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

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

       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

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.

species_id column in the meta table.

Unit-tests passes.

database in new().

translation id can be passed when a new ProteinFeature is created so it can be later stored in the database (protein_feature table)

database names and making sure none of them are picked out when looking
for core (single species) databases.

Reformat of get_all_db_adaptors().

current ensembl/sql/table.sql.

not just "%_core_51".

Using this code on databases not patched up to the v51 schema will fail.

A pre-merge tag was put in place just before this merge:

  pre-multispecies-merge (in ensembl/modules/Bio/EnsEMBL)