MSA skype 20100622

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Mark, Kyle, Andreas

Report from last week:

Mark: last week added global pairwise alignments, added a parallell version. Guide tree building. Committed: concurrency tools, common interface to a shared thread pool. A few interface classes return future objects.

implemented in alignments, which is a static utility class

yesterday: added support for alternate scores

Andreas: We should use an example so one can easily trace how far the module is at the present. Use piwi family as an example.

Would be easier to work with the forester library if we would have also a source-jar. Will ask Scooter if he can provide a copy of the jar with sources attached.

Outlook for this week

basic progressive alignment profile - profile aligner use tree to build up larger and larger profiles from individual sequences

things missing: getting local alignments done. SM

examples for users.

Other things

Andreas: automated build is not ready yet (problems when running it on the production server)

released the RCSB PDB sequence code as a new project in biojava-svn

Kyle: will add it to github

Mark: @override annotation - differences between Java 1.5 and Java 1.6