JSBML is a community-driven project to create a free, open-source, pure Java library for reading, writing, and manipulating SBML files and data streams. It is an alternative to the mixed Java/native code-based interface provided in libSBML. The JSBML project's aim is to provide an SBML parser and programming library that maps all SBML elements to a flexible and extended type hierarchy. Where possible, JSBML strives to attain 100% API compatibility with the libSBML Java API, to facilitate a switch from one library to the other.
The user guide can be found at the JSBML User Guide webpage.
| 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.ontology | |
| org.sbml.jsbml.resources |
Contains classes to deal with and to manage non-Java resources, such as
configuration files.
|
| 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.validator.offline.i18n |
Contains the messages and short messages for the SBML errors in different languages.
|
| org.sbml.jsbml.validator.offline.i18n.fr |
Contains the messages and short messages for the SBML errors in french.
|
| 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.
|
| org.sbml.jsbml.xml.xstream.converter |
Contains classes that uses the XStream to read or write XML.
|