BioJava 1.5 Beta released

The BioJava project released the Beta of the next version 1.5. This version also contains the ExternalProcess class.

Here is the full text of Mark's announcement in the BioJava mailing list:

Dear All -

I have prepared a beta distribution of the much awaited biojava 1.5. The
source, binaries and docs for the release can be obtained from the biojava
site at http://biojava.org/wiki/BioJava:Download

The API docs are also available on line at
http://www.biojava.org/docs/api15b/index.html

There are significant new features in this release:

* biojavax, the biojavax packages are extensions to the basic biojava.
They give access to more detailed objects with better functionality. Most
useful to the average user will be the new file parsers (see
RichSequence.IOTools) and the RichSequence object. See the biojavax docs
for more detail (http://biojava.org/wiki/BioJava:BioJavaXDocs).

* Hibernate interaction with BioSQL. The prefered method of interaction
with BioSQL is now via Hibernate. RichSequence and it's associated objects
have hibernate mappings to biosql databases. This provides a number of the
benefits of Hibernates ORM to biojava, especially control over
transactions and the removal of JDBC code. See
http://biojava.org/wiki/BioJava:BioJavaXDocs#BioSQL_and_Hibernate. for
details.

* Genetic Algorithms. A very flexible genetic algorithm library is
available in the biojavax packages. Simple examples are at
http://biojava.org/wiki/BioJava:BioJavaXDocs#Genetic_Algorithms. but much
more powerful things are possible.

* Several new features are available in the Structure package that allow
manipulation of 3D structure files and objects.

* Non HMM Implementations of the NW and SW alignment algorithms are now
available in the alignment package.

* A new package for handling external processes
(org.biojava.utils.process).

* Dozens of bug fixes.

Please take it out for a spin this weekend and let us know how it works.
You will probably find it more reliable than biojava-1.4 even though this
is technically a beta.

Many thanks to all the volunteers who have contributed to biojava!

Best regards,

- Mark