[Bioperl-l] Bio::SeqFeature::Gene fixes

[Keith James]

Couple of patches.

In Bio/SeqFeature/Gene/Transcript.pm

 Title   : add_exon()
 Usage   : $transcript->add_exon($exon,'initial');

Was ignoring the second arg and not congruent with 

 Title   : add_utr()
 Usage   : $transcript->add_utr($utrobj, 'utr3prime');

Also fixed _add called by add_exon which was discarding the new
primary_tag argument. Accessors which accepted a string "type" were
therefore not returning the values previously set.

In Bio/Tools/Genewise.pm

Exons were not having their coding flag switched on, despite having
protein supporting evidence added.

If nobody shouts against these I'll check them in.

Keith

-- 

- Keith James <kdj at sanger.ac.uk> bioinformatics programming support -
- Pathogen Sequencing Unit, The Wellcome Trust Sanger Institute, UK -