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 #3306135] : the handling to the number NaN (NotANumber) has
    been improved and the correct mathML element is created when saving the
    formula to XML.
  • The attribute denominator on level1v2 SpeciesReferences was never read.
    Thanks to the numerus models in the SBML Test Suite to help us detecting
    this problem.
• Known issues :
  • Reading of more than one RDF Description elements in the RDF annotation
    block (the official SBML annotation scheme) is not supported at the
    moment. Planned for the next major release.