public class ModifierSpeciesReference extends SimpleSpeciesReference
Sometimes a species appears in the kinetic rate formula of a reaction
but is itself neither created nor destroyed in that reaction (for
example, because it acts as a catalyst or inhibitor). In SBML, all such
species are simply called modifiers without regard to the detailed
role of those species in the model. The Reaction
structure provides a
way to express which species act as modifiers in a given reaction. This
is the purpose of the list of modifiers available in Reaction
. The list
contains instances of ModifierSpeciesReference
structures.
The ModifierSpeciesReference
structure inherits the mandatory attribute
'species' and optional attributes 'id' and 'name' from the parent class
SimpleSpeciesReference
. See the description of SimpleSpeciesReference
for more information about these.
The value of the 'species' attribute must be the identifier of a species
defined in the enclosing Model
this species is designated as a modifier
for the current reaction. A reaction may have any number of modifiers.
It is permissible for a modifier species to appear simultaneously in the
list of reactants and products of the same reaction where it is
designated as a modifier, as well as to appear in the list of reactants,
products and modifiers of other reactions in the model.
Constructor and Description |
---|
ModifierSpeciesReference(long level,
long version)
|
ModifierSpeciesReference(SBMLNamespaces sbmlns)
|
Modifier and Type | Method and Description |
---|---|
SBase |
cloneObject()
Creates and returns a deep copy of this
ModifierSpeciesReference object. |
void |
delete()
Explicitly deletes the underlying native object.
|
String |
getElementName()
Returns the XML element name of this object, which for
Species , is
always 'modifierSpeciesReference'. |
int |
getTypeCode()
Returns the libSBML type code for this SBML object.
|
boolean |
hasRequiredAttributes()
Predicate returning
true if
all the required attributes for this ModifierSpeciesReference object
have been set. |
getId, getName, getSpecies, isModifier, isSetId, isSetName, isSetSpecies, renameSIdRefs, setId, setName, setSpecies, unsetId, unsetName, unsetSpecies
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, connectToChild, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData
public ModifierSpeciesReference(long level, long version) throws SBMLConstructorException
level
- a long integer, the SBML Level to assign to this
ModifierSpeciesReference
version
- a long integer, the SBML Version to assign to this
ModifierSpeciesReference
SBMLConstructorException
- Thrown if the given level
and version
combination are invalid
or if this object is incompatible with the given level and version.
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute.public ModifierSpeciesReference(SBMLNamespaces sbmlns) throws SBMLConstructorException
sbmlns
- an SBMLNamespaces
object.
SBMLConstructorException
- Thrown if the given sbmlns
is inconsistent or incompatible
with this object.
SBMLDocument
having a different
combination of SBML Level, Version and XML namespaces than the object
itself will result in an error at the time a caller attempts to make the
addition. A parent object must have compatible Level, Version and XML
namespaces. (Strictly speaking, a parent may also have more XML
namespaces than a child, but the reverse is not permitted.) The
restriction is necessary to ensure that an SBML model has a consistent
overall structure. This requires callers to manage their objects
carefully, but the benefit is increased flexibility in how models can be
created by permitting callers to create objects bottom-up if desired. In
situations where objects are not yet attached to parents (e.g.,
SBMLDocument
), knowledge of the intented SBML Level and Version help
libSBML determine such things as whether it is valid to assign a
particular value to an attribute.public void delete()
In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize()
methods for the objects. The finalize()
methods in turn call the ModifierSpeciesReference.delete()
method on the libSBML object.
This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke ModifierSpeciesReference.delete()
themselves.
delete
 in class SimpleSpeciesReference
public SBase cloneObject()
ModifierSpeciesReference
object.
cloneObject
 in class SBase
ModifierSpeciesReference
object.public int getTypeCode()
LibSBML attaches an identifying code to every kind of SBML object. These
are integer constants known as SBML type codes. The names of all
the codes begin with the characters SBML_
.
In the Java language interface for libSBML, the
type codes are defined as static integer constants in the interface class
libsbmlConstants
. Note that different Level 3
package plug-ins may use overlapping type codes to identify the package
to which a given object belongs, call the getPackageName()
method on the object.
getTypeCode
 in class SBase
SBML_MODIFIER_SPECIES_REFERENCE
(default).
ModifierSpeciesReference.getElementName()
,
SBase.getPackageName()
public String getElementName()
Species
, is
always 'modifierSpeciesReference'.
getElementName
 in class SBase
'modifierSpeciesReference'.
public boolean hasRequiredAttributes()
true
if
all the required attributes for this ModifierSpeciesReference
object
have been set.
The required attributes for a ModifierSpeciesReference
object are:
species
hasRequiredAttributes
 in class SBase
true
if the required attributes have been set, false
otherwise.