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Commits on Jul 27, 2009
  1. Merge branch 'silencio'

    cjlee112 committed Jul 27, 2009
Commits on Jul 25, 2009
  1. added support for no-edgeDB case in mapping.Graph: now defaults to ju…

    cjlee112 committed Jul 25, 2009
    …st save the edge object as-is; see discussion w/ Kenny Daily 7/23/09
Commits on Jul 23, 2009
Commits on Jul 21, 2009
  1. thoughts for future alignments tutorial work.

    Titus Brown
    Titus Brown committed Jul 21, 2009
  2. Added section on storing BLAST results on disk. Done?

    Titus Brown
    Titus Brown committed Jul 21, 2009
  3. minor cleanup

    Titus Brown
    Titus Brown committed Jul 21, 2009
  4. fixed bug that broke BlastxMapping.__getitem__: use seqs to index NLM…

    Titus Brown
    Titus Brown committed Jul 21, 2009
    …SAs!
  5. BlastxMapping.__getitem__ should not be a generator.

    Titus Brown
    Titus Brown committed Jul 21, 2009
  6. test for non-equivalent 'repr's for translationDB sequences & regular…

    Titus Brown
    Titus Brown committed Jul 21, 2009
    … sequences.
  7. fixed bug with empty slices in translationDB.

    Titus Brown
    Titus Brown committed Jul 21, 2009
  8. some basic tests for translationDB.

    Titus Brown
    Titus Brown committed Jul 21, 2009
  9. only return NLMSASlices derived from the query sequence for BlastxMap…

    Titus Brown
    Titus Brown committed Jul 21, 2009
    …ping.
  10. fixes individual sequence queries of BlastxMappings to reference tran…

    Titus Brown
    Titus Brown committed Jul 21, 2009
    …sdb.
  11. check that only NLMSASlices for the translated sequences are returned…

    Titus Brown
    Titus Brown committed Jul 21, 2009
    … from BlastxMapping.__getitem__.
  12. tests for presence of translationdb.annodb in NLMSA produced by Blast…

    Titus Brown
    Titus Brown committed Jul 21, 2009
    …xMapping.
  13. updated alignment tutorial for new BLAST API

    Titus Brown
    Titus Brown committed Jul 21, 2009
Commits on Jul 17, 2009
  1. mask deprecation warning output in test

    Titus Brown
    Titus Brown committed Jul 17, 2009
  2. eliminate bleed-through of formatdb failed output.

    Titus Brown
    Titus Brown committed Jul 17, 2009
  3. show dots again, at lowest verbosity level!

    Titus Brown
    Titus Brown committed Jul 17, 2009
Commits on Jul 16, 2009
  1. Merge branch 'master' into megatests

    Marek Szuba
    Marek Szuba committed Jul 16, 2009
  2. Only switch to the requested verbosity level before running tests, ke…

    Marek Szuba
    Marek Szuba committed Jul 16, 2009
    …eping all filters off otherwise. This is so that messages from the framework itself are not quelled
  3. Merge branch 'master' into silencio

    Marek Szuba
    Marek Szuba committed Jul 16, 2009