Package | Description |
---|---|
org.sbml.jsbml |
Pure Java™ implementation of the data structures to represent all SBML
constructs.
|
org.sbml.jsbml.ext.fbc |
Provides classes for the
Flux Balance Constraints package (FBC).
|
org.sbml.jsbml.ext.fbc.converters | |
org.sbml.jsbml.ext.layout |
Provides classes for the Layout
package.
|
org.sbml.jsbml.ext.multi |
Provides classes for the Multi package.
|
org.sbml.jsbml.ext.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
org.sbml.jsbml.math.compiler | |
org.sbml.jsbml.util |
A collection of handy utilities when working with JSBML classes,
such as classes for String manipulation or mathematical operations.
|
org.sbml.jsbml.util.compilers |
The classes in this package can be used to evaluate the information
represented by abstract syntax trees (ASTNode objects).
|
org.sbml.jsbml.validator.offline.constraints.helper |
Modifier and Type | Method | Description |
---|---|---|
Reaction |
Reaction.clone() |
|
Reaction |
Model.createReaction() |
|
Reaction |
Model.createReaction(java.lang.String id) |
|
Reaction |
KineticLaw.getParent() |
|
Reaction |
KineticLaw.getParentSBMLObject() |
This method is convenient when holding an object nested inside other
objects in an SBML model.
|
Reaction |
Model.getReaction(int n) |
Gets the n-th
Reaction object in this Model. |
Reaction |
Model.getReaction(java.lang.String id) |
Returns the
Reaction of the Model.listOfReactions which has 'id'
as id. |
Reaction |
Model.removeReaction(int n) |
|
Reaction |
Model.removeReaction(java.lang.String id) |
Modifier and Type | Method | Description |
---|---|---|
ListOf<Reaction> |
Model.getListOfReactions() |
Returns the listOfReactions of this
Model . |
ListOf<Reaction> |
Reaction.getParent() |
Modifier and Type | Method | Description |
---|---|---|
boolean |
Model.addReaction(Reaction reaction) |
Adds a Reaction instance to the listOfReactions of this Model.
|
boolean |
Model.removeReaction(Reaction reac) |
Removes a reaction from the model.
|
Modifier and Type | Method | Description |
---|---|---|
void |
Model.setListOfReactions(ListOf<Reaction> listOfReactions) |
Sets the
Model.listOfReactions of this Model to
'listOfReactions'. |
Constructor | Description |
---|---|
KineticLaw(Reaction parentReaction) |
Creates a KineticLaw instance from a given Reaction.
|
Reaction(Reaction reaction) |
Creates a Reaction instance from a given reaction.
|
Modifier and Type | Method | Description |
---|---|---|
Reaction |
FluxBound.getReactionInstance() |
Deprecated.
Only defined in FBC version 1.
|
Reaction |
FluxObjective.getReactionInstance() |
Returns the
Reaction associated with this FluxObjective . |
Modifier and Type | Method | Description |
---|---|---|
FluxObjective |
Objective.createFluxObjective(java.lang.String id,
java.lang.String name,
double coefficient,
Reaction reaction) |
|
void |
FluxBound.setReaction(Reaction reaction) |
Deprecated.
Only defined in FBC version 1.
|
void |
FluxObjective.setReaction(Reaction reaction) |
Sets the
Reaction that this FluxObjective is associated with in the context
of the enclosing Objective class. |
Constructor | Description |
---|---|
FBCReactionPlugin(Reaction extendedSBase) |
Creates a new
FBCReactionPlugin instance. |
Modifier and Type | Method | Description |
---|---|---|
static GeneProductAssociation |
GPRParser.parseGPR(Reaction r,
java.lang.String geneReactionRule,
boolean omitGenericTerms) |
Parses a gene association string as used in COBRA in SBML level 2 into a
GeneProductAssociation
used in SBML level 3. |
static GeneProductAssociation |
GPRParser.parseGPR(Reaction r,
java.lang.String geneReactionRule,
boolean omitGenericTerms,
boolean displayWarning) |
Parses a gene association string as used in COBRA in SBML level 2 into a
GeneProductAssociation
used in SBML level 3. |
Modifier and Type | Method | Description |
---|---|---|
boolean |
Layout.containsGlyph(Reaction reaction) |
|
void |
ReactionGlyph.setReaction(Reaction reaction) |
See setReaction(String)
|
Modifier and Type | Class | Description |
---|---|---|
class |
IntraSpeciesReaction |
Modifier and Type | Method | Description |
---|---|---|
Reaction |
SpatialReactionPlugin.getExtendedSBase() |
Constructor | Description |
---|---|
SpatialReactionPlugin(Reaction rxn) |
Modifier and Type | Method | Description |
---|---|---|
java.lang.String |
HTMLFormula.reactionEquation(Reaction reaction) |
Modifier and Type | Method | Description |
---|---|---|
Reaction |
ModelBuilder.buildReaction(java.lang.String id,
java.lang.String name,
java.lang.String compartment,
boolean fast,
boolean reversible) |
|
Reaction |
ModelBuilder.buildReaction(java.lang.String id,
java.lang.String name,
Compartment compartment,
boolean fast,
boolean reversible) |
Modifier and Type | Method | Description |
---|---|---|
static KineticLaw |
ModelBuilder.buildKineticLaw(Reaction reaction,
java.lang.String formula,
Pair<java.lang.String,java.lang.Double>... localParameters) |
|
static void |
ModelBuilder.buildModifiers(Reaction reaction,
Pair<Species,java.lang.Integer>... modifiers) |
A convenient method to create multiple modifiers in one single step by
passing the
Species along with its role (SBO term) to this method. |
static void |
ModelBuilder.buildProducts(Reaction reaction,
Pair<java.lang.Double,Species>... products) |
Convenient method to build multiple products together with their
stoichiometry in one step.
|
static void |
ModelBuilder.buildReactants(Reaction reaction,
Pair<java.lang.Double,Species>... reactants) |
Convenient method to build multiple reactants together with their
stoichiometry in one step.
|
Modifier and Type | Method | Description |
---|---|---|
java.lang.String |
HTMLFormula.reactionEquation(Reaction reaction) |
Modifier and Type | Method | Description |
---|---|---|
static java.util.Set<java.lang.String> |
ValidationTools.getDefinedSpecies(Reaction r) |