moved ENSEMBL_DB - > DATABASE_CORE and OTHER (non web user dbs) from ENSEMBL_{} -> DATABASE_, and changed the connection stuff to DATABASE_ as well

description for xrefs noew set to text rather than varchar(255) allowing longer descriptions, mainly for swissprot

get_all_DBAdaptors_by_connection():

  Arg [1]    : string, name of database
  Returntype : reference to list of DBAdaptors
  Exceptions : none
  Example    : @dba = @{ Bio::EnsEMBL::Registry
                  ->get_all_DBAdaptors_by_dbname($dbname) };
  Status     : Stable


Some formatting.

having DNA database and analysis database on separate servers:

  In new(), pick the coordinate system internal IDs from a
  CoordSystemAdaptor created from the DNA database (which may be located
  on another database server), then fetch the meta_coord data from the
  adaptor-local database using these.

Passes unit tests.

added a filter parameter to variation call so can also get genotyped snps - this is written generally so that if a new value in the flags column could be tested for

-verbose option added which also need to change run subroutine to get the file/s via a ref to and array then an array

run changed to run_script to get the information via a series of mysql and perl instead of from a local file

config for gorilla gorilla edited

gorilla gorilla added

added new tests to check attributes db_name and db_display_name work properly to retrieve the database_name and the displayable_name from the external database

added 2 new attributes in protein and dna alignFeatures to get the name of the external database and the displayable name

removed helpdesk_draft.txt, analysis_descriptions_draft.txt to avoid confusion. The file to use with load_analysis_descriptions.pl is analysis.descriptions.

Changed format to be tab-separated and added display_label as third column (default is logic name with _ removed).

genes have changed their biotype from eg. D_segment to IG_D_gene.

Changed creation of compara adaptor in get_all_compara_Syntenies and get_all_compara_DnaAlignFeatures to use registry directly.