This release includes general-purpose sequence data storage in BioSQL sequence databases (read and write), adds the missing Blast2Html demo, and includes various documentation fixes.
BioJava 1.2 includes considerable enhancements to the parsers for
Blast output and sequence file formats. There's also an improved
dynamic programming package, which can compile Hidden Markov Models to
Java bytecode, and support for the Distributed Annotation System 1.00.
Pluggable I/O framework for sequence data, parsers for Blast and FASTA output, support for assembly of biological sequences, and a pervasive event model for change notification and veto.
Some bugs were fixed with compiling with javac 1.3 and JBuilder. Support for longer description lines in FASTA files was added. SimpleDistributions can now be trained properly.
