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.

Set gene description to NULL and status back to KNOWN_BY_PROJECTION when deleting previously-projected xrefs.

Refactored - do names and GO terms in one job for those species where both were done separately before. Should reduce the number of jobs.

       all_species

         Args       : NONE
         Example    : @all_species = @{$dba->all_species()};
         Description: Returns the names of all species contained in the
                      database to which this DBAdaptor is connected.
         Returntype : array reference

print out options so to make it easier to keep track of what has been ran. And run the cleanup script after running coordinate mapping so that xrefs only on one coordinate system

a multi-species database.

API passes unit tests.

expensive joins for single-species databases.

no seq_region, so exclude from hack in generic_fetch().

  If called for a Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor object, add
  the seq_region and coord_system tables to the table list and join the
  main feature table to coord_system.species_id through the seq_region
  table.