[Biojava-l] BioJava 4.0.0 released

[Andreas Prlic]

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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