[BioRuby-cvs] bioruby/lib/bio/util/restriction_enzyme/range sequence_range.rb, 1.7, 1.8

[Trevor Wennblom]

Update of /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range
In directory dev.open-bio.org:/tmp/cvs-serv5059/lib/bio/util/restriction_enzyme/range

Modified Files:
	sequence_range.rb 
Log Message:
Added view_ranges parameter to indicate preservation of cut location data in results.


Index: sequence_range.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/util/restriction_enzyme/range/sequence_range.rb,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** sequence_range.rb	5 Apr 2007 23:35:42 -0000	1.7
--- sequence_range.rb	13 May 2007 04:08:02 -0000	1.8
***************
*** 130,133 ****
--- 130,139 ----
    #    3=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[2, 3], p=[]>,
    #    4=>#<struct Bio::RestrictionEnzyme::Range::SequenceRange::Bin c=[4, 5], p=[3, 4, 5]>}
+   #
+   # Note that the bin cannot be easily stored as a range since there may be
+   # nucleotides excised in the middle of a range.
+   #
+   # TODO: Perhaps store the bins as one-or-many ranges since missing
+   # nucleotides due to enzyme cutting is a special case.
    Bin = Struct.new(:c, :p)