Fix missing dependencies, updates to compile with new typespec
Autogenerate most java files from spec, rather than checking them in.
Added some scripts to download necessary binaries
Added script to download 3rd party dbs: Pfam, TIGRFAMs, CDD
and ready them for search
Fixed typos in db prep script
Fixes to db prep script
more cleanup in dp prep script
started to add tests
Got basic test framework working
Got basic test framework working
Merge branch 'dev' of github.com:jmchandonia/gene_families into dev
Started parsing CDD libraries
Added test that runs RPS-BLAST on E. coli vs COG library, and saves
result in file for Marcin to start testing against
Added correct ID for domain to map, as used in Roman's requested output
format for RPS-BLAST
Merge pull request #1 from jmchandonia/dev

gene families update