changed Seq.new argument to hash

[biopieces.git] / code_ruby / lib / maasha / locator.rb

diff --git a/code_ruby/lib/maasha/locator.rb b/code_ruby/lib/maasha/locator.rb
index a2a0db0eff6036f988f8d530e8e497367453d814..f9fae94890e1a3a01e64165ff535b94a28d743d5 100644 (file)
--- a/code_ruby/lib/maasha/locator.rb
+++ b/code_ruby/lib/maasha/locator.rb
@@ -35,7 +35,7 @@ class Locator
   def initialize(locator, seq)
     @locator = locator
     @seq     = seq
-    @subseq  = Seq.new(nil, "", "dna")
+    @subseq  = Seq.new(seq: "", type: :dna)
     parse_locator(locator)
   end
 
@@ -107,25 +107,25 @@ class Locator
           int_beg = $1.to_i - 1
           int_end = $2.to_i - 1
 
-          newseq = Seq.new(nil, @seq.seq[int_beg...int_end], "dna")
+          newseq = Seq.new(seq: @seq.seq[int_beg..int_end], type: :dna)
 
                                        unless newseq.seq.nil?
-                                               newseq.revcomp if comp
+                                               newseq.reverse!.complement! if comp
 
                                                @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
                                        end
         when /^(\d+)$/
           pos = $1.to_i - 1
 
-          newseq = Seq.new(nil, @seq.seq[pos], "dna")
+          newseq = Seq.new(seq: @seq.seq[pos], type: :dna)
 
                                        unless newseq.seq.nil?
-               newseq.revcomp if comp 
+               newseq.reverse!.complement! if comp 
 
                @subseq.seq << (order ? " " + newseq.seq : newseq.seq)
                                        end
         else
-          $stderr.puts "WARNING: Could not match locator -> #{locator}";
+          $stderr.puts "WARNING: Could not match locator ->#{locator}<-";
           @subseq.seq << ""
         end
       end