Uses of Class
de.unirostock.sems.bives.sbml.parser.SBMLSBase

Packages that use SBMLSBase

Package	Description
de.unirostock.sems.bives.sbml.parser

Uses of SBMLSBase in de.unirostock.sems.bives.sbml.parser

Subclasses of SBMLSBase in de.unirostock.sems.bives.sbml.parser

Modifier and Type	Class	Description
class	SBMLAlgebraicRule	The Class SBMLAlgebraicRule used to express equations that are neither assignments of model variables nor rates of change.
class	SBMLAssignmentRule	The Class SBMLAssignmentRule used to express equations that set the values of variables.
class	SBMLCompartment	The Class SBMLCompartment, a bounded space in which species are located.
class	SBMLCompartmentType	The Class SBMLCompartmentType, a grouping construct used to establish a relationship between multiple SBMLCompartments.
class	SBMLConstraint	The Class SBMLConstraint, a mechanism for stating the assumptions under which a model is designed to operate.
class	SBMLEvent	The Class SBMLEvent describes the time and form of instantaneous, discontinuous state changes in the model.
class	SBMLEventAssignment	The Class SBMLEventAssignment.
class	SBMLEventDelay	The Class SBMLEventDelay.
class	SBMLEventPriority	The Class SBMLEventPriority.
class	SBMLEventTrigger	The Class SBMLEventTrigger.
class	SBMLFunctionDefinition	The Class SBMLFunctionDefinition associates an identifier with a function definition.
class	SBMLGenericIdNameObject	The Class SBMLGenericIdNameObject representing a generic object that has an id and a name.
class	SBMLInitialAssignment	The Class SBMLInitialAssignment assigning initial values to entities in a model.
class	SBMLKineticLaw	The Class SBMLKineticLaw defines the speed at which the process defined by the reaction takes place.
class	SBMLListOf	The Class SBMLListOf represents a list of something in SBML.
class	SBMLModel	The Class SBMLModel representing a model encoded in SBML.
class	SBMLParameter	The Class SBMLParameter is used to define a symbol associated with a value; this symbol can then be used in mathematical formulas in a model.
class	SBMLRateRule	The Class SBMLRateRule used to express equations that determine the rates of change of variables.
class	SBMLReaction	The Class SBMLReaction represents any kind of process that can change the quantity of one or more species in a model.
class	SBMLRule	The abstract Class SBMLRule.
class	SBMLSimpleSpeciesReference	The Class SBMLSimpleSpeciesReference representing a link to a species (mainly for modifiers, parent class for substrates and products).
class	SBMLSpecies	The Class SBMLSpecies representing a species in an SBML document.
class	SBMLSpeciesReference	The Class SBMLSpeciesReference representing a link to a species.
class	SBMLSpeciesType	The Class SBMLSpeciesType representing type of species (level < 3).
class	SBMLUnit	The Class SBMLUnit representing a factor based on a unit:
class	SBMLUnitDefinition	The Class SBMLUnitDefinition.

Methods in de.unirostock.sems.bives.sbml.parser that return SBMLSBase

Modifier and Type	Method	Description
SBMLSBase	SBMLModel.getFromMetaId(String metaId)	Gets an entity given its meta id.
SBMLSBase	SBMLModel.getFromNode(de.unirostock.sems.xmlutils.ds.TreeNode node)	Gets an entity given its tree node.
SBMLSBase	SBMLInitialAssignment.getSymbol()	Gets the symbol.
SBMLSBase	SBMLAssignmentRule.getVariable()	Gets the corresponding variable.
SBMLSBase	SBMLEventAssignment.getVariable()	Gets the variable of interest.
SBMLSBase	SBMLRateRule.getVariable()	Gets the variable of interest.
SBMLSBase	SBMLModel.resolveSymbol(String symbol)	Resolve certain symbol.
SBMLSBase	SBMLModel.resolveSymbole(String symbol)	Deprecated. as of version 1.3.6, replaced by SBMLModel.resolveSymbol(String)
protected SBMLSBase	SBMLEventAssignment.resolveVariable(String ref)	Resolve variable.
protected SBMLSBase	SBMLRule.resolveVariable(String ref)	Resolves a variable.

Methods in de.unirostock.sems.bives.sbml.parser that return types with arguments of type SBMLSBase

Modifier and Type	Method	Description
HashMap<String,List<SBMLSBase>>	SBMLModel.getOntologyMappings()	Gets the ontology mappings which group entities by there pointers into ontologies.

Methods in de.unirostock.sems.bives.sbml.parser with parameters of type SBMLSBase

Modifier and Type	Method	Description
static String	SBMLModel.getSidName(SBMLSBase ref)	Gets the SId.
void	SBMLModel.mapNode(de.unirostock.sems.xmlutils.ds.DocumentNode node, SBMLSBase sbase)	Map node model node to its entity.