Package 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:

java.io.Serializable, java.lang.Cloneable, javax.swing.tree.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

JSBML_WRONG_SBO_TERM

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
Input	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.
java.lang.String	getQualitativeSpecies()
QualitativeSpecies	getQualitativeSpeciesInstance()
Sign	getSign()
int	getThresholdLevel()
InputTransitionEffect	getTransitionEffect()
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	isQualitativeSpeciesMandatory()
boolean	isSetQualitativeSpecies()
boolean	isSetSign()
boolean	isSetThresholdLevel()
boolean	isSetTransitionEffect()
boolean	isThresholdLevelMandatory()
boolean	isTransitionEffectMandatory()
boolean	readAttribute(java.lang.String attributeName, java.lang.String prefix, java.lang.String value)	Sets the given attribute in this SBase.
void	setQualitativeSpecies(java.lang.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()
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

isValidId

Methods inherited from class org.sbml.jsbml.AbstractSBase

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

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 interface org.sbml.jsbml.NamedSBase

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

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, 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

Methods inherited from interface javax.swing.tree.TreeNode

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

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

Constructor Detail

Input

public Input()

Creates a new Input instance.

Input

public Input(java.lang.String id)

Creates a new Input instance.

Parameters:

id - the id to be set.

Input

public Input(java.lang.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(java.lang.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(java.lang.String id,
             java.lang.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()

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

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()

Description copied from interface: SBase

Returns true if the identifier of this SBase is required to be defined (i.e., not null) in the definition of SBML.

Specified by:

isIdMandatory in interface NamedSBase

Specified by:

isIdMandatory in interface SBase

Overrides:

isIdMandatory in class AbstractSBase

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:

if the qualitative species is set

getQualitativeSpecies

public java.lang.String getQualitativeSpecies()

Returns:

the qualitativeSpecies

getQualitativeSpeciesInstance

public QualitativeSpecies getQualitativeSpeciesInstance()

setQualitativeSpecies

public void setQualitativeSpecies(java.lang.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(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 AbstractSBase

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 AbstractSBase

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 AbstractSBase

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 AbstractSBase

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.