[BioRuby-cvs] bioruby/lib/bio sequence.rb,0.47,0.48

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio
In directory pub.open-bio.org:/tmp/cvs-serv11009/lib/bio

Modified Files:
	sequence.rb 
Log Message:
* added forward_complement(!) and reverse_complement(!) methods
* changed complement(!) methods to aliases of reverse_complement(!) methods


Index: sequence.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/sequence.rb,v
retrieving revision 0.47
retrieving revision 0.48
diff -C2 -d -r0.47 -r0.48
*** sequence.rb	15 Nov 2005 14:58:57 -0000	0.47
--- sequence.rb	22 Nov 2005 00:32:59 -0000	0.48
***************
*** 46,50 ****
  
    def self.auto(str)
!     moltype = guess(str)
      if moltype == NA
        NA.new(str)
--- 46,50 ----
  
    def self.auto(str)
!     moltype = self.guess(str)
      if moltype == NA
        NA.new(str)
***************
*** 259,279 ****
      end
  
!     # Returns a reverse complement sequence (including the universal codes).
!     def complement
        s = self.class.new(self)
!       s.complement!
        s
      end
  
!     def complement!
        if self.rna?
-         self.reverse!
          self.tr!('augcrymkdhvbswn', 'uacgyrkmhdbvswn')
        else
-         self.reverse!
          self.tr!('atgcrymkdhvbswn', 'tacgyrkmhdbvswn')
        end
        self
      end
  
      # Translate into the amino acid sequence from the given frame and the
--- 259,296 ----
      end
  
!     # Returns complement sequence without reversing ("atgc" -> "tacg")
!     def forward_complement
        s = self.class.new(self)
!       s.forward_complement!
        s
      end
  
!     # Convert to complement sequence without reversing ("atgc" -> "tacg")
!     def forward_complement!
        if self.rna?
          self.tr!('augcrymkdhvbswn', 'uacgyrkmhdbvswn')
        else
          self.tr!('atgcrymkdhvbswn', 'tacgyrkmhdbvswn')
        end
        self
      end
+ 
+     # Returns reverse complement sequence ("atgc" -> "gcat")
+     def reverse_complement
+       s = self.class.new(self)
+       s.reverse_complement!
+       s
+     end
+ 
+     # Convert to reverse complement sequence ("atgc" -> "gcat")
+     def reverse_complement!
+       self.reverse!
+       self.forward_complement!
+     end
+ 
+     # Aliases for short
+     alias complement reverse_complement
+     alias complement! reverse_complement!
+ 
  
      # Translate into the amino acid sequence from the given frame and the