[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.44,0.45

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv29278/lib/bio

Modified Files:
	sequence.rb 
Log Message:
* Bio::Sequence.auto method is added
* Bio::Sequence#blast and Bio::Sequence#fasta methods are removed


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.44
retrieving revision 0.45
diff -C2 -d -r0.44 -r0.45
*** sequence.rb	26 Sep 2005 13:00:04 -0000	0.44
--- sequence.rb	5 Nov 2005 08:22:52 -0000	0.45
***************
*** 34,37 ****
--- 34,65 ----
    class Sequence < String
  
+     def self.auto(str)
+       moltype = guess(str)
+       if moltype == NA
+         NA.new(str)
+       else
+         AA.new(str)
+       end
+     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 to_s
        String.new(self)
***************
*** 75,86 ****
      end
  
-     def fasta(factory, header = nil)
-       factory.query(self.to_fasta(header))
-     end
- 
-     def blast(factory, header = nil)
-       factory.query(self.to_fasta(header))
-     end
- 
      def window_search(window_size, step_size = 1)
        i = 0
--- 103,106 ----
***************
*** 108,130 ****
        end
        return count
-     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
  
--- 128,131 ----