updateing seq.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1058 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/code_ruby/Maasha/lib/seq.rb b/code_ruby/Maasha/lib/seq.rb
index ff5bd4425bc4f1a60ada30276168af1faf03144f..4ce1e019ab79ebb75841b779f3b0ba5d4d92a317 100644 (file)
--- a/code_ruby/Maasha/lib/seq.rb
+++ b/code_ruby/Maasha/lib/seq.rb
@@ -4,41 +4,41 @@ class Seq < String
        def guess_type
                raise ArgumentError, "No sequence." if self.empty?
 
-               seq_beg = self[ 0, 100 ].upcase
+               seq_beg = self[0, 100].upcase
 
                if seq_beg.count( "FLPQIE" ) > 0
-                       Seq::AA.new( self )
-               elsif seq_beg.count( "U" ) > 0
-                       Seq::NA::RNA.new( self )
+                       Seq::AA.new(self)
+               elsif seq_beg.count("U") > 0
+                       Seq::NA::RNA.new(self)
                else
-                       Seq::NA::DNA.new( self )
+                       Seq::NA::DNA.new(self)
                end
        end
 
        # Method to wrap a sequence to a given width using a given delimiter.
-       def wrap( width = 80, delimit = "\n" )
-               raise ArgumentError, "Cannot wrap sequence to negative width: #{ width }." if width <= 0
+       def wrap(width = 80, delimit = $/)
+               raise ArgumentError, "Cannot wrap sequence to negative width: #{width}." if width <= 0
 
-               self.delete!( " \t\n\r" )
-               self.gsub( /.{#{ width }}(?!$)/, "\\0#{ delimit }" )
+               self.delete!(" \t\n\r")
+               self.gsub(/.{#{width}}(?!$)/, "\\0#{delimit}")
        end
 
        # Method to wrap and replace a sequence to a given width using a given delimiter.
-       def wrap!( width = 80, delimit = "\n" )
-               self.replace( self.wrap( width, delimit ) )
+       def wrap!(width = 80, delimit = $/)
+               self.replace(self.wrap(width, delimit))
        end
 
        # Method that generates a random sequence of a given length.
-       def generate( length )
-               raise ArgumentError, "Cannot generate negative sequence length: #{ length }." if length <= 0
+       def generate(length)
+               raise ArgumentError, "Cannot generate negative sequence length: #{length}." if length <= 0
 
                alph = self.residues
-               Array.new( length ) { alph[ rand( alph.size ) ] }.join( "" )
+               Array.new(length) { alph[rand(alph.size)] }.join("")
        end
 
        # Method that replaces sequence with a randomly generated sequence of a given length.
-       def generate!( length )
-               self.replace( self.generate( length ) )
+       def generate!(length)
+               self.replace(self.generate(length))
        end
 
        # Class containing methods specific for amino acid (AA) sequences.