Package | Description |
---|---|
org.sbml.jsbml |
Pure Java™ implementation of the data structures to represent all SBML
constructs.
|
org.sbml.jsbml.ext.arrays.compiler | |
org.sbml.jsbml.ext.arrays.util | |
org.sbml.jsbml.ext.arrays.validator | |
org.sbml.jsbml.ext.arrays.validator.constraints | |
org.sbml.jsbml.ext.comp |
Provides classes for the
Hierarchical Model Composition package.
|
org.sbml.jsbml.ext.fbc |
Provides classes for the
Flux Balance Constraints package (FBC).
|
org.sbml.jsbml.ext.groups |
Provides classes for the Groups
package.
|
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.render.director |
This package contains interfaces and classes to create an implementation
to create a graphical representation of the
Layout
of a SBML document. |
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.util.converters | |
org.sbml.jsbml.validator |
This package provides methods to validate the content of SBML models, whether
given in a file or as a data structure.
|
org.sbml.jsbml.validator.offline.constraints.helper |
Modifier and Type | Method | Description |
---|---|---|
Model |
Model.clone() |
|
Model |
SBMLInputConverter.convertModel(T model) |
Takes a model in an arbitrary (but type-secure) format and delivers a
corresponding JSBML-compliant model.
|
Model |
SBMLDocument.createModel() |
Creates a new Model inside this
SBMLDocument , and returns a
pointer to it. |
Model |
SBMLDocument.createModel(java.lang.String id) |
Creates a new instance of Model from id and the level and version of this
SBMLDocument.
|
Model |
AbstractSBase.getModel() |
|
Model |
SBase.getModel() |
|
Model |
SBMLDocument.getModel() |
Returns the model of this
SBMLDocument . |
Modifier and Type | Method | Description |
---|---|---|
static java.lang.String |
JSBML.addUnitDefinitionIfNotContained(Model model,
UnitDefinition units) |
Adds the given
UnitDefinition to the given model or returns the
identifier of an equivalent UnitDefinition that is already part
of the model. |
static boolean |
Unit.isValidUnit(Model model,
java.lang.String unit) |
|
void |
SBMLDocument.setModel(Model model) |
Constructor | Description |
---|---|
Model(Model model) |
Creates a Model instance from a Model.
|
Constructor | Description |
---|---|
StaticallyComputableCompiler(Model model) |
Constructs a new StaticallyComputableCompiler object
|
VectorCompiler(Model model) |
|
VectorCompiler(Model model,
boolean useId) |
|
VectorCompiler(Model model,
boolean useId,
java.util.Map<java.lang.String,ASTNode> idToVector) |
|
VectorCompiler(Model model,
NamedSBase sbase,
boolean useId) |
Modifier and Type | Method | Description |
---|---|---|
static boolean |
ArraysMath.checkVectorAssignment(Model model,
MathContainer mathContainer) |
|
static boolean |
ArraysMath.checkVectorMath(Model model,
MathContainer mathContainer) |
|
static boolean |
ArraysMath.evaluateIndexBounds(Model model,
Index index) |
Checks if the index math does not go out of bounds.
|
static boolean |
ArraysMath.evaluateIndexBounds(Model model,
SBase reference,
int arrayDim,
ASTNode math,
java.util.Map<java.lang.String,java.lang.Double> dimSizes) |
|
static boolean |
ArraysMath.evaluateIndexBounds(Model model,
SBase parent,
java.lang.String refAttribute,
ASTNode math,
int arrayDim) |
|
static boolean |
ArraysMath.evaluateSelectorBounds(Model model,
MathContainer mathContainer) |
Checks if the arguments of a selector function does not go out of bounds.
|
static java.util.Map<java.lang.String,java.lang.Double> |
ArraysMath.getDimensionSizes(Model model,
ArraysSBasePlugin arraysSBasePlugin) |
Maps a dimension id to the size of the dimension object.
|
static int |
ArraysMath.getSize(Model model,
Dimension dimension) |
Gets the size of a Dimension object.
|
static java.util.Map<java.lang.Integer,java.lang.Integer> |
ArraysMath.getVectorDimensionSizes(Model model,
ASTNode math) |
Returns a map containing a pair of array depth level and its size.
|
static boolean |
ArraysMath.isStaticallyComputable(Model model,
ASTNode math,
java.lang.String... constantIds) |
Determines whether a
MathContainer object is
statically computable given a list of ids that can appear in the math. |
static boolean |
ArraysMath.isStaticallyComputable(Model model,
Index index) |
Determines whether a
MathContainer object is statically computable. |
static boolean |
ArraysMath.isStaticallyComputable(Model model,
MathContainer mathContainer) |
Determines whether a
MathContainer object is statically computable. |
static boolean |
ArraysMath.isStaticallyComputable(Model model,
MathContainer mathContainer,
java.lang.String... constantIds) |
Determines whether a
MathContainer object is statically computable given
a list of ids that can appear in the math. |
static boolean |
ArraysMath.isVectorBalanced(Model model,
MathContainer mathContainer) |
Modifier and Type | Method | Description |
---|---|---|
static java.util.List<SBMLError> |
ArraysMathValidator.validate(Model model,
MathContainer math) |
Validates the given
SBase object. |
static java.util.List<SBMLError> |
DimensionValidator.validate(Model model,
Dimension dim) |
Validates the given
SBase object. |
static java.util.List<SBMLError> |
ExtendedSBaseValidator.validate(Model model,
SBase sbase) |
Validates the given
SBase object. |
static java.util.List<SBMLError> |
IndexValidator.validate(Model model,
Index index) |
Validates the given
SBase object. |
Constructor | Description |
---|---|
ArraysConstraint(Model model) |
Constructs an ArraysConstraint with a model.
|
ArraysMathCheck(Model model,
MathContainer mathContainer) |
|
DimensionArrayDimCheck(Model model,
SBase sbase) |
Creates a DimensionArrayDimCheck with a model and sbase.
|
DimensionIDCheck(Model model,
SBase sbase) |
|
DimensionSizeCheck(Model model,
Dimension dim) |
|
IndexArrayDimCheck(Model model,
SBase sbase) |
Creates a new
IndexArrayDimCheck instance with a model and sbase |
IndexAttributesCheck(Model model,
Index index) |
|
SBaseWithDimensionCheck(Model model,
SBase sbase) |
Creates a new SBaseWithDimensionCheck with a model and sbase.
|
Modifier and Type | Class | Description |
---|---|---|
class |
ModelDefinition |
Holder class for model definitions, which are
Model s. |
Modifier and Type | Method | Description |
---|---|---|
Model |
CompSBMLDocumentPlugin.createModelDefinition() |
Creates a new ModelDefinition element and adds it to the ListOfModelDefinitions list
|
Model |
CompSBMLDocumentPlugin.createModelDefinition(java.lang.String id) |
Creates a new
ModelDefinition element and adds it to the ListOfModelDefinitions list |
Model |
ExternalModelDefinition.getReferencedModel() |
Resolves the external
Model referenced by this and returns that
model, under the assumption that the containing SBMLDocument a)
exists and b) has a valid locationURI set (cf
SBMLDocument.isSetLocationURI() ). |
Model |
ExternalModelDefinition.getReferencedModel(java.net.URI absoluteContainingURI) |
Resolves the external
Model referenced by this and
returns that model, for a given path to the directory containing the
SBML-file wherein this
ExternalModelDefinition was made/the root directory for references
by relative paths. |
Constructor | Description |
---|---|
CompModelPlugin(Model model) |
Creates a new
CompModelPlugin instance, associated with the given Model |
ModelDefinition(Model model) |
Creates a new
ModelDefinition instance cloned from the given core Model instance. |
Modifier and Type | Method | Description |
---|---|---|
Model |
FBCModelPlugin.getParent() |
|
Model |
FBCModelPlugin.getParentSBMLObject() |
Constructor | Description |
---|---|
FBCModelPlugin(Model model) |
Creates a new
FBCModelPlugin instance. |
Constructor | Description |
---|---|
GroupsModelPlugin(Model model) |
Creates a new
GroupsModelPlugin instance |
Modifier and Type | Method | Description |
---|---|---|
Model |
LayoutModelPlugin.getModel() |
Constructor | Description |
---|---|
LayoutModelPlugin(Model model) |
Creates a new instance
LayoutModelPlugin associate it with the given Model . |
Modifier and Type | Method | Description |
---|---|---|
Model |
MultiModelPlugin.getModel() |
Returns the
Model |
Constructor | Description |
---|---|
MultiModelPlugin(Model model) |
Modifier and Type | Method | Description |
---|---|---|
Model |
QualModelPlugin.getModel() |
Returns the
Model |
Constructor | Description |
---|---|
QualitativeModel(Model model) |
Deprecated.
use
QualModelPlugin instead. |
QualModelPlugin(Model model) |
Creates a new
QualModelPlugin instance |
Constructor | Description |
---|---|
GlyphCreator(Model model) |
Modifier and Type | Method | Description |
---|---|---|
Model |
SpatialModelPlugin.getExtendedSBase() |
|
Model |
AbstractSpatialSBasePlugin.getModel() |
Constructor | Description |
---|---|
SpatialModelPlugin(Model model) |
Constructor | Description |
---|---|
UnitsCompiler(Model model) |
Modifier and Type | Method | Description |
---|---|---|
Model |
ModelBuilder.buildModel(java.lang.String id,
java.lang.String name) |
|
Model |
ModelBuilder.getModel() |
Modifier and Type | Method | Description |
---|---|---|
static void |
SBMLtools.addPredefinedUnitDefinitions(Model model) |
|
static SBMLDocument |
SubModel.generateSubModel(Model model,
java.lang.String[] compartmentsIds,
java.lang.String[] speciesIds,
java.lang.String[] reactsIds) |
Generates a sub-model containing the elements passed as argument and all
the necessary dependencies.
|
static SBMLDocument |
SubModel.generateSubModel(Model model,
java.lang.String[] compartmentsIds,
java.lang.String[] speciesIds,
java.lang.String[] reactsIds,
java.lang.String[] rulesIds,
java.lang.String[] eventsIds) |
Generates a sub-model containing the elements passed as argument and all
the necessary dependencies.
|
static java.lang.String[] |
SubModel.getRelatedCompartments(Model model,
java.lang.String[] compartmentsIds,
java.lang.String[] speciesIds) |
|
static java.lang.String[] |
SubModel.getRelatedReactions(Model model,
java.lang.String[] reactsIds,
java.lang.String[] speciesIds) |
Returns an array of reaction id related to the
reactsIds or speciesIds . |
static java.lang.String[] |
SubModel.getRelatedSpecies(Model model,
java.lang.String[] reactsIds,
java.lang.String[] compartmentsIds,
java.lang.String[] speciesIds) |
|
static java.lang.String |
SBMLtools.nextId(Model model) |
Generate a valid SBML identifier using UUID.
|
Constructor | Description |
---|---|
UnitsCompiler(Model model) |
|
UnitsCompiler(Model model,
boolean allowInvalidModel) |
|
UnitsCompiler(Model model,
ValidationContext ctx) |
Modifier and Type | Method | Description |
---|---|---|
static ASTNode |
ExpandFunctionDefinitionConverter.expandFunctionDefinition(Model m,
ASTNode math) |
Expands the
FunctionDefinition used in the given ASTNode . |
Constructor | Description |
---|---|
OverdeterminationValidator(Model model) |
Creates a new OverdeterminationValidator for the given model
|
Modifier and Type | Method | Description |
---|---|---|
static boolean |
ValidationTools.checkUnit(ValidationContext ctx,
Model m,
java.lang.String units) |
Checks that the given units is a valid units in the
Model (validation rule 10313). |
static UnitDefinition |
ValidationTools.getDerivedExtendUnitDefinition(Model m) |
Returns the extend
UnitDefinition for the given Model . |
static UnitDefinition |
ValidationTools.getDerivedSubstanceUnitDefinition(Model m) |
Returns the substance
UnitDefinition for the given Model . |
static UnitDefinition |
ValidationTools.getDerivedTimeUnitDefinition(Model m) |
Returns the time
UnitDefinition for the given Model . |
static boolean |
ValidationTools.isSpeciesReference(Model m,
java.lang.String name) |