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  1. 13 Jul, 2010 1 commit
  2. 14 Jun, 2010 1 commit
  3. 08 Jun, 2010 1 commit
  4. 03 Jun, 2010 1 commit
  5. 02 Jun, 2010 1 commit
  6. 06 May, 2010 1 commit
    • 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
  7. 04 May, 2010 1 commit
  8. 14 Apr, 2010 1 commit
  9. 16 Mar, 2010 1 commit
  10. 03 Feb, 2010 1 commit
  11. 02 Feb, 2010 1 commit
  12. 26 Jan, 2010 2 commits
  13. 04 Dec, 2009 2 commits
  14. 02 Dec, 2009 4 commits
  15. 25 Nov, 2009 2 commits
  16. 17 Nov, 2009 2 commits
    • Andreas Kusalananda Kähäri's avatar
      Add to documentation of get_species_and_object_type(): · 5be7a5e3
      Andreas Kusalananda Kähäri authored
        NOTE: No validation is done to see if the stable ID actually exists.
      5be7a5e3
    • Andreas Kusalananda Kähäri's avatar
      Rewrite of get_species_and_object_type(): · 43ea3ea9
      Andreas Kusalananda Kähäri authored
        Description:  Get the species name, object type (gene, transcript,
                      translation, or exon etc.), and database type for a
                      stable ID.
      
        Arg[1]     :  String
                      The stable ID to find species and object type for.
      
        Example    :  my ( $species, $object_type, $db_type ) =
                        $registry->get_species_and_object_type('ENST00000326632');
      
        Return type:  Array consisting of the species name, object type,
                      and database type.  The array may be empty if no
                      match is found.
      
        Exceptions :  none
        Status     :  At Risk.
      43ea3ea9
  17. 13 Nov, 2009 1 commit
  18. 07 Oct, 2009 1 commit
  19. 22 Sep, 2009 1 commit
  20. 12 Aug, 2009 1 commit
  21. 11 Aug, 2009 1 commit
  22. 10 Aug, 2009 2 commits
  23. 10 Jul, 2009 1 commit
    • Andreas Kusalananda Kähäri's avatar
      Change the organization of %registry_register slightly to make it easier · e57f4250
      Andreas Kusalananda Kähäri authored
      to merge copies of it; added a _SPECIES and a _TYPE section to the hash.
      
      Added the subroutine load_registry_from_multiple_dbs():
      
         Arg [1]   : Array of hashes, each hash being a set of arguments to
                     load_registry_from_db() (see above).
      
         Example   :
      
           $registry->load_registry_from_multiple_dbs( {
               '-host'    => 'ensembldb.ensembl.org',
               '-user'    => 'anonymous',
               '-verbose' => '1'
             },
             {
               '-host'     => 'server.example.com',
               '-user'     => 'anonymouse',
               '-password' => 'cheese',
               '-verbose'  => '1'
             } );
      
         Description:  Will call load_registry_from_db() (see above)
                       multiple times and merge the resulting registries
                       into one, effectively allowing a user to connect to
                       databases on multiple database servers from within
                       one program.
      
                       If a database is found on more than one server, the
                       first found instance of that database will be used.
      e57f4250
  24. 23 Jun, 2009 1 commit
  25. 18 Jun, 2009 1 commit
    • Anne Parker's avatar
      · f1139c8d
      Anne Parker authored
      Fixed error in error message :)
      f1139c8d
  26. 15 Jun, 2009 2 commits
  27. 03 Jun, 2009 2 commits
  28. 29 May, 2009 1 commit
  29. 05 May, 2009 1 commit
  30. 17 Mar, 2009 1 commit