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  1. 04 Jun, 2007 3 commits
  2. 03 Jun, 2007 3 commits
  3. 01 Jun, 2007 2 commits
    • Andreas Kusalananda Kähäri's avatar
      From request by Laura. · 08a95cf6
      Andreas Kusalananda Kähäri authored
      
      From the code:
      
      # This parser will read Direct Xrefs from a simple tab-delimited file.
      # The columns of the file should be the following:
      #
      # 1)    Accession ID
      # 2)    Ensembl ID
      # 3)    Type (one of 'transcript', 'gene', or 'translation',
      #       will default to 'gene')
      # 4)    Display label (will default to the Accession ID in column 1)
      # 5)    Description (will default to the empty string)
      # 6)    Version (will default to '1')
      #
      # Columns 1 and 2 are obligatory.
      08a95cf6
    • Ian Longden's avatar
      21f86e14
  4. 31 May, 2007 3 commits
  5. 30 May, 2007 5 commits
    • Ian Longden's avatar
      bug fix, be more specific when getting xref · 6573d90d
      Ian Longden authored
      6573d90d
    • Andreas Kusalananda Kähäri's avatar
      Collapse all eval() calls into one. · 0cf4505d
      Andreas Kusalananda Kähäri authored
      Only clear old registry configuration if we have a configuration file
      name and if that file exists.
      0cf4505d
    • Patrick Meidl's avatar
      - changed MAX_ROWS to 30 · 700b88c4
      Patrick Meidl authored
      - rewrote fetch_by_stable_id*() methods to look up current versions of stable
        IDs in *_stable_id tables
      - new method lookup_current() to assist the former (also replaces
        _lookup_version())
      - new method add_all_current_to_history() to implement this behaviour for
        StableIdHistoryTree
      
      - new methods to get properties of current db:
        - get_current_release()
        - get_current_assembly()
      
      - fixed _resolve_type() to copy with non Ensembl-style stable IDs (e.g.
        Anopheles)
      
      - removed deprecated methods
      700b88c4
    • Patrick Meidl's avatar
      - added new methods: · 722bec70
      Patrick Meidl authored
        - get_latest_StableIdEvent(): find latest Event in tree for a given stable ID
        - getters/setters for current db properties:
          - current_release()
          - current_assembly()
          - current_dbname()
        - is_incomplete(): flag to indicate incomplete trees
      722bec70
    • Patrick Meidl's avatar
      - added new methods: · 813f08cb
      Patrick Meidl authored
        - current_version(): retrieves current version of stable ID from db
        - is_current(): test if this is the current version
        - get_latest_incarnation(): get latest incarnation of stable ID from db
        - is_latest(): test if this is the latest version
      
      - version() no longer lazy-loaded (now always set by adaptor)
      
      - removed deprecated methods
      813f08cb
  6. 29 May, 2007 2 commits
  7. 25 May, 2007 1 commit
  8. 24 May, 2007 4 commits
  9. 23 May, 2007 7 commits
  10. 22 May, 2007 5 commits
  11. 21 May, 2007 1 commit
  12. 17 May, 2007 2 commits
  13. 16 May, 2007 1 commit
  14. 15 May, 2007 1 commit