[Biojava-l] [Biojava-dev] BioJava 4.0.0 released

[Spencer Bliven]

Great! Thanks, Andreas, for performing the release and getting it to work
on Maven Central! And to all the other contributors, of course!

On Fri, Jan 30, 2015 at 9:59 PM, Andreas Prlic <andreas at sdsc.edu> wrote:

> BioJava 4.0.0 has been released and is available from Maven Central as
> well as from http://biojava.org/wiki/BioJava:Download.
>
> BioJava 4.0.0 is a major release, with many new features as well as core
> API changes. In accordance with semantic versioning nomenclature, the jump
> to 4.x.x indicates that existing applications may need to be modified (e.g.
> due to the removal of deprecated methods). In most cases there should be a
> clearly documented replacement method. See below for details on how to
> upgrade.
>
> This release contains over 500 commits from 17 authors:
>
> @andreasprlic @benjamintboyle @christiam @dmyersturnbull @Elinow
> @emckee2006 @jgrzebyta @josemduarte @kevinwu1 @pibizza @heuermh @paolopavan
> @parit @pwrose @sbliven @sroughley @willishf
>
> *New Features:*
>
>    - General
>       - Consistent error logging. SLF4J is used for logging and provides
>       adaptors for all major logging implementations. (many contributors,
>       including @benjamintboyle and @josemduarte)
>       - Improved handling of exceptions (@dmyersturnbull)
>       - Removed deprecated methods
>       - Expanded the BioJava tutorial (@andreasprlic, @josemduarte, and
>       @sbliven)
>       - Updated dependencies where applicable
>       - Available on Maven Central (@andreasprlic and @heuermh)
>    - biojava3-core
>       - Improved Genbank parser, including support for feature records,
>       qualifiers, and nested locations. (@paolopavan and @jgrzebyta)
>    - biojava3-structure
>       - Better support for crystallographic information, including
>       crystallographic operators, unit cells, and protein-protein interfaces.
>       (@josemduarte)
>       - Better organization of downloaded structure files (set using the
>       PDB_DIR and PDB_CACHE_DIR environmental variables) (@sbliven)
>       - Better command-line tools for structure alignment (@sbliven)
>       - New algorithm for symmetry detection in biological assemblies
>       (@pwrose)
>       - New algorithm for fast contact calculation, both intra-chain and
>       inter-chain (@josemduarte)
>       - Support for Accessible Surface Area (ASA) calculation through and
>       implementation of the Shrake & Rupley algorithm, both single-thread and
>       parallel (memory permitting) (@josemduarte)
>       - Support for large structures (memory permitting) and
>       multi-character chain IDs.
>       - Default to mmCIF file format, as recommended by the wwPDB
>
> This version is compatible with Java 6, 7, and 8.
>
> *Upgrading*
>
> Since we renamed all package names to be consistent across the whole
> project, there will be import errors when upgrading to this version. These
> can automatically get resolved using IDEs such as Eclipse or IntelliJ by
> selecting the *Optimize Import* menu item.
>
> *About BioJava:*
>
> BioJava is a mature open-source project that provides a framework for
> processing of biological data. BioJava contains powerful analysis and
> statistical routines, tools for parsing common file formats, and packages
> for manipulating sequences and 3D structures. It enables rapid
> bioinformatics application development in the Java programming language.
>
> Happy BioJava-ing,
>
> Andreas
>
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>
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