
boolean	isQualitativeSpeciesMandatory()
boolean	isSetQualitativeSpecies()
boolean	isSetSign()
boolean	isSetThresholdLevel()
boolean	isSetTransitionEffect()
boolean	isThresholdLevelMandatory()
boolean	isTransitionEffectMandatory()
boolean	readAttribute(String attributeName, String prefix, String value)
void	setQualitativeSpecies(String qualitativeSpecies) The required attribute qualitativeSpecies is used to identify the QualitativeSpecies that is the input of this Transition.
void	setSign(Sign sign) The sign of type Sign can be used as an indication as to whether the contribution of this Input is positive, negative, both (dual) or unknown.
void	setThresholdLevel(int thresholdLevel) The thresholdLevel is a non-negative integer that can be used to set the threshold level of the particular input.
void	setTransitionEffect(InputTransitionEffect transitionEffect) Each Input has a required attribute transitionEffect of type InputTransitionEffect which describes how the QualitativeSpecies referenced by the Input is affected by the Transition.
boolean	unsetQualitativeSpecies()
boolean	unsetSign()
boolean	unsetThresholdLevel()
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

Input

public Input()

Creates a new Input instance.

Input

public Input(String id)

Creates a new Input instance.

Parameters:

id - the id to be set.

Input

public Input(String id,
             QualitativeSpecies qualitativeSpecies,
             InputTransitionEffect transitionEffect)

Creates a new Input instance.

Parameters:

id - the id to be set.

qualitativeSpecies - the QualitativeSpecies that is linked to this Input.

transitionEffect - the transition effect.

Input

public Input(int level,
             int version)

Creates a new Input instance.

Parameters:

level - the SBML level

version - the SBML version

Input

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

Creates a new Input instance.

Parameters:

id - the id to be set.

level - the SBML level

version - the SBML version

Input

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

Creates a new Input instance.

Parameters:

id - the id to be set.

name - the name to be set.

level - the SBML level

version - the SBML version

Input

public Input(Input in)

Creates a new Input instance cloned from the given Input.

Parameters:

in - the Input instance to clone.

Method Detail

initDefaults

public void initDefaults()

clone

public Input clone()

Specified by:

clone in interface SBase

Overrides:

clone in class AbstractSBase

setSign

public void setSign(Sign sign)

The sign of type Sign can be used as an indication as to whether the contribution of this Input is positive, negative, both (dual) or unknown. This enables a model to distinguish between stimulation and inhibition and can facilitate interpretation of the model without the mathematics. The sign is particularly used for visualization purposes and has no impact on the mathematical interpretation. This attribute is optional.

Parameters:

sign - the sign to set

isSetSign

public boolean isSetSign()

Returns:

getSign

public Sign getSign()

Returns:

the sign

unsetSign

public boolean unsetSign()

Returns:

true if unset the sign attribute was successful

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:

if the qualitative species is set

getQualitativeSpecies

public String getQualitativeSpecies()

Returns:

the qualitativeSpecies

getQualitativeSpeciesInstance

public QualitativeSpecies getQualitativeSpeciesInstance()

setQualitativeSpecies

public void setQualitativeSpecies(String qualitativeSpecies)

The required attribute qualitativeSpecies is used to identify the QualitativeSpecies that is the input 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:

if the qualitative species was unset

isTransitionEffectMandatory

public boolean isTransitionEffectMandatory()

Returns:

isSetTransitionEffect

public boolean isSetTransitionEffect()

Returns:

if the transitionEffect is set

getTransitionEffect

public InputTransitionEffect getTransitionEffect()

Returns:

the transitionEffect

setTransitionEffect

public void setTransitionEffect(InputTransitionEffect transitionEffect)

Each Input has a required attribute transitionEffect of type InputTransitionEffect which describes how the QualitativeSpecies referenced by the Input is affected by the Transition. It should be noted that in logical models the transitionEffect is always set to "none", while in Petri nets, it can be set to "none" (indicating a read arc) or to "consumption".

Parameters:

transitionEffect - the transitionEffect to set

unsetTransitionEffect

public boolean unsetTransitionEffect()

Returns:

isThresholdLevelMandatory

public boolean isThresholdLevelMandatory()

Returns:

false

isSetThresholdLevel

public boolean isSetThresholdLevel()

Returns:

getThresholdLevel

public int getThresholdLevel()

Returns:

the thresholdLevel

setThresholdLevel

public void setThresholdLevel(int thresholdLevel)

The thresholdLevel is a non-negative integer that can be used to set the threshold level of the particular input. This attribute relates to the contribution of this input required for the transition to take place. In logical regulatory models, it refers to the threshold level that must be reached or exceeded in order for the regulation to take place, while in a Petri net, it refers to the number of tokens required to enable the transition (weight of the arc connecting the input place to the transition). Whether the level of a QualitativeSpecies should reach or exceed the thresholdLevel in order for the Transition to occur will be encoded in the math elements of the FunctionTerms listed for the given Transition. The thresholdLevel is used by the FunctionTerms associated with the containing Transition to determine the applicable resultLevel that should be applied. The id of the Input represents this value and can be used in the math element of a FunctionTerm. When defined, this attribute should be coherent with the content of the FunctionTerm, i.e. if a number is used in the FunctionTerm to compare the current level of a species, this number must correspond to the thresholdLevel of the corresponding Input. Since a number can be used within the FunctionTerm to represent the thresholdLevel of an Input it is not compulsory to use this attribute to specify the value. A missing thresholdLevel attribute merely implies that the threshold is incorporated into the FunctionTerm using a number.

Parameters:

thresholdLevel - the thresholdLevel to set

unsetThresholdLevel

public boolean unsetThresholdLevel()

Returns:

true if unset the threholdLevel attribute was successful

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