Package | Description |
---|---|
org.sbml.jsbml |
Pure Java™ implementation of the data structures to represent all SBML
constructs.
|
org.sbml.jsbml.ext |
The base package for all SBML extensions.
|
org.sbml.jsbml.ext.arrays | |
org.sbml.jsbml.ext.arrays.compiler | |
org.sbml.jsbml.ext.arrays.flattening | |
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.comp.util | |
org.sbml.jsbml.ext.distrib | |
org.sbml.jsbml.ext.distrib.util | |
org.sbml.jsbml.ext.dyn |
Provides classes for the
Dynamic Structures package.
|
org.sbml.jsbml.ext.fbc |
Provides classes for the
Flux Balance Constraints package (FBC).
|
org.sbml.jsbml.ext.fbc.converters | |
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.multi.util | |
org.sbml.jsbml.ext.qual |
Provides classes for the Qualitative Models package.
|
org.sbml.jsbml.ext.render |
Provides classes for the render package, see the specification at sbml.org.
|
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.req | |
org.sbml.jsbml.ext.spatial |
Provides classes for the
Spatial Geometries and Processes package.
|
org.sbml.jsbml.math | |
org.sbml.jsbml.math.compiler | |
org.sbml.jsbml.math.parser |
Provides classes to parse formula
Strings and to convert these into abstract syntax tree data structures.
|
org.sbml.jsbml.text.parser |
Provides classes to parse formula
Strings and to convert these into abstract syntax tree data structures.
|
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.util.filters |
Filters are useful to decide whether or not to accept a certain item.
|
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 |
Provides classes to validate any kind of object offline.
|
org.sbml.jsbml.validator.offline.constraints |
Any validation constraints related to the multi package.
|
org.sbml.jsbml.validator.offline.constraints.helper | |
org.sbml.jsbml.validator.offline.factory | |
org.sbml.jsbml.xml |
This package provides classes and methods to deal with SBML in form of XML
elements, i.e., here you can find parsers and writers for SBML and also
elements to define XML nodes to be used for notes or annotations.
|
org.sbml.jsbml.xml.parsers |
Contains classes that implement
ReadingParser
and/or WritingParser to read or write some
specific parts of an SBML file. |
org.sbml.jsbml.xml.stax |
Contains classes that use the Streaming API for XML (StAX)
to read or write an SBML file.
|
Class | Description |
---|---|
AbstractMathContainer |
Base class for all the SBML components which contain MathML nodes.
|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractNamedSBaseWithUnit |
This simple implementation of the interfaces
NamedSBaseWithDerivedUnit and SBaseWithUnit defines elements
that can be addressed by their identifier and are or can be associated with a
defined Unit or UnitDefinition . |
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
AlgebraicRule |
Represents the algebraicRule XML element of a SBML file.
|
Annotation |
An Annotation represents the annotations of an
SBase element. |
AnnotationElement |
A common super class for all those elements that can be part of an
Annotation . |
Assignment |
An
Assignment can be seen as a mathematical equation with a
Variable on the left hand side and an equation on the right hand side
that assigns a value to the Variable . |
AssignmentRule |
Represents the assignmentRule XML element of a SBML file.
|
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
ASTNode.Type |
An enumeration of all possible types that can be represented by an
abstract syntax tree node.
|
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
CompartmentalizedSBase | |
CompartmentType |
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
|
Constraint |
Represents the constraint XML element of a SBML file.
|
Creator | |
CVTerm |
Contains all the MIRIAM URIs for a MIRIAM qualifier in the annotation element
of a SBML component.
|
CVTerm.Qualifier |
This
enum list all the possible MIRIAM qualifiers. |
CVTerm.Type |
This enum list all the possible MIRIAM qualifiers type.
|
Delay |
Represents the delay subnode of an event element.
|
Event |
Represents the event XML element of a SBML file.
|
EventAssignment |
Represents the eventAssignment XML element of a SBML file.
|
ExplicitRule |
An explicit
Rule is a rule that explicitly declares its variable
element. |
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
History | |
IdentifierException |
This exception is thrown when trying to set or add an identifier to an
instance of
NamedSBase but if the given identifier is already
registered in the containing Model . |
InitialAssignment |
Represents the initialAssignment XML element of a SBML file.
|
KineticLaw |
Represents the kineticLaw XML element of a SBML file.
|
LevelVersionError | |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
ListOf.Type |
This enum lists all the possible names of the listXXX components.
|
LocalParameter |
A local parameter can only be used to specify a constant within a
KineticLaw . |
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
Model |
JSBML implementation of SBML's
Model construct. |
ModifierSpeciesReference |
Represents the modifierSpeciesReference XML element of a SBML file.
|
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
NamedSBaseWithDerivedUnit |
All objects that implement this interface can be referenced in abstract
syntax trees as implemented in
ASTNode . |
Parameter |
Represents a globally valid parameter in the model, i.e., a variable that
may change during a simulation or that provides a constant value.
|
Priority |
This class represents the priority element in SBML.
|
PropertyException |
This is an error of an undefined property or value for a property in some
instance of
SBase . |
PropertyNotAvailableException |
An error that indicates that a property of an
SBase is
not available for the current SBML Level/Version combination. |
Quantity |
A quantity is an element that represents a value with an associated unit that
can be addressed through the identifier or name attribute of this element.
|
QuantityWithUnit |
This object represents an element with identifier and name, a value, and a
defined unit.
|
RateRule |
Represents the rateRule XML element of a SBML file.
|
Reaction |
Represents the reaction XML element of a SBML file.
|
Rule | |
SBase |
The interface to implement for each SBML element.
|
SBaseWithDerivedUnit |
This type represents an SBase object that is associated to a unit.
|
SBaseWithUnit |
Defines a kind of
SBase that is equipped with a defined unit. |
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
SBMLError |
Representation of errors, warnings and other diagnostics.
|
SBMLError.SEVERITY | |
SBMLErrorLog |
Log of errors and other events encountered during SBML processing.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
SBMLException.Category |
Category of this exception.
|
SBMLException.Code |
Error codes.
|
SBMLException.Type | |
SBMLReader |
Provides methods for reading SBML from files, text strings or streams.
|
SBMLWriter |
Provides methods for writing SBML to files, text strings or streams.
|
SimpleSpeciesReference |
The base class of
SpeciesReference and
ModifierSpeciesReference . |
Species |
Represents the species XML element of a SBML file.
|
SpeciesReference |
Represents the speciesReference XML element of a SBML file.
|
SpeciesType |
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
|
StoichiometryMath |
Deprecated.
Since SBML Level 3 Version 1 use
AssignmentRule with
instances of SpeciesReference as Variable
instead. |
Symbol | |
TidySBMLWriter |
Provides methods for writing SBML to files, text strings or streams.
|
Trigger |
Represents the trigger XML element of a SBML file.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Unit |
Represents the unit XML element of a SBML file.
|
Unit.Kind |
This enumeration contains an exhaustive list of all available unit kinds
within all Levels and Versions of SBML.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Variable |
A variable of the system is a
Quantity whose value may change during
a simulation. |
Class | Description |
---|---|
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
SBase |
The interface to implement for each SBML element.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
Class | Description |
---|---|
AbstractMathContainer |
Base class for all the SBML components which contain MathML nodes.
|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
NamedSBaseWithDerivedUnit |
All objects that implement this interface can be referenced in abstract
syntax trees as implemented in
ASTNode . |
SBase |
The interface to implement for each SBML element.
|
SBaseWithDerivedUnit |
This type represents an SBase object that is associated to a unit.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Class | Description |
---|---|
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
Model |
JSBML implementation of SBML's
Model construct. |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
Class | Description |
---|---|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
Class | Description |
---|---|
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
Model |
JSBML implementation of SBML's
Model construct. |
SBase |
The interface to implement for each SBML element.
|
Class | Description |
---|---|
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
Model |
JSBML implementation of SBML's
Model construct. |
SBase |
The interface to implement for each SBML element.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
SBMLError |
Representation of errors, warnings and other diagnostics.
|
Class | Description |
---|---|
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
Model |
JSBML implementation of SBML's
Model construct. |
SBase |
The interface to implement for each SBML element.
|
SBMLError |
Representation of errors, warnings and other diagnostics.
|
Class | Description |
---|---|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
Model |
JSBML implementation of SBML's
Model construct. |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
SBase |
The interface to implement for each SBML element.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Class | Description |
---|---|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
Class | Description |
---|---|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
SBase |
The interface to implement for each SBML element.
|
SBaseWithDerivedUnit |
This type represents an SBase object that is associated to a unit.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Class | Description |
---|---|
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
SBase |
The interface to implement for each SBML element.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
Class | Description |
---|---|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
Event |
Represents the event XML element of a SBML file.
|
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
SBase |
The interface to implement for each SBML element.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Class | Description |
---|---|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
Model |
JSBML implementation of SBML's
Model construct. |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
Parameter |
Represents a globally valid parameter in the model, i.e., a variable that
may change during a simulation or that provides a constant value.
|
Reaction |
Represents the reaction XML element of a SBML file.
|
SBase |
The interface to implement for each SBML element.
|
Species |
Represents the species XML element of a SBML file.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Class | Description |
---|---|
Reaction |
Represents the reaction XML element of a SBML file.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
Class | Description |
---|---|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
Model |
JSBML implementation of SBML's
Model construct. |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
SBase |
The interface to implement for each SBML element.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Class | Description |
---|---|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
CompartmentalizedSBase | |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
Model |
JSBML implementation of SBML's
Model construct. |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
Reaction |
Represents the reaction XML element of a SBML file.
|
SBase |
The interface to implement for each SBML element.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
SimpleSpeciesReference |
The base class of
SpeciesReference and
ModifierSpeciesReference . |
Species |
Represents the species XML element of a SBML file.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Class | Description |
---|---|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
CompartmentalizedSBase | |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
Model |
JSBML implementation of SBML's
Model construct. |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
NamedSBaseWithDerivedUnit |
All objects that implement this interface can be referenced in abstract
syntax trees as implemented in
ASTNode . |
Reaction |
Represents the reaction XML element of a SBML file.
|
SBase |
The interface to implement for each SBML element.
|
SBaseWithDerivedUnit |
This type represents an SBase object that is associated to a unit.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
SimpleSpeciesReference |
The base class of
SpeciesReference and
ModifierSpeciesReference . |
Species |
Represents the species XML element of a SBML file.
|
SpeciesReference |
Represents the speciesReference XML element of a SBML file.
|
SpeciesType |
Deprecated.
Only valid in SBML Level 2 for Versions 2 through 4.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Class | Description |
---|---|
SBase |
The interface to implement for each SBML element.
|
Class | Description |
---|---|
AbstractMathContainer |
Base class for all the SBML components which contain MathML nodes.
|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
CompartmentalizedSBase | |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
Model |
JSBML implementation of SBML's
Model construct. |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
NamedSBaseWithDerivedUnit |
All objects that implement this interface can be referenced in abstract
syntax trees as implemented in
ASTNode . |
SBase |
The interface to implement for each SBML element.
|
SBaseWithDerivedUnit |
This type represents an SBase object that is associated to a unit.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
Species |
Represents the species XML element of a SBML file.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Class | Description |
---|---|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
SBase |
The interface to implement for each SBML element.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Class | Description |
---|---|
Model |
JSBML implementation of SBML's
Model construct. |
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
Class | Description |
---|---|
AbstractNamedSBase |
Base abstract class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
SBase |
The interface to implement for each SBML element.
|
Class | Description |
---|---|
AbstractMathContainer |
Base class for all the SBML components which contain MathML nodes.
|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
Model |
JSBML implementation of SBML's
Model construct. |
NamedSBase |
Base class for all the SBML components with an id and a name (optional or
not) in SBML Level 3 Version 1 or lower.
|
Parameter |
Represents a globally valid parameter in the model, i.e., a variable that
may change during a simulation or that provides a constant value.
|
Reaction |
Represents the reaction XML element of a SBML file.
|
SBase |
The interface to implement for each SBML element.
|
SBaseWithDerivedUnit |
This type represents an SBase object that is associated to a unit.
|
SBaseWithUnit |
Defines a kind of
SBase that is equipped with a defined unit. |
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
Species |
Represents the species XML element of a SBML file.
|
UniqueNamedSBase |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model before SBML Level 3 Version 2. |
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Unit |
Represents the unit XML element of a SBML file.
|
Unit.Kind |
This enumeration contains an exhaustive list of all available unit kinds
within all Levels and Versions of SBML.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Class | Description |
---|---|
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
ASTNode.Type |
An enumeration of all possible types that can be represented by an
abstract syntax tree node.
|
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Class | Description |
---|---|
ASTNode.Type |
An enumeration of all possible types that can be represented by an
abstract syntax tree node.
|
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
Model |
JSBML implementation of SBML's
Model construct. |
Reaction |
Represents the reaction XML element of a SBML file.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
Unit |
Represents the unit XML element of a SBML file.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Class | Description |
---|---|
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
Class | Description |
---|---|
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
Class | Description |
---|---|
AbstractSBase |
The base class for each
SBase component. |
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
KineticLaw |
Represents the kineticLaw XML element of a SBML file.
|
ListOf |
This list implementation is a Java
List that extends
AbstractSBase . |
Model |
JSBML implementation of SBML's
Model construct. |
Parameter |
Represents a globally valid parameter in the model, i.e., a variable that
may change during a simulation or that provides a constant value.
|
Reaction |
Represents the reaction XML element of a SBML file.
|
SBase |
The interface to implement for each SBML element.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
Species |
Represents the species XML element of a SBML file.
|
UniqueSId |
This interface is used to tag all those elements
whose identifier must be unique within an SBML
Model . |
Unit |
Represents the unit XML element of a SBML file.
|
Unit.Kind |
This enumeration contains an exhaustive list of all available unit kinds
within all Levels and Versions of SBML.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Class | Description |
---|---|
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
ASTNode.Type |
An enumeration of all possible types that can be represented by an
abstract syntax tree node.
|
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
Compartment |
Represents the compartment in a model, i.e., a variable element with name,
identifier, unit, and value that may change during a simulation.
|
FunctionDefinition |
Represents the functionDefinition XML element of a SBML file.
|
Model |
JSBML implementation of SBML's
Model construct. |
Reaction |
Represents the reaction XML element of a SBML file.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
Unit |
Represents the unit XML element of a SBML file.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Class | Description |
---|---|
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
Model |
JSBML implementation of SBML's
Model construct. |
SBase |
The interface to implement for each SBML element.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
Class | Description |
---|---|
CVTerm.Qualifier |
This
enum list all the possible MIRIAM qualifiers. |
Species |
Represents the species XML element of a SBML file.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Class | Description |
---|---|
Model |
JSBML implementation of SBML's
Model construct. |
SBase |
The interface to implement for each SBML element.
|
SBMLErrorLog |
Log of errors and other events encountered during SBML processing.
|
Class | Description |
---|---|
SBase |
The interface to implement for each SBML element.
|
SBMLError |
Representation of errors, warnings and other diagnostics.
|
SBMLErrorLog |
Log of errors and other events encountered during SBML processing.
|
Class | Description |
---|---|
SBase |
The interface to implement for each SBML element.
|
SBMLError |
Representation of errors, warnings and other diagnostics.
|
Class | Description |
---|---|
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
Assignment |
An
Assignment can be seen as a mathematical equation with a
Variable on the left hand side and an equation on the right hand side
that assigns a value to the Variable . |
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
CallableSBase |
The interface
CallableSBase represents an SBase that can be
called in mathematical expressions, i.e., ASTNode , via its
identifier. |
KineticLaw |
Represents the kineticLaw XML element of a SBML file.
|
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
Model |
JSBML implementation of SBML's
Model construct. |
Reaction |
Represents the reaction XML element of a SBML file.
|
SBase |
The interface to implement for each SBML element.
|
SBaseWithDerivedUnit |
This type represents an SBase object that is associated to a unit.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
Species |
Represents the species XML element of a SBML file.
|
UnitDefinition |
Represents the unitDefinition XML element of a SBML file.
|
Variable |
A variable of the system is a
Quantity whose value may change during
a simulation. |
Class | Description |
---|---|
SBase |
The interface to implement for each SBML element.
|
SBMLError |
Representation of errors, warnings and other diagnostics.
|
Class | Description |
---|---|
AbstractTreeNode |
A basic implementation of the
TreeNode interface. |
Class | Description |
---|---|
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
SBase |
The interface to implement for each SBML element.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|
Class | Description |
---|---|
ASTNode |
A node in the Abstract Syntax Tree (AST) representation of a mathematical
expression.
|
MathContainer |
Base interface for all the SBML components which contain MathML nodes.
|
SBase |
The interface to implement for each SBML element.
|
SBMLDocument |
Represents the 'sbml' root node of a SBML file.
|
SBMLException |
This class roughly corresponds to libSBML's SBMLError class.
|