@niko-rodrigue niko-rodrigue released this Aug 16, 2018 · 9 commits to master since this release

Assets 4

We are pleased to announce the release of JSBML-1.4, which is now available for download from GitHub (above) and from SourceForge.

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 the JSBML project home page:

http://sbml.org/Software/JSBML

The main new feature in this release is the development of the offline validator. We have also started to write some converters that transform SBML documents. Some progress were made on the offline validator, you can get a detailed report of what is left to be done in a separate wiki page.

You can find a detailed list of the user-visible new features and bug fixes since JSBML version 1.3 on the NEWS file.

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

The JSBML team.

@niko-rodrigue niko-rodrigue released this Dec 19, 2017 · 432 commits to master since this release

Assets 4

We are pleased to announce the release of JSBML-1.3.1, which is now available for download from GitHub (above) and from SourceForge.

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 the JSBML project home page:

http://sbml.org/Software/JSBML

The main new feature in this release is the support for SBML Level 3 Version 2 and the development of the offline validator. We have also started to write some converters that transform SBML documents. In particular, a converter that expands function definitions that was requested several times by our community. Some very good progress was made on the offline validator, you can get a detailed report of what is left to be done in a separate wiki page. Since the last release, we made the offline validator more user-friendly by provided error messages similar to libSBML with a first part that explains the specification and a second part that describe the element and why it failed the rule. We hope to have the offline validator complete by the end of next year when it will be used by default.

You can find a detailed list of the user-visible new features and bug fixes since JSBML version 1.2 on the NEWS file.

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

The JSBML team.

@niko-rodrigue niko-rodrigue released this Dec 13, 2017 · 442 commits to master since this release

Assets 4

We are pleased to announce the release of JSBML-1.3, which is now available for download from GitHub (above) and SourceForge.

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 the JSBML project home page:

http://sbml.org/Software/JSBML

@niko-rodrigue niko-rodrigue released this Dec 13, 2016 · 710 commits to master since this release

Assets 4

We are pleased to announce the release of JSBML-1.2, which is now available for download from GitHub (above) and from SourceForge.

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 the JSBML project home page:

http://sbml.org/Software/JSBML

The main new feature in this release is the support for SBML Level 3 Version 2 (RC2). This involved some changes in the class hierarchy of JSBML. A notable SBML change introduced in SBML Level 3 Version 2 is that every SBase object can have an id and a name attribute. In JSBML, for compatibility reasons, we did not change the NamedSBase interface, so not every SBase is a NamedSBase. Only SBML elements that had id and name in SBML Levels/Versions below L3V2 will extend NamedSBase. So, when implementing support for SBML L3V2, we recommend that developers try to avoid using NamedSBase and just use SBase instead. The same is true for the JSBML classes UniqueNamedSBase and UniqueSId. If you were using the UniqueNamedSBase class, please try to use UniqueSId instead. As part of the upgrade to support SBML L3V2, users should also consider checking how they access InitialAssignment, Rule and EventAssignment objects, as often the methods make use of the variable or symbol attribute instead of the id attribute.

We have upgraded the minimum JDK requirement to 1.7 for this release, to be able to use the latest versions of the third-party libraries needed by JSBML. As the number of third-party libraries having JDK 1.8 as a minimum requirement increases, we may need to increase the minimum JDK requirement to 1.8 for next year's JSBML releases. (Please let us know in advance if you think requiring JDK 1.8 will be a problem for you.)

The method toString() available on most JSBML classes has been replaced by a generic method, so you may find some differences in the output produced by the JSBML classes compared to previous versions. One method we did not change for now is ASTNode.toString(), because doing so could cause many side effects. As part of the upgrade to SBML L3V2 and JSBML 1.2, we advise users to make sure they use ASTNode.toFormula() when they want to show/store the infix formula representation of an ASTNode, and to not rely on the toString() method for that purpose. Don't hesitate to provide us with some feedback about this change. We tried to keep any significantly different toString() method under a different name, starting with print and followed by the class name, for example Unit.printUnit() will produce the same output as the Unit.toString() method in JSBML 1.1.

Since the time of the last JSBML release, we have moved the JSBML source code repository to GitHub. Although we provide the main download files from GitHub, we will continue to distribute the releases from SourceForge until we develop a suitable release replacement scheme using either GitHub or sbml.org.

You can find a detailed list of the user-visible new features and bug fixes since JSBML version 1.1 on the NEWS file.

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

The JSBML team.

@niko-rodrigue niko-rodrigue released this Oct 26, 2016 · 846 commits to master since this release

Assets 5

JSBML-1.2-beta1

We are pleased to announce the release of JSBML-1.2-beta1, which is now available for download from github below and from sourceforge.

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

The main new feature in this release is the support for SBML Level 3 Version 2 (RC1). This involved some changes in the class hierarchy of JSBML. A notable SBML change introduced in SBML Level 3 Version 2 is that every SBase object can have an 'id' and a 'name' attribute. In JSBML, for compatibility reasons, we did not change the NamedSBase interface, so not every SBase is a NamedSBase. Only SBML elements that had 'id' and 'name' in SBML Levels/Versions below L3V2 will extend NamedSBase. So, when implementing support for SBML L3V2, we recommend that developers try to avoid using NamedSBase and just use SBase instead. The same is true for the JSBML classes UniqueNamedSBase and UniqueSId. If you were using the UniqueNamedSBase class, please try to use UniqueSId instead. As part of the upgrade to support SBML L3V2, users should also consider checking how they access InitialAssignment, Rule and EventAssignment objects, as often the methods make use of the 'variable' or 'symbol' attribute instead of the 'id' attribute.

We have upgraded the minimum JDK requirement to 1.7 for this release, to be able to use the latest versions of the third-party libraries needed by JSBML. As the number of third-party libraries requiring JDK 1.8 as a minimum requirement increases, we may need to increase the minimum JDK requirement to 1.8 for next year's JSBML releases. (Please let us know in advance if you think requiring JDK 1.8 will be a problem for you.)

The toString() method of most JSBML classes has been replaced by a generic method so you may find some changes in the output produced by the JSBML classes. One method we did not change for now is ASTNode.toString(), because doing so could cause many side effects. As part of the upgrade to SBML L3V2 and JSBML 1.2, we advise users to make sure they use ASTNode.toFormula() when they want to show/store the infix formula representation of an ASTNode, and to not rely on the toString() method for that purpose. Don't hesitate to provide us with some feedback about this change. We tried to keep any significantly different toString method under a different name, starting with 'print' and followed by the class name, for example Unit.printUnit() will produce the same output as the Unit.toString() method in JSBML 1.1.

Since the time of the last JSBML release, we have moved the JSBML source code repository to github.com. Although we provide the main download files from GitHub, we will continue to distribute the releases from SourceForge until we develop a suitable release replacement scheme using either GitHub or sbml.org.

You can find a detailed list of the user-visible new features and bug fixes since JSBML version 1.1 on the NEWS file.

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

The JSBML team.

@niko-rodrigue niko-rodrigue released this May 23, 2016 · 1551 commits to master since this release

Assets 2

JSBML-1.0

We are pleased to announce the final release of JSBML-1.0, which is now available for downloading from

 https://sourceforge.net/projects/jsbml/files/jsbml/1.0

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-beta1 and 1.0-rc1.

The most important new feature of JSBML-1.0 is the support for the SBML Level 3 packages. The list below explains which ones are supported exactly and which ones are experimental. An experimental package support is provided when the SBML Level 3 package specifications have not yet been finalized, and the package implementations are themselves in a state of development and provided 'as-is' for experimental development only.

An other major change is that now the XML annotation element is read as an XMLNode object class instead of String. This will hopefully make it easier to manipulate nonstandard annotations.

Other notable changes include: the manipulation and merging of units have been significantly improved, the modules for CellDesigner plugins and libSBML input/output have been rewritten, bugs have been fixed in the cloning of whole SBMLDocument and their subcomponents, and bug fixes have been fixed in the notification of change listeners.

For people using jsbml-0.8, the link below will highlight the api changes since 0.8:

http://sbml.org/Special/Software/JSBML/1.0/doc/JSBML_API_changes_0.8_to_1.0/changes.html

Release plan: We will try to have shorter release from now on. We will start working on the support for SBML L3V2, L2V5 that should arrive quickly and we will soon merge into trunk the work done on refactoring the ASTNode class.

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

The JSBML team.

Version 1.0 (09-12-2014)

  • New Features:
    • Added a new module that contains a tidy SBMLWriter that uses
      the jtidy library to correct the formatting of the XML file
      before writing it out.
    • Created a new class SyntaxChecker that corresponds to the class in
      libSBML and moved pattern matching for id comparisons and e-mail
      addresses into this class.
    • Updated JSBML to create identifiers.org URIs instead of URNs for
      units.
    • Support for SBML Level 3 'Dynamic Structures (dyn)' package:
    • First draft of JSBML implementation done (experimental).
  • Bug Fixes:
    • Solved error #82 in Unit.removeMultiplier. Thanks to Christian
      Thöns for pointing this out.
    • The registerChild method now returns a boolean value to indicate if
      the operation was successfully completed. This prevents users from
      adding duplicates to ListOf objects.
    • Improvements made to the java API documentation (javadoc).
    • Added a check to write only the necessary namespaces when writing
      CVTerm to XML.
    • Support for SBML Level 3 'Hierarchical Model Composition (comp)'
      package:
    • Registering SBaseRef correctly in the document. Corrected the clone
      constructor of SBaseRef that did not copy the recursive SBaseRef.
    • Added all the missing equals and hashCode methods in the comp
      package.
    • Support for SBML Level 3 'Arrays' package:
    • Several fixes and improvements in the validation code and the
      flattening code.

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.

@niko-rodrigue niko-rodrigue released this May 23, 2016 · 1306 commits to master since this release

Assets 5

JSBML-1.1 DOI

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.

@niko-rodrigue niko-rodrigue released this May 23, 2016 · 1632 commits to master since this release

Assets 2

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.

@niko-rodrigue niko-rodrigue released this May 23, 2016 · 1928 commits to master since this release

Assets 2

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 elements, they won't be kept
      in memory or went writing back the model to a file. The final release
      should be able to handle unknown packages.

@niko-rodrigue niko-rodrigue released this May 23, 2016 · 2515 commits to master since this release

Assets 2

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.