[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.42,0.43

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv23142

Modified Files:
	sequence.rb 
Log Message:
* Bio::Sequence::NA#gc_percent is changed returns integer instead of float
* Bio::Sequence::NA#gc method is removed
* added Bio::Sequence#guess and Bio::Sequence.guess
* plugin - modified to use new guess method


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.42
retrieving revision 0.43
diff -C2 -d -r0.42 -r0.43
*** sequence.rb	20 Sep 2005 02:00:15 -0000	0.42
--- sequence.rb	23 Sep 2005 14:27:59 -0000	0.43
***************
*** 110,113 ****
--- 110,132 ----
      end
  
+     def guess(threshold = 0.9)
+       cmp = self.composition
+ 
+       bases = cmp['A'] + cmp['T'] + cmp['G'] + cmp['C'] + 
+               cmp['a'] + cmp['t'] + cmp['g'] + cmp['c']
+ 
+       total = self.length - cmp['N'] - cmp['n']
+ 
+       if bases.to_f / total > threshold
+         return NA
+       else
+         return AA
+       end
+     end 
+ 
+     def self.guess(str, *args)
+       self.new(str).guess(*args)
+     end
+ 
      def randomize(hash = nil)
        length = self.length
***************
*** 229,236 ****
          at = count['a'] + count['t'] + count['u']
          gc = count['g'] + count['c']
!         gc = format("%.1f", gc.to_f / (at + gc) * 100)
!         return gc.to_f
        end
-       alias :gc :gc_percent
  
        def illegal_bases
--- 248,254 ----
          at = count['a'] + count['t'] + count['u']
          gc = count['g'] + count['c']
!         gc = 100 * gc / (at + gc)
!         return gc
        end
  
        def illegal_bases