GitLab

the Ensembl Genomes project.

Formatting.

earlier.

Skip projection of genes from sources with "clone" in the db name - should stop mouse clone names being projected to rat & kangaroo rat.

make sure if we use clone name for the gene name that we only get each clone anem once, else add -201 at the end and increment for each one.

reset_DBADaptor also handles absent adaptor nicely, as well as an extra parameters hash for passing to the DBAdaptor constructor

throw() instead of die()  if program can't be found ......

In translate():

  Allow for seq_region attributes 'complete5' and 'complete3' to be
  fetched and used.  These will be fetched from the slice and used in
  the call to Bio::PrimarySeqI::translate() (see the documentation for
  that BioPerl module).

  Formatting.

  Be explicit, using defined() and scalar().

  Use index() rather than more expensive regular expression match for
  fixed string matching.

now imports throw() method out of Bio::EnsEMBL::Utils::Exception to
properly compile after changes done on  29-Oct-08 r 1.27