associated with the transcript.

  Args       : None
  Example    :

    my @alt_translations =
      @{ $transcript->get_all_alternative_translations() };

  Description:  Fetches all alternative translations defined for this
                transcript.  The canonical translation is not returned.

  Returntype : Array reference to Bio::EnsEMBL::Translation
  Exceptions : None
  Caller     : General
  Status     : Stable


Added method add_alternative_translation():

  Args       : Bio::EnsEMBL::Translation $translation
  Example    :

    $transcript->add_alternative_translation($translation);

  Description: Adds an alternative translation to this transcript.
  Returntype : None
  Exceptions : None
  Caller     : General
  Status     : Stable

simple sanity check for human and mouse to make sure the core/vega links are up to date with each other

Use registry to get vega and core databases. Plus now only take the core -> vega mapping and not vice versa (to be consistent)

Add PRINTS back as it is needed for the protein alignments but store the source in the  interpro table as this is usefull information, that allows us to ignore PRINTS later.

Store the databases type in the interpro table so that we can easily see where they came from. i.e. PRINTS, PFAM etc

use the registry to get the core and vega databses that way we dont have to remember to update this file for every release and changing the release number. You can still use the old way as well in case you have to, i.e. on different servers

from the gene table, not dna_align_feature table.

DEFAULT values.  No schema patch file necessary.

the depricated table option "TYPE=MyISAM".

"missing".