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.layout |
Provides classes for the Layout
package.
|
org.sbml.jsbml.ext.multi |
Provides classes for the Multi package.
|
org.sbml.jsbml.ext.qual |
Provides classes for the Qualitative Models package.
|
org.sbml.jsbml.ext.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
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.filters |
Filters are useful to decide whether or not to accept a certain item.
|
org.sbml.jsbml.validator.offline.constraints.helper |
Modifier and Type | Method | Description |
---|---|---|
Species |
Species.clone() |
|
Species |
Model.createSpecies() |
|
Species |
Model.createSpecies(java.lang.String id) |
|
Species |
Model.createSpecies(java.lang.String id,
java.lang.String name,
Compartment c) |
|
Species |
Model.createSpecies(java.lang.String id,
Compartment c) |
|
Species |
Model.getSpecies(int n) |
Gets the n-th
Species object in this Model. |
Species |
Model.getSpecies(java.lang.String id) |
Gets the
Species of the Model.listOfSpecies which has 'id' as
id. |
Species |
SimpleSpeciesReference.getSpeciesInstance() |
|
Species |
Model.removeSpecies(int i) |
|
Species |
Model.removeSpecies(java.lang.String id) |
Modifier and Type | Method | Description |
---|---|---|
ListOf<Species> |
Model.getListOfSpecies() |
Returns the
Model.listOfSpecies of this Model . |
Modifier and Type | Method | Description |
---|---|---|
boolean |
Model.addSpecies(Species spec) |
Adds a Species instance to the listOfSpecies of this Model.
|
ModifierSpeciesReference |
Reaction.createModifier(java.lang.String id,
Species species) |
Creates a new
ModifierSpeciesReference with the given
id as its identifier, which points to the given
Species , adds it to this Reaction 's
Reaction.listOfModifiers , and returns a pointer to it. |
ModifierSpeciesReference |
Reaction.createModifier(Species species) |
Creates a new
ModifierSpeciesReference , which points to the given
Species , adds it to this Reaction 's
Reaction.listOfModifiers , and returns a pointer to it. |
SpeciesReference |
Reaction.createProduct(java.lang.String id,
Species species) |
Creates a new
SpeciesReference with the given id as
its identifier, which points to the given Species , adds it to
this Reaction 's Reaction.listOfProducts and returns a pointer to
it. |
SpeciesReference |
Reaction.createProduct(Species species) |
Creates a new
SpeciesReference , which points to the given
Species , adds it to this Reaction 's
Reaction.listOfProducts and returns a pointer to it. |
SpeciesReference |
Reaction.createReactant(java.lang.String id,
Species species) |
Creates a new
SpeciesReference with the given id as
identifier, which points to the given Species and adds it to the
Reaction.listOfReactants . |
SpeciesReference |
Reaction.createReactant(Species species) |
|
boolean |
Reaction.hasModifier(Species s) |
|
boolean |
Reaction.hasProduct(Species s) |
|
boolean |
Reaction.hasReactant(Species s) |
|
boolean |
Reaction.involves(Species s) |
Convenient test if the given species takes part in this reaction as a
reactant, product, or modifier.
|
boolean |
Model.removeSpecies(Species spec) |
Removes a species from the model.
|
void |
SimpleSpeciesReference.setSpecies(Species species) |
Sets the speciesID to the id of the
Species 'species'. |
Modifier and Type | Method | Description |
---|---|---|
void |
Model.setListOfSpecies(ListOf<Species> listOfSpecies) |
Sets the listOfSpecies of this
Model to 'listOfSpecies'. |
Constructor | Description |
---|---|
ModifierSpeciesReference(Species species) |
Creates a
ModifierSpeciesReference instance from a given Species . |
SimpleSpeciesReference(Species species) |
Creates a SimpleSpeciesReference instance from a given Species.
|
Species(Species species) |
Creates a Species instance from a Species.
|
SpeciesReference(Species species) |
Creates a SpeciesReference instance from a Species.
|
Modifier and Type | Method | Description |
---|---|---|
ListOf<Species> |
FBCSpeciesPlugin.getParent() |
|
ListOf<Species> |
FBCSpeciesPlugin.getParentSBMLObject() |
Constructor | Description |
---|---|
FBCSpeciesPlugin(Species species) |
Creates an
FBCSpeciesPlugin instance |
Modifier and Type | Method | Description |
---|---|---|
boolean |
Layout.containsGlyph(Species species) |
|
void |
SpeciesGlyph.setSpecies(Species species) |
Constructor | Description |
---|---|
MultiSpeciesPlugin(Species species) |
Creates a new
MultiSpeciesPlugin instance, connected to the given 'core'
Species . |
Modifier and Type | Method | Description |
---|---|---|
QualitativeSpecies |
QualModelPlugin.createQualitativeSpecies(java.lang.String id,
java.lang.String metaId,
Species species) |
Creates a new
QualitativeSpecies , based on an existing Species ,
adds it to this QualModelPlugin and returns it. |
Constructor | Description |
---|---|
QualitativeSpecies(Species species) |
Creates a new
QualitativeSpecies instance. |
Modifier and Type | Method | Description |
---|---|---|
Species |
SpatialSpeciesPlugin.getExtendedSBase() |
|
Species |
ParameterType.getSpeciesInstance() |
Returns the
Species instance associated with ParameterType.variable . |
Constructor | Description |
---|---|
SpatialSpeciesPlugin(Species sp) |
Modifier and Type | Method | Description |
---|---|---|
Species |
ModelBuilder.buildSpecies(java.lang.String id,
java.lang.String name,
java.lang.String compartmentId,
boolean hasOnlySubstanceUnits,
boolean boundaryCondition,
boolean constant,
double initialConcentration,
java.lang.String substanceUnits) |
|
Species |
ModelBuilder.buildSpecies(java.lang.String id,
java.lang.String name,
Compartment compartment,
boolean hasOnlySubstanceUnits,
boolean boundaryCondition,
boolean constant,
double initialConcentration,
java.lang.String substanceUnits) |
|
Species |
ModelBuilder.buildSpecies(java.lang.String id,
java.lang.String name,
Compartment compartment,
boolean hasOnlySubstanceUnits,
boolean boundaryCondition,
boolean constant,
double initialConcentration,
Unit.Kind substanceUnits) |
|
Species |
ModelBuilder.buildSpecies(java.lang.String id,
java.lang.String name,
Compartment compartment,
boolean hasOnlySubstanceUnits,
boolean boundaryCondition,
boolean constant,
double initialConcentration,
UnitDefinition substanceUnits) |
Constructor | Description |
---|---|
SpeciesReferenceFilter(Species species) |
Creates a new
SpeciesReferenceFilter that only accepts instances of
SpeciesReference pointing to the id of the given Species . |
Modifier and Type | Method | Description |
---|---|---|
static UnitDefinition |
ValidationTools.getDerivedSubstanceUnitDefinition(Species sbase) |
Returns the substance only derived
UnitDefinition for the given Species . |