fixed bad tests in match.rb

[biopieces.git] / code_ruby / lib / maasha / align / match.rb

diff --git a/code_ruby/lib/maasha/align/match.rb b/code_ruby/lib/maasha/align/match.rb
index 784a2d12f2a1916adb8a216c821769683697a19a..47a5fbd523aecba4ab81b51394a656eb4362c770 100644 (file)
--- a/code_ruby/lib/maasha/align/match.rb
+++ b/code_ruby/lib/maasha/align/match.rb
@@ -23,7 +23,6 @@
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
 require 'inline'
-require 'maasha/math_aux'
 
 # Class for describing a match between two sequences q and s.
 class Match
@@ -58,20 +57,8 @@ class Match
     self
   end
 
-  def redundant?(matches)
-    # Speed-up with binary search
-
-    matches.each do |m|
-      if Math.dist_point2line(self.q_beg, self.s_beg, m.q_beg, m.s_beg, m.q_end, m.s_end) == 0
-        return true
-      end
-    end
-
-    false
-  end
-
   def to_s(seq = nil)
-    s = "q: #{@q_beg}, s: #{@s_beg}, l: #{@length}, s: #{@score}"
+    s = "q: #{@q_beg} #{self.q_end} s: #{@s_beg} #{self.s_end} l: #{@length} s: #{@score}"
     s << " #{seq[@q_beg .. q_end]}" if seq
 
     s