[Biojava-l] Announce: BioJava1.3.1 released

[Schreiber, Mark]

Hi All -

The biojava 1.3.1 release has finally been posted to the biojava website and is obtainable from http://biojava.org/download/ This represents an interim release that is partway between biojava1.3 and biojava-live (from which the biojava1.4 release will be built). Your xmas present has arrived early this year :)

This release features:

* lots of bug fixes from the main branch
* Faster GUI rendering code
* Some new GUI code for circular sequence rendering
* Lots of bug fixes to improve SeqIO from flatfiles esp the protein based sequences
* Improved Serialization support (esp for Protein based sequences)
* LSID naming of core symbols to allow unambiguous deserialization
* Bug fixes to HMM/ DP code that prevent continuous loops when training profile HMMs
* Improved CircularLocation API
* Other stuff I have forgotten

One nice thing is that there have been very few changes or breaks to the API. The only thing that a few people may notice is that SimpleSequence and ViewSequence are now in org.biojava.bio.seq.impl. The recommended way of accessing these from now on is to use SequenceTools. This is in line with what happens in biojava-live.

Another change that almost no-one will notice unless they provide custom alphabets via XML files is that Symbols named in these files must now use a full LSID as there name (see AlphabetManager.xml for examples). If you make these changes everything else will work fine.

Known Issues:

* At the time of writing the output of Sequences in SwissProt and GenPept format is weak
* Biojava 1.3.1 only supports the Capetown version of the OBDA protocols. If you need more up to date support use biojava-live
* Theres bound to be other stuff so make sure you test your programs!

Details:

Java Docs are at http://biojava.org/download/docs/ in both tar.gz and zip format
Binaries are at http://biojava.org/download/binaries/ in jar format
Source is at http://biojava.org/download/source/ in both tar.gz and zip format

Future Releases:
<speaking entirely for myself, these views may not represent those of the group>
At this stage the future of the biojava 1.3.x branch is unclear. It will probably pick up a few more bugfixes but it is increasingly hard to incorporate everything from the main branch especially parts that have dependencies on new functionality such as the ontology package. My personal prefence is to vastly increase the converage of the unit tests in biojava-live and aim to have regular stable releases from the live branch (in line with the XP approach to programming). We'll see what happens. Anyhow there will probably be a 1.3.2 release at least before a 1.4 arrives.

Finally:

A big thanks to everyone who contributed code and told use when it didn't work. A lot of the bug fixes came about due to an increasing number of people using parts of the API that don't often get used in anger. This is encouraging as it means people actually seem to be interested and find biojava useful and are prepared to help identify and often help to fix bugs.

Enjoy!

- Mark
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