JSBML 1.1 release

---

JSBML-1.1

We are pleased to announce the release of JSBML-1.1.

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.

For more details, please visit

http://sbml.org/Software/JSBML

At the end of this message, you can find a detailed list of the
user-visible new features and bug fixes since 1.0.

Thank you for your interest and support of JSBML and SBML in general.

The JSBML team.

Version 1.1 (09-12-2015)

• New Features:
  • Implemented the ability to support multiple version of SBML Level 3
    package definitions.
  • Improved the Maven pom files, and changed the Maven group ids and
    artifact ids. They should be stable now. With these changes in place,
    we can update the Maven repository much more quickly and easily. Next
    steps are to make JSBML available in Maven Central.
  • Added some utility classes to improve support for SBML files written by
    the Cobra toolbox before the SBML Level 3 FBC package was created. The
    CobraFormulaParser class can parse properly the Cobra gene associations
    String into an ASTNode. The CobraUtils class contain a method to parse
    the SBML notes into a Java Properties object.
  • Updated the implementation of the SBML Level 3 Groups package to the
    Groups version 0.7 specification.
• Bug Fixes:
  • The compartment 'units' attribute was not written in SBML L1. This is
    corrected now.
  • SBML L1 rules were not correctly written: the wrong XML element name
    was used. Now it uses the correct L1 names and attributes.
  • The clone constructor for the Species class did not copy the
    speciesType attribute. Thanks to Olivier Martin who reported the
    problem.
  • The clone constructor for the FunctionDefinition class did not copy the
    id attribute.
    • Since the merge with the astnode2 branch in 1.1-beta1, the attributes
      on mathML elements where processed before calling the main
      processAttributes method and as a consequence, some of them where not
      processed at all, like 'sbml:units'. Thanks to Matthias König who
      reported the problem.

Version 1.1-beta1 (12-10-2015)

• New Features:
  • Changed the default JSBML formula compiler. WARNING: this changes the
    default output for comparison operators. The parsing is now very close
    to what the libSBML L3 parser is doing.
  • Added support for the nested CVTerms introduced in SBML L2V5 and
    L3V2. We created some new methods in the CVTerm class to be able to
    manipulate nested terms.
  • Merged with the ASTNode2 branch (experimental). This is not used by
    default, but it is starting to work well. We were able to pass all tests
    from the SBML Test Suite using the ASTNode facade that uses the ASTNode2
    classes underneath. We made this work so that no API change is needed --
    old code should work without modifications.
  • Changed the printing of ASTNode in SimpleTreeNodeChangeListener to
    avoid many exceptions being printed when reading an XML file and the
    log4j DEBUG is activated (SF.net tracker item #88).
  • Improved CellDesigner LayoutConverter.
  • Added a new class, PackageUtil, to check and fix the package versions and
    namespaces if needed. This method is called after we read a file from
    XML or before we write the model to XML. In the near future, the method
    SBase.registerChild will take care of setting everything properly.
  • Added a default load of the parsers for environment not setup properly
    for it (Eclipse, Matlab dynamic path, OSGi, ...).
  • Modified the way we initialize the XML factories so that it is explicit
    (to OSGi for example) which classes and packages are used. Then there
    is no more need to define the System properties about the XML factories
    which solve an other reported problem with OSGi bundles. Thanks to all
    users who reported and tested problems related to OSGi.
  • Implemented a new interface CompartmentalizedSBase and changed all
    elements that can have a compartment so that they extend it.
  • Added a createCurve method to ReactionGlyph.
  • Improvements in the arrays flattening code.
  • Updated spatial to implement version 0.90 of the draft specifications.
  • Implemented FBC version 2.
  • Implemented distrib version 1 draft 0.16.
  • Modified the SBMLReader so that we are able to parse some UncertML
    Strings as XMLNode, even when they are on their own, via
    org.sbml.jsbml.xml.XMLNode.convertStringToXMLNode(String).
  • Added a new class DistribModelBuilder to help users to create distrib
    elements, including uncertML XMLNode.
  • Implemented the multi draft rev 459 (Nov 2014).
• Bug Fixes:
  • Methods that accepted Double/Integer/Boolean values or returned those
    where updated to double/integer/boolean in the spatial and render
    package. Instead of null values PropertyUndefinedExceptions are now
    thrown when necessary.
  • Tracker item #83: the equals method from StringBuilder is
    not implemented so we have to compare the content of the StringBuilder
    or use other utility method to compare properly the StringBuilders.
  • Tracker item #84: corrected and improved the XMLNode.toString method.
  • Tracker item #85: removing spaces with the String.trim() method in
    org.sbml.jsbml.Creator.setEmail(String) before checking the validity
    of the email address. Thanks to Camille Laibe who reported this
    problem.
  • Tracker item #87: changed HashMap to Map in the SBMLValidator API.
  • When writing math formula, in some cases, parentheses were not generated
    properly surrounding relational expressions. This is now fixed. Thanks
    to Miguel de Alba for reporting this problem.

---

J S B M L 1.1

JSBML is a free, open-source programming library to help you read, write,
manipulate, translate, and validate SBML files and data streams. It is not
an application itself (though it does come with example programs), but
rather a library you can embed in your own applications.

This is the a short description of the JSBML 1.1 final release files.
Here you will find the following:

jsbml-1.1.jar -- jar file containing the classes of JSBML-1.1

jsbml-1.1-with-dependencies.jar -- jar file containing the
classes of JSBML-1.1 including all of the currently supported
SBML L3 packages and any needed dependencies libraries classes.

jsbml-1.1-full.zip -- full distribution of JSBML-1.1
containing the two jars file described above plus the sources and
documentation along with the build script to be able to compile the
library. Contain also the jsbml modules sources and binaries.

For more information about JSBML, please visit the JSBML website at

               http://sbml.org/Software/JSBML

Thank you for your interest in JSBML!

The JSBML Team.

jsbml-1.0-rc1

Version 1.0-rc1 (24-09-2014)

• New Features:
  • Changed the default behaviour of the parsing of math infix formula.
    The methods concerned are JSBML#parseFormula and
    ASTNode#parseFormula.
    The changes include a different operator precedence, to match the
    one used in the L3 libSBML parser. The parsing is also case
    sensitive for mathML elements. Boolean operators are now
    differently interpreted: '&&' and '||' are used instead of 'and'
    and 'or'. Please consult the JavaDoc of those methods for more
    details, it is also explain there what to do if you want to keep
    the old behaviour.
  • Added two new BioModels.net qualifiers, bqmodel:isIntanceOf and
    bqmodel:hasInstance.
  • BioJava was updated to the latest version and the dependency is
    now to biojava3-ontology.
  • Added removeCVTerm methods in Annotation and SBase.
  • An IdManager interface has been introduced to help deal with the
    different id namespace in SBML core and in the different packages.
  • JSBML now provides a convenient ModelBuilder that can be used to
    create SBML models with a significantly lower number of lines of
    code for the end user.
  • Improved Java source code documentation (in particular CVTerm).
  • The SBMLDocument has now a convenient method to access all metaIds
    within the document in form of an unmodifiable Collection.
  • The SBO class provides more methods to access those terms that are
    of particular interest for SBGN displays.
  • A general Pair of arbitrary values now generalizes ValuePair.
  • The toString() methods in UnitDefinition and SpeciesReferences
    have been improved and are now more informative.
  • Internally, JSBML no longer creates Unit objects that lack
    required attributes when reading models. (However, this does not
    prevent users from creating new Unit objects without such
    attributes.)
  • Species and Compartment 'containsUndeclaredUnits' method has been
    overridden because in SBML L3 Species and Compartments can inherit
    a default unit from the Model. This is now considered. In this
    case, containsUndeclaredUnits will return false even if the object
    itself does not explicitly declare its unit. This is important
    because the unit of the element is not undefined.
  • Added some missing methods to manipulate EvenAssignment in Event
    and improved the JavaDoc of the Event class.
  • Added some missing getter in the L3 packages classes.
  • Support for SBML Level 3 'Arrays' package:
  • Arrays package implemented, version 05/05/14. Only selector and
    vector supported for now. Validations, flattening available.
  • Added support for vector and selector infix parsing to support the
    arrays package.
  • Support for SBML Level 3 'Layout' package:
  • Added missing methods to remove GeneralGlyph objects from a Layout
    object.
  • Added further missing remove or unset methods in the layout
    package.
  • Support for SBML Level 3 'Qualitative Models (qual)' package:
  • The class QualitativeModel in the qual package has been marked
    deprecated and should no longer be used. Aiming to achieve better
    compatibility to libSBML, the new class QualModelPlugin has been
    created to be used instead.
  • Support for SBML Level 3 'Spatial Processes (spatial)' package:
  • Updated to implement version 0.88 of the draft specifications.
• Bug Fixes:
  • Corrected the method AbstractSBase#getExtensionCount that was
    always returning 0.
  • Corrected the SBMLWriter so that disabled packages are not written
    to XML any more (they are still cloned).
  • Corrected the method SBase.appendNotes that contained several
    problems.
  • Corrected a bug when cloning a text XMLToken.
  • Fixed the AbstractSBase equals method that could throw a
    NullPointerException in some cases and was not testing all fields.
  • Fixed the CVTerm.removeResource(String) method. Thanks to Camille
    Laibe who reported the problem (tracker item #80).
  • Corrected the method ASTNode.parseFormula so that they catch any
    Exception or Error and throw a ParseException instead.
  • Added the support for the 'root' function in the parsing of math
    formula.
  • The FormulaParserLL3 was not reading properly formula like
    'kf * S0 * S1'. Only two arguments were read instead of three or
    more. Thanks to Chris J. Myers for reporting this problem.
  • Corrected a bug in Event#setListOfEventAssignments method that
    prevented the listOfEventAssignments to be registered properly in
    the model (ids and metaids registered).
  • Corrected the removeFromParent method to make it working for
    SBasePlugin instances.
  • The ListOf.remove(String) will not throw a ClassCastException
    anymore when used on list that do not contain elements with id.
  • The static method JSBML.read(String) was not calling the right
    helper method.
  • ASTNode threw a NullPointerException when trying to un-set its
    variable.
  • The AbstractTreeNode recursive method
    removeTreeNodeChangeListener(TreeNodeChangeListener, boolean) was
    not actually recursive.
  • Solved source for potential NullPointerException in LaTeXCompiler.
  • Support for SBML Level 3 'Hierarchical Model Composition (comp)'
    package:
  • Fixed several issues when cloning 'comp' elements and L3 packages
    elements in general. Thanks to Chris J. Myers and the iBioSim team
    for their help to find and fix all issues.
  • Support for SBML Level 3 'Flux Balance Constraints (fbc)' package:
  • The required flag for the fbc package was set to true instead of
    false, thanks to Chris J. Myers for reporting this problem.
  • Support for SBML Level 3 'Layout' package:
  • The implementation of the layout package contained unnecessary
    classes that all represented a Point object (Start, End, Position,
    BasePoint1, BasePoint2). In order to avoid confusion and to
    simplify the implementation, those classes have all been deleted.
  • Corrected the method Layout#setListOfAdditionalGraphicalObjects to
    avoid the warnings when cloning the list and to avoid to create a
    new list when not needed.
  • Support for SBML Level 3 'Qualitative Models (qual)' package:
  • The SBML qual attribute Output.outputLevel was not read properly
    from XML.
  • Support for SBML Level 3 'Rendering (render)' package:
  • Fixed severals bugs in the experimental render package. Renamed
    the Group class to RenderGroup and the Curve class to RenderCurve.
    Added the possibility to add children to a RenderGroup and
    corrected the way it was written to XML.

jsbml-1.0-beta1

Version 1.0-beta1 (06-03-2014)

• New Features:
  • The main addition to JSBML 1.0 is support for the SBML Level 3 packages,
    as described below.
  • JSBML is no longer compliant with Java 1.5, and now requires Java 1.6 as
    a minimum. We believe this is reasonable given the widespread
    availability of Java virtual machines version 1.6 on diverse platforms.
  • Support for the SBML Qualitative Models package (qual) has been
    implemented, following the Version 1 Release 1 specification (17 May
    2013).
  • Support for the SBML Flux Balance Constraints package (fbc) has been
    implemented, following the Version 1 Release 1 spec. (11 February 2013).
  • Support for the SBML Hierarchical Model Composition package (comp) has
    been implemented, following the Version 1 Release 3 spec. (14 November
    2013).
  • Support for the SBML Layout package (layout) has been implemented,
    following the Version 1 Release 1 specification (13 August 2013).
  • (Experimental) support for the SBML Required Elements package (req) has
    been implemented, following the draft Version 1 Release 0.5 spec. (30 May
    2013).
  • (Experimental) support for the SBML Spatial Processes package (spatial)
    has been implemented, following the working specification Version 1
    release 0.80 (latest version is release 0.85, 13 December 2013).
  • (Experimental) support for the SBML Groups package (groups) has been
    implemented, following the draft Version 1 Release 0.4 spec. (17 May 2013).
  • (Experimental) support for the SBML Render package (render) has been
    implemented, trying to follow the SBML Level 2 specification.
  • Support for arrays, distrib and multi is not yet available but planned
    for the final JSBML 1.0 release.
  • A ParserManager class has been implemented to register SBML Level 3
    package parsers. This manager also allows JSBML to enable automatically
    the packages into the SBMLDocument so there is no longer a need to set
    the package namespace or the 'required' attribute manually.
  • Reading more than one RDF Description element in the RDF annotation
    block (the official SBML annotation scheme) is now supported. The whole
    annotation is parsed first into an XMLNode object, and then the official
    SBML annotations are extracted, if any are found.
  • A new convenience method, removeFromParent, has been added to SBase and
    TreeNodeWithChangeSupport. It offers the ability to remove any element
    from the JSBML tree from its parent.
  • An alternative class to parse mathematical formula has been implemented.
    It is named FormulaParserLL3 and it respects the same syntax as the
    libSBML L3 parser.
  • Some filter methods have been added to TreeNodeWithChangeSupport (and
    thus to SBase as well); they allow for recursive queries in the entire
    data structure.
  • A new filter, XMLNodeFilter, is available to facilitate the manipulation
    of XMLNode. It allow to do a search similar to the DOM
    Element#getElementsByTagNameNS(String, String) method on XMLNode.
  • There is now a new ProgressListener utility class that enables tracking
    the progress of computationally intensive tasks.
  • For better localization support and to separate source code from user
    messages, a new resource manager has been implemented and is being used
    in some JSBML classes already.
  • The CVTerm API has been improved with new methods that should simplify
    the code needed to manipulate CVTerm objects. The javadoc documentation
    indicates which methods could be used to replace the existing ones.
  • The libSBMLio module for reading and writing SBML using libSBML as an
    input and output module has been revised and completely re-implemented.
  • The CellDesigner plugin module has been completely re-written and has
    become significantly more efficient. This facilitates the creation of
    CellDesigner plugins for existing JSBML-based programs with very little
    overhead.
  • MAVEN support has been improved. Thanks to Aurélien Naldi for providing
    several POM.xml files for JSBML.
  • Syntax checking for SBML 'metaid' attributes have been added to the
    setMetaId method.
  • SBasePlugin now implements the TreeNodeWithChangeSupport interface.
  • Validation checks for e-mail addresses have been added to Creator.
  • A quick Hash-based search method to access elements in a model based on
    their identifier is now available. In the same way, any SBase can be
    found in the SBMLDocument based on its metaId in constant time.
  • In order to make the API more Java-like, for each getNumXXX method a
    corresponding getXXXCount method has been created.
  • The userObject in ASTNode has been replaced by a more general map of
    userObjects that is located in TreeNodeWithChangeSupport. In this way,
    any JSBML object that is part of the SBML tree can now be attached with
    user- defined objects. These will not be written to SBML later on.
  • The Unit class has the new methods removeMultiplier: it merges multiplier
    and scale. This can only be done if the logarithm to the base 10 of the
    multiplier is nearly an integer number, i.e., if the distance to the next
    integer falls below the ensured double precision.
  • The multiplyWith and divideBy methods in UnitDefinition have been
    improved to better combine units by using the merge method.
  • The Species class now ensures that its spatial size units can only be set
    if its surrounding compartment does not have zero dimensions and if its
    hasOnlySubstanceUnits attribute is false. This behavior is specified by
    the SBML documents for Level 2 Versions 1 and 2, but was not yet
    implemented.
  • When deriving its UnitDefinition, the Species class searches for a
    suitable existing unit from the model, rather than creating a new
    instance. To this end, inherited Level 3 units from the Model are now
    taken into account.
  • A new JUnit test class helps to check if simplification and merging of
    Units and UnitDefinitions works correctly.
• Bug Fixes:
  • When writing SBML to files, the streams created by JSBML were not closed
    in all cases. Fixed. Thanks to Akira Funahashi for pointing this out.
  • Appending text in an XMLToken did not have an effect if there was already
    some text. Fixed.
  • When trying to remove a modifier, reactant, or product from a reaction using
    the id of the element, where no such element was present before, a
    NullPointerException was thrown. This has been solved. Thanks to Curtis
    Madsen for detecting this bug.
  • In the Reaction class, the setReversible method accepted Boolean, instead
    of boolean. This has been changed.
  • Removed old note comment from the SubModel class.
  • JSBML did not write negative infinity into SBML files correctly. Fixed.
  • Detected and fixed a source of possible NullPointerExceptions within the
    hashCode method in ASTNode.
  • There was a bug in KineticLaw that prevented a correct iteration through
    all children. Instead of looking at the listOfLocalParameters, it
    returned the math element twice (if there was one).
  • When cloning entire models or SBMLDocuments, JSBML assigned the identical
    TreeNodeChangeListeners to the new data structure. This could lead to
    unexpected behavior because listeners were receiving change events from
    data structures to which these have not been explicitly added by a user.
  • Cloning caused problems because in some cases the recursive method that
    registers all local parameters and other entities with an id did not do a
    full recursion. Hence, some entities could not be found in the model
    later on when searching for a certain id.
  • When calling the method setSymbol in InitialAssignment with an instance
    of Variable as argument, the listeners were sometimes not correctly
    informed about changes.
  • The setParent method caused an incorrect and in many cases duplicate call
    of the nodeAdded method in TreeNodeChangeListeners. Instead of
    registering a property change (the parent link) the parent node has been
    passed to the nodeAdded method.
  • QuantityWithUnit did not fire update events when changing its value.
  • The unsetUnits method in ExplicitRule now correctly notifies the listeners.
  • The Model class lacked an unsetSubstanceUnits method. Thanks to Robert
    Byrnes for reporting this problem.
  • The Compartment class did not override the method getDerivedUnitDefinition
    from its superclass. Hence, Level 3 units could not be inherited from the
    model. Fixed.
  • Merging of Units did not correctly work in cases where the scales of two
    units could not be evenly merged: just one of both was used and the other
    was ignored. In the corrected version, both scales removed represented by
    a double-valued multiplier in the merged unit. In particular, this error
    occurred in the addition or subtraction of ASTNodes.
  • If during the simplification of UnitDefinitions a dimensionless unit was
    created by canceling terms, its scale was always set to 0 and multiplier to
    1, which could lead to errors. Additional checks now yield correct results.
  • The units of formulae containing Advogadro's number could not be derived.
    This is now fixed.
  • In some cases, containsUndeclaredUnits() in ASTNode yielded incorrect
    results. These are now fixed.
  • [Tracker item #6]: a NullPointerException was returned when using the
    method Model.findLocalParameters(String) unless at least one
    LocalParameter was registered in the model.
  • It was sometimes possible to unregister elements from a model using
    cloned elements that did not belong to the model.
  • SBMLValidator fixed according to the changes made on the sbml.org
    validator to add package information.
• Known issues:
  • If you don't have the code handling a package in your classpath,
    jsbml-1.0-beta1 will loose the package elemen...

jsbml-0.8-rc1

Version 0.8-rc1 (14-12-2011)

• New Features:
  • NamedSBase has now the new method isIdMandatory in order to check
    whether the identifier of this element must be defined in the SBML
    representation.
  • The SBMLReader can now be used in connection with a
    TreeNodeChangeListener. This allows users to keep track about the
    parsing process of XML files.
  • The new interface TreeNodeWithChangeSupport separates manipulation
    of change listeners from SBase, allowing multiple implementations.
  • The JavaDoc has been extended: It now also includes a statement
    when ever a method might throw a PropertyNotAvailableException.
    This class was called PropertyNotAvailableError before. In order
    to avoid confusion with Java Errors, this class has been renamed.
    Also the super type XMLError has been renamed to XMLException in
    order to come closer to the default Java naming convention in
    JSBML.
  • ASTNode has now a userObject attribute through which any
    computation result or other additional information can be stored
    in the tree.
  • Restructured the extension package: There is now one extra
    directory including a specialized source folder for each extension.
    The core does no longer contain the ext package. Besides the source
    folder, there is also an extra doc folder that contains the
    description of the type hierarchy of the implementation for this
    package.
  • Data structures for the spatial extension are implemented.
  • When accessing the i-th child of an AbstractSBase, it is no longer
    necessary to sort all extension packages as these are now
    maintained in a sorted data structure.
  • The compile method in ASTNode has become more efficient now by
    restructuring its case distinctions.
  • Implemented the hashCode method for all elements belonging to the
    hierarchical SBML data structure (SBase, Annotation, ASTNode
    etc.).
  • In order to get closer to the Java package structure, the change
    listener for SBML objects is now located in the package
    org.sbml.jsbml.util package. For the sake of more similarity to
    standard Java classes and a greater flexibility, the
    SBaseChangedListener has been renamed to TreeNodeChangeListener
    and now extends the PropertyChangeListener in the package
    java.beans. The same holds for the corresponding
    SBaseChangedEvent that is now called TreeNodeChangeEvent and also
    located in the package org.sbml.jsbml.util. Furthermore, all
    elements of the SBML tree, including annotations, ASTNodes etc.
    now make use of change events and notify their listeners, which
    are now organized in a list instead of a set to make sure that
    they are always called in the same order. The management of these
    listeners is now performed in AbstractTreeNode, the new super
    class for all recursive elements in JSBML. Thanks to Sarah Rachel
    Müller vom Hagen to support this effort.
  • Notes, annotations, and extension packages are now part of the tree
    representation of the JSBML data structure.
  • The new super class AnnotationElement has been introduced to gather
    all those elements that can be used to annotate instances of SBase.
  • The new Type AbstractTreeNode implements basic recursive functions
    and is now used as the new super class for ASTNode, AbstractSBase,
    the new type AnnotationElement, and XMLToken (as the super class of
    XMLNode). In this way, recursion and iteration over child elements
    within the SBML data structure now follow a unified structure and
    can be accessed uniquely within all such elements, including
    annotations and extensions. Furthermore, the new interface
    TreeNodeWithChangeSupport that is extended by SBase and
    AbstractTreeNode gathers methods to add, remove, and notify listeners
    about changes within the data structure (such as adding, removing
    or exchanging child nodes, or change of any attributes).
  • A simple implementation of AbstractTreeNode, the class
    TreeNodeAdapter has been implemented that contains some methods
    also present in the interface MutableTreeNode. However, it does not
    fully implement this interface because there are also some methods
    that are not suitable for JSBML purposes. The TreeNodeAdapter works
    as a wrapper class for elements that are part of the SBML data
    hierarchy but that do not implement the TreeNode interface. With this
    adapter, it is possible to include the list of Creators within a
    history that is not a ListOf object, or the list of CVTerms in an
    annotation in the hierarchy.
  • Sebastian Fröhlich provided some contributions to the parser for the
    SBML level 3 layout extension package. JSBML now supports experimental
    reading for this package. The full stable API for reading/writing of
    SBML level 3 packages is planned for the next release of JSBML.
  • The SBMLReader now follows the factory pattern by providing static
    methods to directly read SBML content from Files, InputStreams, or
    Strings. Thanks to Martin Gräßlin for this idea in tracker issue
    #3300433.
  • JSBML now provides a Maven script file. Thanks to Igor Rodchenkov
    for contributing this file.
  • Where necessary, initDefaults has been complemented with an
    additional method, for which the level/version combination can be
    directly specified, i.e., it is now possible for those elements to
    set their defaults as these would be for the specified
    level/version combination.
  • A basic check to avoid setting the same meta identifier more than
    once has been implemented. It maintains a set of metaIds on the
    SBMLDocument. Thanks to Stefan Hoops for making clear that such a
    check is mandatory.
  • A check for duplicate identifiers has been implemented. JSBML now
    registers all elements that might have an identifier in hashes
    mapping the id to the object itself. Different rules depending on
    the specifications of the levels and versions of SBML ensure that
    only allowable identifiers can be accepted. To this end, the new
    interface UniqueNamedSBase tags all those elements whose id is
    intended to be unique within one model.
  • When adding an element with undefined Level/Version combination
    or at least with undefined Version to an element whose L/V
    configuration has been defined, JSBML now recursively updates this
    configuration for the child element. In case of differing L/V
    configurations an exception will be thrown on adding the element.
• Bug Fixes:
  • Corrected mistakes in the org.sbml.jsbml.util.Maths class, where
    some trigonometric functions were incorrectly calculated.
  • When writing SBML Level 1 the name attribute (which has become the
    id attribute in later SBML versions) was never written because JSBML
    uses the id only as an internal representation. The check for
    Level 1 name attributes was not correct.
  • In SBML Level 1 MathML code was written in KineticLaws although
    in this SBML version formulas are represented in infix notation only.
  • When creating a Parameter object using the constructor that takes
    a LocalParameter as its only argument, a call to setConstant(true)
    was always performed, irrespective of the fact that for Level = 1
    models this method throws a PropertyNotAvailableError. Thanks to
    Sarah R. Müller vom Hagen for reporting this problem.
  • [Tracker issue #3323886]: The units of Species were not derived
    correctly because if the units were not explicitly defined, the method
    getDerivedUnitsInstance() always returned the predefined unit
    "substance", or null for models in Level 3. Now it considers the
    surrounding compartment, the hasOnlySubstanceUnits, and spatialSizeUnits
    attributes depending on the Level/Version configuration.
  • Cloning of SBMLDocuments was not done correctly: The set of already
    existing metaIds was initialized after adding the model to the document.
    In the mean time, there could already be access to this set.
  • When reading SBML content from a file or writing JSBML data structures
    as SBML to a file, the SBMLReader/Writer did not close streams after
    finishing. This caused that sometimes files could not be opened by other
    programs although writing was already done. Unfortunately, by correcting
    this bug, an IOException needs to be thrown, but previously, a
    FileNotFoundException was already sufficient. Hence, users need to catch
    a different exception now when reading/writing SBML.
  • Renamed the getters for Creator and ModifiedDates in History to
    getListOfCreators() and getListOfModifiedDates (before it was spelled
    without "Of", for the sake of having equal names for all such getters.
  • If the Level/Version combination was not set, the identifier of
    NamedSBases was sometimes not written to an SBML file.
  • [Tracker issue #3300430]: In some condition, the JVM was not checking
    the type of an Object before adding it to a typed variable which later
    lead to some ClassCastException that prevented jsbml to save some
    models. Thanks to Martin Graesslin to report the bugs alongside some
    unit tests and to help resolved it.
  • [Tracker issue #3300490] : The method SBase.getNotesString() was
    returning null instead of the empty string, as stated in the java
    documentation. This has been corrected and the empty String is returned
    now. Thanks to Martin Graesslin to report the bugs alongside some
    unit tests.
  • The SBML level 1 rules were incorrectly read, now when the 'type'
    attribute is set to 'rate', a RateRule is properly created.
  • The SubModel utility class was fixed and an example of how to use it
    added.
  • Corrected the clone method for listOf objects. The typeOfList was
    not set in the clone so it was not possible to save a model that contain
    a cloned list.
  • [Tracker item...

jsbml-0.8-b2

Version 0.8-b2 (18-04-2011)

New Features:

• The new interface CallableSBase ensures that only instances of this type may be referenced in ASTNodes. In this way, it is no longer possible to refer to Events from ASTNodes.
• Additional type of error: abstract PropertyError with its two subtypes PropertyNotAvailableError and PropertyUndefinedError. The PropertyNotAvailableError one indicates that a certain property of an SBase is not defined for its current Level/Version combination, whereas the latter one indicates that the value belonging to a mandatory property, for which there is no default value has not been defined. At least in the Trigger class, PropertyUndefinedErrors are now thrown when attempting to access the value of the persistent or initialValue attribute for models with Level >= 3 and an undeclared value. Thanks to Roland Keller and Lucian Smith for pointing out this necessity.

Bug Fixes:

• The class Maths, a compilation of useful mathematical functions, provided an implementation of the factorial function that took a double as its argument. However, for this purpose, the Gamma function must be implemented. We changed this function to take integer values only.
• A NullPointerException could occur when deriving the unit of an expression containing a call to the factorial function. Thanks to Roland Keller for reporting this.
• [Tracker issue #3208887] : When trying to access the previously set value for UseValuesFromTriggerTime it was possible that a NullPointerException could occur due to the attempt to clone this element. This has been fixed. Thanks to Sebastian Fröhlich for reporting this.
• [Tracker issue #3208903] : Priority elements were properly read and written. Thanks to Sebastian Fröhlich for reporting this.
• [Tracker issue #3204275] : It was impossible to set the size of a compartment for models in Level 3 if the spatial dimensions was undefined, i.e., NaN. Since it is only prohibited to set the size if the dimensions equal 0, we provided another test in the set method in Compartment to allow for this.
• Corrected a typo in the method SBO.getAntisenseRNA(), the method was always returning -1. It is now returning the correct value (317), thanks to Anushya Muruganujan for reporting this.
• [Tracker issue #3175906] : Removed plenty of unused methods in the Annotation class that were dealing with writing the annotation as XML. Everything is handle now in the stax SBMLWriter. The getAnnotationString method was not present in the SBase interface, it is now added and should be the only method used to get the Annotation as XML.
• [Tracker issue #3175911] : compartment.spatialDimensions type changed to double to be consistent with the SBML level 3 specifications, as a consequence the return type of the getSpatialDimensions as been changed.
• [Tracker issue #3176548] : id containing underscores were not parsed properly by the infix formula parser, this is now fix and any valid SId should work. Thanks to Goksel Misirli for reporting this.
• [Tracker issue #3175833] : annotation tags were not properly closed when a mathML element was present on the same element. Thanks to Goksel Misirli for reporting this.
• A new interface, CallableSBase, was introduced to encompass all the different SBML elements that can be referenced inside a mathML 'ci' element. As a consequence, some methods signature have changed.
• [Tracker issue #3175833] : in some cases, an empty annotation was written if a metaid was defined. Some methods were added to the Annotation class to test which part of the annotation is defined.
• [Tracker issue #3196284] : the unit exponent was incorrectly always read as an integer. This has been corrected and if the level of the model is 3, the exponent is read as a double.
• [Tracker issue #3196638] : the message constraint was not properly read, it was stored in the notes instead of the message ! This is now corrected, thanks to the person who reported that.
• Corrected several bugs in the SBMLValidator and implemented properly all the classes related to SBMLdocument.checkConsistency() so that is works as expected.
• [Tracker issue #3199792] : localParameter were not parsed correctly in SBML level 3. Thanks for the persons who reported it.
• [Tracker issue #3216183] : all the XML elements that were belonging to the RDF namespace were sent to a parser that understood only the specific SBML RDF annotations. This as been fixed and we can now have some RDF elements anywhere in the annotation.

Known issues :

• SBML level 1 rules when the 'type' attribute is equal to 'rate' are created as AssignmentRule instead of RateRule.
• The support for the mathML elements notanumber and infinity is not complete.
• Reading of more than one RDF Description elements in the RDF annotation block (the official SBML annotation scheme) is not supported at the moment.

JSBML 0.8-β1

Version 0.8-b1 (04-02-2011)

This the first beta release of JSBML 0.8, 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.

For more details, please visit http://sbml.org/Software/JSBML

Bug Fixes:

• [Tracker issue #3137967] Namespaces in the sbml element were incorrectly parsed, some known namespaces like html were not kept for examples. This is fixed, thanks to Paulo Maia for reporting this.

Known issues:

• problem of output indentation for notes, when there is several top level elements.
• the method SBMLDocument.checkConsistency() is not working. There is a problem in the parsing of the XML return by the sbml.org validator.
• dependency on the sbml.org validator which might not be robust enough (you cannot submit a file bigger 15MB for example). It would be better to be able to install your own localy or at least have several mirrors. We will have to see how it performs.
• in a mathML block, if one 'ci'element is suppose to represent a functionDefinition but the id is not a valid id, the type of the ASTNode is not set properly, so there are some errors when trying to use the corresponding ASTNode tree. (cf model generated by COBRA)