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
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
.JSBML_WRONG_SBO_TERM
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) |
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) |
|
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) |
|
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. |
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 Input()
Input
instance.public Input(java.lang.String id)
Input
instance.id
- the id to be set.public Input(java.lang.String id, QualitativeSpecies qualitativeSpecies, InputTransitionEffect transitionEffect)
Input
instance.id
- the id to be set.qualitativeSpecies
- the QualitativeSpecies
that is linked to this Input
.transitionEffect
- the transition effect.public Input(int level, int version)
Input
instance.level
- the SBML levelversion
- the SBML versionpublic Input(java.lang.String id, int level, int version)
Input
instance.id
- the id to be set.level
- the SBML levelversion
- the SBML versionpublic Input(java.lang.String id, java.lang.String name, int level, int version)
Input
instance.id
- the id to be set.name
- the name to be set.level
- the SBML levelversion
- the SBML versionpublic void initDefaults()
public Input clone()
SBase
SBase
with the same
properties
like this one.clone
in interface SBase
clone
in class AbstractSBase
public void setSign(Sign sign)
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.sign
- the sign to setpublic boolean isSetSign()
public Sign getSign()
public boolean unsetSign()
true
if unset the sign attribute was successfulpublic 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()
public QualitativeSpecies getQualitativeSpeciesInstance()
public void setQualitativeSpecies(java.lang.String qualitativeSpecies)
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.qualitativeSpecies
- the qualitativeSpecies to setpublic boolean unsetQualitativeSpecies()
public boolean isTransitionEffectMandatory()
public boolean isSetTransitionEffect()
public InputTransitionEffect getTransitionEffect()
public void setTransitionEffect(InputTransitionEffect transitionEffect)
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".transitionEffect
- the transitionEffect to setpublic boolean unsetTransitionEffect()
public boolean isThresholdLevelMandatory()
public boolean isSetThresholdLevel()
public int getThresholdLevel()
public void setThresholdLevel(int thresholdLevel)
QualitativeSpecies
should reach or exceed the
thresholdLevel in order for the Transition
to occur will be encoded in the math elements
of the FunctionTerm
s listed for the given Transition
.
The thresholdLevel is used by the FunctionTerm
s 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.thresholdLevel
- the thresholdLevel to setpublic boolean unsetThresholdLevel()
true
if unset the threholdLevel attribute was successfulpublic 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.