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  1. 08 Jun, 2010 1 commit
  2. 07 Jun, 2010 1 commit
  3. 04 Jun, 2010 3 commits
  4. 03 Jun, 2010 1 commit
  5. 02 Jun, 2010 4 commits
  6. 24 May, 2010 1 commit
  7. 21 May, 2010 4 commits
  8. 19 May, 2010 1 commit
  9. 17 May, 2010 1 commit
  10. 07 May, 2010 1 commit
  11. 06 May, 2010 5 commits
    • Andreas Kusalananda Kähäri's avatar
      Added new 'species' argument to load_registry_from_db(): · 4b3a1051
      Andreas Kusalananda Kähäri authored
      Arg [SPECIES]:  (optional) string
                      By default, all databases that are found on the server
                      and that corresponds to the correct release are probed
                      for aliases etc.  For some people, depending on where
                      they are in the world, this might be a slow operation.
                      With the '-species' argument, one may reduce the startup
                      time by restricting the set of databases that are probed
                      to those of a particular species.
      
                      Note that the latin name of the species is required,
                      e.g., 'homo sapiens', 'gallus gallus', 'callithrix
                      jacchus' etc.  It may be the whole species name, or only
                      the first part of the name, e.g. 'homo', 'gallus', or
                      'callithrix'.  This will be used in matching against the
                      name of the databases.
      4b3a1051
    • Eugene Kulesha's avatar
      another typo · d10f6768
      Eugene Kulesha authored
      d10f6768
    • Eugene Kulesha's avatar
      fixed a typo · cc5830e9
      Eugene Kulesha authored
      cc5830e9
    • Ian Longden's avatar
      LRGSlice fixes · 4a9b9a8d
      Ian Longden authored
      4a9b9a8d
    • Ian Longden's avatar
      fixes for LRGSlices and new methods to find nearest gene to a feature (this... · 5bd6ce87
      Ian Longden authored
      fixes for LRGSlices and new methods to find nearest gene to a feature (this will change greatly as this is a very simple case)
      5bd6ce87
  12. 05 May, 2010 3 commits
  13. 04 May, 2010 4 commits
  14. 22 Apr, 2010 3 commits
    • Andreas Kusalananda Kähäri's avatar
      In get_all_alternative_translations(): · 755ce7c3
      Andreas Kusalananda Kähäri authored
        We know that fetch_all_by_Transcript() (on a TranslationAdaptor) will
        return a list of translations, where the first one will always be the
        canonical translation (if there is one).  Make use of this fact to
        make the routine slightly quicker.
      755ce7c3
    • Andreas Kusalananda Kähäri's avatar
      In store(): · f8abbac7
      Andreas Kusalananda Kähäri authored
        * Use fetch_all_by_Transcript() rather than translation() on the
          transcript to get the canonical translation (and any alternative
          translations).
      
        * ... then store the translation and any alternative translations.
      
      Solves a problem stopping genebuilders from copying genes from one
      database to another.
      f8abbac7
    • Andreas Kusalananda Kähäri's avatar
      In fetch_all_by_Transcript(): · a74758df
      Andreas Kusalananda Kähäri authored
        * Correct documentation.
        * Use fetch_by_Transcript() to get canonical translation.
        * Modify SQL not to get canonical translation.
      a74758df
  15. 21 Apr, 2010 1 commit
  16. 20 Apr, 2010 3 commits
  17. 14 Apr, 2010 1 commit
  18. 01 Apr, 2010 1 commit
  19. 31 Mar, 2010 1 commit