[Bioperl-guts-l] bioperl-live/Bio/Graphics/Glyph cds.pm,1.24,1.25

Scott Cain scain at pub.open-bio.org
Fri Jun 17 15:59:28 EDT 2005


Update of /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph
In directory pub.open-bio.org:/tmp/cvs-serv14219

Modified Files:
	cds.pm 
Log Message:
modified the cds glyph to support a 'sub_part' option.  This is important for
chado objects, because mRNA objects may contain UTRs and introns and they
should not be drawn in the cds glyph, so in a gbrowse/chado contect, the option
'sub_part = CDS' can be used.


Index: cds.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Graphics/Glyph/cds.pm,v
retrieving revision 1.24
retrieving revision 1.25
diff -C2 -d -r1.24 -r1.25
*** cds.pm	27 Jul 2004 17:24:44 -0000	1.24
--- cds.pm	17 Jun 2005 19:59:25 -0000	1.25
***************
*** 82,85 ****
--- 82,89 ----
      my $part    = $parts[$i];
      my $feature = $part->feature;
+ 
+     my $type = $feature->method;
+     next if ($self->option('sub_part') && $type ne $self->option('sub_part'));
+ 
      my $pos     = $feature->start;
      my $phase   = eval {$feature->phase} || 0;
***************
*** 300,303 ****
--- 304,311 ----
                unless it is a feature
                subpart.
+ 
+   -sub_part   For objects with multiple	   undef
+               subpart types, defines which
+               is the CDS part.
  
    -codontable   Codon table to use           1 (see Bio::Tools::CodonTable)



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