ensembl-59'.

Sprout from master 2010-07-27 13:05:46 UTC Javier Herrero <jh7@sanger.ac.uk> 'Add ancestral_sequences (production-like name) as an alias for Ancestral sequences'
Delete:
    misc-scripts/protein_match/process_pmach.pl

Adding a new method as a result of benchmarking to keep developers using SqlHelper with very large data sets. We now can allow the developer to define how they wish to iterate through a result set

_merge_ajoining_coords added to make sure that having more than one coord is wrong. Andy Yates wrote the code i just checked it and added it.

Addition of utility classes for use in the Ensembl API. The first are shortcuts for asserting object/ref types and the second is a class which removes boilerplate from working with databases.

on new species (i.e. species without previous stable IDs).

Untested at the moment.

-  @seqeds = sort { $b->start() <=> $a->start() } @seqeds;
+  # HACK:   The translation ENSP00000420939 somehow makes the next line
+  #         bomb out ($a or $b becomes undef) if the start() method
+  #         is used.  I haven't been able to find out why.  It has 10
+  #         Selenocysteine seqedits that looks correct.
+  #         /Andreas (release 59)
+  my @seqeds = sort { $b->{'start'} <=> $a->{'start'} } @seqeds;

Undefined value warnings on $species_suffix usage and lowercasing input to allow for matching on registry stored aliases

mapping and other things specific to the Ensembl Genomes people.

Might have broken Ensembl stable ID mapping (in which case I clean it up
later).

transcript had to be fetched from the database.  If this happens, the
user is likely working in a translation-centric way, i.e. not going
through transcripts.  If the reference is weakened, the reference to
the transcript will be undef after the end of the code block, as the
transcript passes out of scope.