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external DB type strings contains '%' and use "LIKE" or "=" accordingly.
Document this behaviour in the POD of the method.  Also, safely quote
strings inserted into SQL.

In _type_by_external_db_id(): Fix documentation for method.

Both pointed out by Michael S.

<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.

Formatting of SYNOPSIS code.

Passes unit tests.

changes introduced in release 52: new column description in external_db and new column in dna_align_feature

  When testing for existance of an object xref entry with
  linkage_annotation, treat NULLs as equals.

+ some formatting.

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)

registry and not get_XXXAdaptor() explicitly.

Slightly more elegant way of collecting results in
_type_by_external_id() and in _type_by_external_db_id().

(MySQL v5 knows how to do index merges) in _type_by_external_id():

  # decrease in time by 35%
  $dbea->list_transcript_ids_by_extids('BRCA2');

  # decrease in time by 28%
  $dbea->list_translation_ids_by_extids('GO:0004835');

  # decrease in time by 24%
  $dbea->list_gene_ids_by_extids('ARSE');


Also some formatting.

fetchrow_arrayref() to speed up DB fetching by approx. 100 rows/sec.

  If there are no synonyms, return an empty list, not a list containing
  a reference to an empty list.

  Add an optional fourth boolean argument, $ignore_release:

    If unset or zero, will require that the release string of the
    DBEntry object is identical to the release of the external database.
    If set and non-zero, will ignore the release information.

fetch_all_by_external_name() in GeneAdaptor.pm, TranscriptAdaptor.pm,
and in TranslationAdaptor.pm.

This will limit the returned genes, transcripts, or translations, to
those that originates from the named external database.

This also means adding the optional argument to
list_gene_ids_by_extids(), list_transcript_ids_by_extids(),
list_translation_ids_by_extids(), and to _type_by_external_id() in
DBEntryAdaptor.pm.

The matching is done on 'db_name' in the 'external_db' table with LIKE
and an appended '%' to the given $external_db_name.

added NOTE about fetching by primary accession not being bothered about what the external database is

Added optional argument to get_all_DBEntries and get_all_DBLinks which is the database name. Use like in sql statment so percentage sign can be used for wild cards etc.