Modifier and Type | Class and Description |
---|---|
class |
AlgebraicRule
Implementation of SBML's AlgebraicRule construct.
|
class |
AssignmentRule
Implementation of SBML's AssignmentRule construct.
|
class |
Association |
class |
BoundingBox |
class |
Compartment
Implementation of SBML's Compartment construct.
|
class |
CompartmentGlyph |
class |
CompartmentType
Implementation of SBML's Level 2's CompartmentType construct.
|
class |
CompBase |
class |
Constraint
Implementation of SBML's Constraint construct.
|
class |
CubicBezier |
class |
Curve |
class |
Delay
Implementation of SBML's Delay construct for Event.
|
class |
Deletion |
class |
Dimensions |
class |
Event
Implementation of SBML's Event construct.
|
class |
EventAssignment
Implementation of SBML's EventAssignment construct for Event.
|
class |
ExternalModelDefinition |
class |
FluxBound |
class |
FluxObjective |
class |
FunctionDefinition
Implementation of SBML's FunctionDefinition construct.
|
class |
GeneAssociation |
class |
GeneralGlyph |
class |
GraphicalObject |
class |
InitialAssignment
Implementation of SBML's InitialAssignment construct.
|
class |
KineticLaw
Implementation of SBML's KineticLaw construct.
|
class |
Layout |
class |
LineSegment |
class |
ListOf
Parent class for the various SBML 'ListOfXYZ' classes.
|
class |
ListOfCompartmentGlyphs |
class |
ListOfCompartments
Implementation of SBML Level 2's ListOfCompartments construct.
|
class |
ListOfCompartmentTypes
Implementation of SBML's ListOfCompartmentTypes construct.
|
class |
ListOfConstraints
Implementation of SBML's ListOfConstraints construct.
|
class |
ListOfDeletions |
class |
ListOfEventAssignments
Implementation of SBML's ListOfEventAssignments construct.
|
class |
ListOfEvents
Implementation of SBML's ListOfEvents construct.
|
class |
ListOfExternalModelDefinitions |
class |
ListOfFluxBounds |
class |
ListOfFluxObjectives |
class |
ListOfFunctionDefinitions
Implementation of SBML's ListOfFunctionDefinitions construct.
|
class |
ListOfGeneAssociations |
class |
ListOfGraphicalObjects |
class |
ListOfInitialAssignments
Implementation of SBML's ListOfInitialAssignments construct.
|
class |
ListOfLayouts |
class |
ListOfLineSegments |
class |
ListOfLocalParameters
Implementation of SBML Level 3's ListOfLocalParameters construct.
|
class |
ListOfModelDefinitions |
class |
ListOfObjectives |
class |
ListOfParameters
Implementation of SBML's ListOfParameters construct.
|
class |
ListOfPorts |
class |
ListOfReactionGlyphs |
class |
ListOfReactions
Implementation of SBML's ListOfReactions construct.
|
class |
ListOfReferenceGlyphs |
class |
ListOfReplacedElements |
class |
ListOfRules
Implementation of SBML's ListOfRules construct.
|
class |
ListOfSpecies
Implementation of SBML Level 2's ListOfSpecies construct.
|
class |
ListOfSpeciesGlyphs |
class |
ListOfSpeciesReferenceGlyphs |
class |
ListOfSpeciesReferences
Implementation of SBML's ListOfSpeciesReferences construct.
|
class |
ListOfSpeciesTypes
Implementation of SBML's ListOfSpeciesTypes construct.
|
class |
ListOfSubmodels |
class |
ListOfTextGlyphs |
class |
ListOfUnitDefinitions
Implementation of SBML's ListOfUnitDefinitions construct.
|
class |
ListOfUnits
Implementation of SBML's ListOfUnits construct.
|
class |
LocalParameter
Implementation of SBML Level 3's LocalParameter construct.
|
class |
Model
Implementation of SBML's Model construct.
|
class |
ModelDefinition |
class |
ModifierSpeciesReference
Implementation of SBML's ModifierSpeciesReference construct.
|
class |
Objective |
class |
Parameter
Implementation of SBML's Parameter construct.
|
class |
Point |
class |
Port |
class |
Priority
Implementation of SBML Level 3's Priority construct
for
Event . |
class |
RateRule
Implementation of SBML's RateRule construct.
|
class |
Reaction
Implementation of SBML's Reaction construct.
|
class |
ReactionGlyph |
class |
ReferenceGlyph |
class |
ReplacedBy |
class |
ReplacedElement |
class |
Replacing |
class |
Rule
Implementation of SBML's Rule construct.
|
class |
SBaseRef |
class |
SBMLDocument
Container for an SBML document and interface for global operations
on SBML documents.
|
class |
SimpleSpeciesReference
Implementation of SBML's SimpleSpeciesReference construct.
|
class |
Species
Implementation of SBML's Species construct.
|
class |
SpeciesGlyph |
class |
SpeciesReference
Implementation of SBML's SpeciesReference construct.
|
class |
SpeciesReferenceGlyph |
class |
SpeciesType
Implementation of SBML Level 2's SpeciesType construct.
|
class |
StoichiometryMath
Implementation of SBML Level 2's StoichiometryMath construct.
|
class |
Submodel |
class |
TextGlyph |
class |
Trigger
Implementation of SBML's Trigger construct for Event.
|
class |
Unit
Implementation of SBML's Unit construct.
|
class |
UnitDefinition
Implementation of SBML's UnitDefinition construct.
|
Modifier and Type | Method and Description |
---|---|
SBase |
ReplacedBy.cloneObject()
Creates and returns a deep copy of this
SBase object. |
SBase |
Submodel.cloneObject()
Creates and returns a deep copy of this
SBase object. |
SBase |
SBase.cloneObject()
Creates and returns a deep copy of this
SBase object. |
SBase |
ModifierSpeciesReference.cloneObject()
Creates and returns a deep copy of this
ModifierSpeciesReference
instance. |
SBase |
Deletion.cloneObject()
Creates and returns a deep copy of this
SBase object. |
SBase |
ExternalModelDefinition.cloneObject()
Creates and returns a deep copy of this
SBase object. |
SBase |
ReplacedElement.cloneObject()
Creates and returns a deep copy of this
SBase object. |
SBase |
Port.cloneObject()
Creates and returns a deep copy of this
SBase object. |
SBase |
SBaseRef.cloneObject()
Creates and returns a deep copy of this
SBase object. |
SBase |
CompSBMLDocumentPlugin.createObject(XMLInputStream stream) |
SBase |
CompSBasePlugin.createObject(XMLInputStream stream) |
SBase |
CompModelPlugin.createObject(XMLInputStream stream) |
SBase |
FbcModelPlugin.createObject(XMLInputStream stream) |
SBase |
LayoutExtension.DowncastSBase(long cPtr,
boolean owner)
SBMLExtension derived classes must override this method
|
SBase |
CompExtension.DowncastSBase(long cPtr,
boolean owner) |
SBase |
FbcExtension.DowncastSBase(long cPtr,
boolean owner) |
SBase |
ListOfReplacedElements.get(long n)
Get an item from the list.
|
SBase |
SBaseList.get(long n) |
SBase |
ListOf.get(long n)
Get an item from the list.
|
SBase |
ListOfSubmodels.get(long n)
Get an item from the list.
|
SBase |
ListOfPorts.get(long n)
Get an item from the list.
|
SBase |
ListOfModelDefinitions.get(long n)
Get an item from the list.
|
SBase |
ListOfExternalModelDefinitions.get(long n)
Get an item from the list.
|
SBase |
ListOfDeletions.get(long n)
Get an item from the list.
|
SBase |
SBase.getAncestorOfType(int type)
Returns the first ancestor object that has the given SBML type code.
|
SBase |
SBase.getAncestorOfType(int type,
String pkgName)
Returns the first ancestor object that has the given SBML type code.
|
SBase |
CompSBMLDocumentPlugin.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
Submodel.getElementByMetaId(String metaid)
Returns the first child element it can find with a specific 'metaid'
attribute value, or
null if no such object is found. |
SBase |
SBase.getElementByMetaId(String metaid)
Returns the first child element it can find with a specific 'metaid'
attribute value, or
null if no such object is found. |
SBase |
UnitDefinition.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
SBasePlugin.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
Reaction.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
ListOf.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
Objective.getElementByMetaId(String metaid)
Returns the first child element it can find with a specific 'metaid'
attribute value, or
null if no such object is found. |
SBase |
CompSBasePlugin.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
CompModelPlugin.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
Event.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
SBaseRef.getElementByMetaId(String metaid)
Returns the first child element it can find with a specific 'metaid'
attribute value, or
null if no such object is found. |
SBase |
SBMLDocument.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or itself if it has the given metaid , or null if no such object is found. |
SBase |
KineticLaw.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
Model.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or
null if no such object is found. |
SBase |
FbcModelPlugin.getElementByMetaId(String metaid)
Returns the first child element it can find with the given
metaid , or null if no such object is found. |
SBase |
CompSBMLDocumentPlugin.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
Submodel.getElementBySId(String id)
Returns the first child element found that has the given
id in the
model-wide SId namespace, or null if no such object is found. |
SBase |
SBase.getElementBySId(String id)
Returns the first child element found that has the given
id in the
model-wide SId namespace, or null if no such object is found. |
SBase |
UnitDefinition.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
SBasePlugin.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
Reaction.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
ListOfEventAssignments.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
ListOfInitialAssignments.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
ListOfLocalParameters.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
ListOf.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
ListOfUnitDefinitions.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
Objective.getElementBySId(String id)
Returns the first child element found that has the given
id in the
model-wide SId namespace, or null if no such object is found. |
SBase |
CompSBasePlugin.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
ListOfPorts.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
CompModelPlugin.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
Event.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
ListOfRules.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
SBaseRef.getElementBySId(String id)
Returns the first child element found that has the given
id in the
model-wide SId namespace, or null if no such object is found. |
SBase |
SBMLDocument.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
KineticLaw.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
Model.getElementBySId(String id)
Returns the first child element found that has the given
id in the
model-wide SId namespace, or null if no such object is found. |
SBase |
FbcModelPlugin.getElementBySId(String id)
Returns the first child element found that has the given
id in the model-wide SId namespace, or null if no such object is found. |
SBase |
CompSBMLDocumentPlugin.getModel(String sid) |
SBase |
SBase.getParentSBMLObject()
Returns the parent SBML object containing this object.
|
SBase |
SBasePlugin.getParentSBMLObject()
Returns the parent
SBase object to which this plugin
object connected. |
SBase |
ASTNode.getParentSBMLObject()
Returns the parent SBML object.
|
SBase |
SBaseRef.getReferencedElement() |
SBase |
ReplacedElement.getReferencedElementFrom(Model model) |
SBase |
SBaseRef.getReferencedElementFrom(Model model) |
SBase |
ListOfReplacedElements.remove(long n)
Removes the nth item from this
ListOf items and returns a
pointer to it. |
SBase |
SBaseList.remove(long n) |
SBase |
ListOf.remove(long n)
Removes the nth item from this
ListOf items and returns a
pointer to it. |
SBase |
ListOfSubmodels.remove(long n)
Removes the nth item from this
ListOf items and returns a
pointer to it. |
SBase |
ListOfPorts.remove(long n)
Removes the nth item from this
ListOf items and returns a
pointer to it. |
SBase |
ListOfModelDefinitions.remove(long n)
Removes the nth item from this
ListOf items and returns a
pointer to it. |
SBase |
ListOfExternalModelDefinitions.remove(long n)
Removes the nth item from this
ListOf items and returns a
pointer to it. |
SBase |
ListOfDeletions.remove(long n)
Removes the nth item from this
ListOf items and returns a
pointer to it. |
Modifier and Type | Method and Description |
---|---|
void |
SBaseList.add(SBase item) |
int |
ListOf.append(SBase item)
Adds item to the end of this
ListOf . |
int |
ListOf.appendAndOwn(SBase item)
Adds item to the end of this
ListOf . |
static XMLNode |
RDFAnnotationParser.createCVTerms(SBase obj)
Takes a list of
CVTerm objects and creates a the RDF 'Description'
element. |
static Model |
CompBase.getParentModel(SBase child) |
int |
ListOf.insert(int location,
SBase item)
Inserts the item at the given position of this
ListOf |
int |
ListOf.insertAndOwn(int location,
SBase item)
Inserts the item at the given position of this
ListOf |
boolean |
SBase.matchesRequiredSBMLNamespacesForAddition(SBase sb)
Returns
true if this object's set of XML namespaces are a subset
of the given object's XML namespaces. |
boolean |
SBase.matchesSBMLNamespaces(SBase sb)
Returns
true if this object's set of XML namespaces are the same
as the given object's XML namespaces. |
static XMLNode |
RDFAnnotationParser.parseCVTerms(SBase obj)
Takes a list of
CVTerm objects and creates a complete SBML annotation
around it. |
static XMLNode |
RDFAnnotationParser.parseModelHistory(SBase obj)
Reads the model history and cvTerms stored in
obj and creates the
XML structure for an SBML annotation representing that metadata if
there is a model history stored in obj . |
static XMLNode |
RDFAnnotationParser.parseOnlyModelHistory(SBase obj)
Reads the model history stored in
obj and creates the
XML structure for an SBML annotation representing that history. |
void |
SBaseList.prepend(SBase item) |
boolean |
FbcModelPlugin.readOtherXML(SBase parentObject,
XMLInputStream stream) |
int |
Submodel.replaceElement(SBase toReplace,
SBase replacement) |
int |
Replacing.replaceWithAndMaybeDelete(SBase replacement,
boolean deleteme,
ASTNode conversionFactor) |