This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git. Pull mirroring updated .
  1. 26 May, 2004 1 commit
  2. 21 May, 2004 1 commit
  3. 14 May, 2004 1 commit
  4. 11 May, 2004 1 commit
  5. 24 Mar, 2004 1 commit
  6. 17 Feb, 2004 1 commit
  7. 13 Jan, 2004 3 commits
  8. 12 Jan, 2004 1 commit
  9. 09 Jan, 2004 1 commit
  10. 29 Aug, 2003 1 commit
  11. 11 Jun, 2003 2 commits
  12. 10 Jun, 2003 1 commit
  13. 12 Feb, 2003 1 commit
    • Laura Clarke's avatar
      · 82899b0d
      Laura Clarke authored
      altered sub version so it doesn't not set the value for no good reason
      82899b0d
  14. 10 Dec, 2002 1 commit
  15. 25 Nov, 2002 1 commit
  16. 30 Oct, 2002 1 commit
  17. 17 Oct, 2002 1 commit
  18. 16 Oct, 2002 2 commits
    • Laura Clarke's avatar
      · 47491ad3
      Laura Clarke authored
      Translation and TranslationAdaptor start_exon and end_exon to start_Exon and end_Exon
      
      DBEntryAdaptor check to see if gene has a stable id before trying to used it to get info
      47491ad3
    • Graham McVicker's avatar
      lists -> listrefs · cb9c682b
      Graham McVicker authored
      cb9c682b
  19. 23 Jul, 2002 1 commit
  20. 10 Jul, 2002 1 commit
  21. 14 Jun, 2002 1 commit
    • Alistair Rust's avatar
      More inner workings for slice related things. · 244a44c6
      Alistair Rust authored
      The main focus of the debugging has been to implement the get_all_Genes method.
      
      For genes with transcripts containing non-sticky exons then things work fine:
       - get gene
       - get all transcripts
       - get all exons
       - transform exons from raw to assembly coordinates
       - re-jiggle the exons to which the translation points
       - re-jiggle the exons to which the transcript points
       - check that everything translates nicely
      
      Sticky exon'ed transcripts are however not playing nicely.  This may be a
      feature of the test database - one of the contigs on which the sticky exon
      lies may be wrong.  The translations of the current test sticky exon is just
      plain wrong.  Retrieving subseqs on the exons are wrong to begin with -
      pointing therefore at the contig seq.  Needs debugging / checking in here.
      The re-jiggling of translation start/end points for sticky exons needs checking
      too.
      
      The other major related changes are in the seq methods.  These now return
      dna as txt rather than a primary seq object.  This makes calls such as
      seq->seq redundant now.  This change has yet to be checked across all modules
      for consistency yet.
      244a44c6
  22. 18 Apr, 2002 1 commit
  23. 30 Oct, 2001 1 commit
  24. 07 Sep, 2001 1 commit
    • Michele Clamp's avatar
      Moved core code to FeatureAdaptor and AnalysisAdaptor · 4167cfe7
      Michele Clamp authored
      tests will not work as I havent' changed the dumps yet.
      
      Changed the way genscans are stored and retrieved
      
      Clone
       - removed Feature_Obj and Gene_Obj use statements
      
      Exon
       - inherits from Bio::EnsEMBL::SeqFeature to use the extra gubbins
       - added temporary_id as for Transcript and Gene
      
      SeqFeature
       - debug
      
      Transcript
       - debug
      
      Translation
       - added temporary_id
      
      ContigI
       - removed string checking - takes *far too long for big contigs
      
      FeatureAdaptor
       - debug on inserts
      
      RawContig
       - removed Feature_Obj and Gene_Obj use statements - changed to AnalysisAdaptor and FeatureAdaptor
       - changed analysis to analysisprocess in several methods
       - removed Feature_Obj - changed to AnalysisAdaptor
       - changed the way genscans are fetched.
      
      Utils
       - added fset2transcript_3frame method
      
      StaticContig
       - changed analysis to analysisprocess
       - gets analysis by AnalysisAdaptor and not Feature_Obj
       - gets genscans differently
      4167cfe7
  25. 26 Jul, 2001 1 commit
  26. 31 Mar, 2001 1 commit
  27. 01 Feb, 2001 1 commit
  28. 25 Oct, 1999 1 commit