This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated .
  1. 16 Oct, 2002 1 commit
  2. 28 Aug, 2002 1 commit
  3. 29 Jul, 2002 1 commit
  4. 12 Jul, 2002 1 commit
  5. 01 May, 2002 1 commit
    • Laura Clarke's avatar
      AnalysisAdaptor - logic_name must be unique so fetch_by_logic_name now only... · 4fbe162b
      Laura Clarke authored
      AnalysisAdaptor - logic_name must be unique so fetch_by_logic_name now only returns one analysis object
      DnaAlignFeatureAdaptor - formatting print statements etc
      ProteinAlignFeatureAdaptor - Now follows the same format as DnaAlignFeatureAdaptor, has methods to fetch by contig, slice and assembly location and when constrainted by score
      or percent id all methods can take an optional type which is logic name
      RepeatFeatureAdaptor
      PredictionTranscriptAdaptor all have methods which fetch by slice, contig_id and assembly location and each method has optional type which should be logic_name
      SimpleFeatureAdaptor
      4fbe162b
  6. 18 Apr, 2002 1 commit
  7. 08 Feb, 2002 1 commit
  8. 22 Jan, 2002 1 commit
  9. 04 Dec, 2001 1 commit
  10. 11 Oct, 2001 1 commit
  11. 10 Oct, 2001 1 commit
    • wormpipe's avatar
      some changes to the exists method: · a6e55012
      wormpipe authored
        returns now the dbID of th analysis or undef
      
        changed the while loop into a foreach loop
        (since this iteration was over a global variable,
         a new "iteration" started where the old one stopped,
         rather than at the beginning)
      
      ms2
      a6e55012
  12. 07 Sep, 2001 2 commits
  13. 23 Aug, 2001 1 commit
  14. 26 Jul, 2001 2 commits
  15. 20 Jul, 2001 1 commit
    • Michele Clamp's avatar
      Most important change - added an option to create a DBAdaptor with · 09237b7a
      Michele Clamp authored
      a dna database handle.  All the dna fetching is done through this extra
      dna handle.  This allows us to create new databases with fresh features
      and genes without having to use up 4Gb worth of disk space.  All deleting
      from the dna table is disallowed.  Arne will probably shout at me for not
      using a proper adaptor.
      
      Added percent_id,p_value,phase to supporting evidence in ExonAdaptor
      
      Removed debug from ExternalWrapper
      
      Gene_Obj - writes phase,p_value,percent_id from supporting features
      
      Raw_Contig :
      	   removed call to got_overlaps
      	   removed calls to get_left_overlap (and right)
      	   removed load_overlaps
      	   removed unnecessary joiun to dna table
      	   removed string checking (slow)
      	   remove feature_file method
      	   removed get_extra_features method
      	   removed analysis method
      	   removed filter_features method
      	   all dna is fetched through the dna adaptor and
                 no deleting is allowed from the dna table.
      
      Utils:
      	refixed phase problem
      
      CloneAdaptor
      
              removed overlaps
              added warning about deleting from dna table if using
              a remote dna database
      09237b7a
  16. 13 Jul, 2001 1 commit
  17. 07 Jul, 2001 1 commit
  18. 19 Jun, 2001 1 commit
    • James Gilbert's avatar
      · 55bef973
      James Gilbert authored
      Tidy up of DBAdaptor
      Addition of get_all_SimpleFeatures methods to Virtual::StaticContig
      55bef973
  19. 31 May, 2001 1 commit
  20. 18 Apr, 2001 1 commit
  21. 29 Jan, 2001 2 commits
  22. 26 Jan, 2001 1 commit