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fixes when identifying other stops -  1) ribosomal frameshift ignored, 2) stop codon being automatically annotated as a seleno and 3) non numerical values in comments

CV: ---------------------------------------------------------------------

ensembl-63'.

Sprout from master 2011-06-21 09:41:22 UTC Laurent Gil <lgil@ebi.ac.uk> 'Remove the Variation Bio::EnsEMBL::Variation::Utils::Constants import'
Delete:
    misc-scripts/protein_match/process_pmach.pl

- Add a new optional @colour tag, to colour the tables (if you want to be consistent with colours used in your database schema).
- Add a colour legend at the bottom of the HTML page, if colours are found.
- You can disable this feature using the option '-c 0'

Updated code to get the list of taxIds from xref_config.ini and check the PHIbase mapping based on all returned taxIds rather then just the spiecies_id

Updated methods store_on_ and remove_from_ to undefine Slice->{'circular'} SliceAdaptor->{'is_circular'} and SliceAdaptor->{'circular_sr_id_cache'} when the attribute code is 'circular_seq' and object is a slice