[BioRuby-cvs] bioruby/lib/bio/data aa.rb,0.9,0.10 na.rb,0.10,0.11

[Katayama Toshiaki]

Update of /home/repository/bioruby/bioruby/lib/bio/data
In directory pub.open-bio.org:/tmp/cvs-serv28702/lib/bio/data

Modified Files:
	aa.rb na.rb 
Log Message:
* AminoAcid#to_re method is added
* clean up


Index: aa.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/data/aa.rb,v
retrieving revision 0.9
retrieving revision 0.10
diff -C2 -d -r0.9 -r0.10
*** aa.rb	7 Aug 2005 09:58:21 -0000	0.9
--- aa.rb	7 Aug 2005 23:28:14 -0000	0.10
***************
*** 136,139 ****
--- 136,145 ----
        end
  
+       # backward compatibility
+       def names
+         Names
+       end
+       alias :aa :names
+ 
        def name(x)
          str = Names[x]
***************
*** 212,217 ****
--- 218,233 ----
        end
  
+       def to_re(seq)
+         str = seq.to_s.upcase
+         str.gsub!(/[^BZACDEFGHIKLMNPQRSTVWYU]/, ".")
+         str.gsub!("B", "[DN]")
+         str.gsub!("Z", "[EQ]")
+         Regexp.new(str)
+       end
+ 
+ 
        private
  
+ 
        def reverse
          hash = Hash.new
***************
*** 236,249 ****
      Weight = Data::Weight
  
-     def aa
-       Names
-     end
- 
-     def self.names
-       Names
-     end
  
      private
  
      alias :orig_reverse :reverse
      def reverse
--- 252,260 ----
      Weight = Data::Weight
  
  
      private
  
+ 
+     # override when used as an instance method to improve performance
      alias :orig_reverse :reverse
      def reverse
***************
*** 300,304 ****
    p aa.to_3('A')
  
- 
    puts "# Bio::AminoAcid.one2three('A')"
    p Bio::AminoAcid.one2three('A')
--- 311,314 ----
***************
*** 330,333 ****
--- 340,346 ----
    puts "# aa.name2three('alanine')"
    p aa.name2three('alanine')
+ 
+   puts "# Bio::AminoAcid.to_re('BZACDEFGHIKLMNPQRSTVWYU')"
+   p Bio::AminoAcid.to_re('BZACDEFGHIKLMNPQRSTVWYU')
  
  end

Index: na.rb
===================================================================
RCS file: /home/repository/bioruby/bioruby/lib/bio/data/na.rb,v
retrieving revision 0.10
retrieving revision 0.11
diff -C2 -d -r0.10 -r0.11
*** na.rb	7 Aug 2005 09:58:21 -0000	0.10
--- na.rb	7 Aug 2005 23:28:14 -0000	0.11
***************
*** 114,117 ****
--- 114,123 ----
        end
  
+       # backward compatibility
+       def names
+         Names
+       end
+       alias :na :names
+ 
        def name(x)
          Names[x.to_s.upcase]
***************
*** 144,154 ****
      Weight = Data::Weight
  
-     def na
-       Names
-     end
- 
-     def self.names
-       Names
-     end
  
    end
--- 150,153 ----