From: martinahansen <martinahansen@74ccb610-7750-0410-82ae-013aeee3265d>
Date: Tue, 11 Sep 2012 10:04:45 +0000 (+0000)
Subject: working on pair.rb
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=5cd784d5cb9b87e5162dd592892d58e4382bd870;p=biopieces.git

working on pair.rb

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1921 74ccb610-7750-0410-82ae-013aeee3265d
---

diff --git a/code_ruby/lib/maasha/align/pair.rb b/code_ruby/lib/maasha/align/pair.rb
index c948673..6e2dcad 100644
--- a/code_ruby/lib/maasha/align/pair.rb
+++ b/code_ruby/lib/maasha/align/pair.rb
@@ -279,14 +279,14 @@ module PairAlign
         s_gaps += diff.abs
       end
 
-      @matches[1 .. -1].each do |match|
-        diff = (q_gaps + match.q_beg) - (s_gaps + match.s_beg)
+      @matches[1 .. -1].each do |m|
+        diff = (q_gaps + m.q_beg) - (s_gaps + m.s_beg)
 
         if diff < 0
-          @q_entry.seq.insert(match.q_beg + q_gaps, "-" * diff.abs)
+          @q_entry.seq.insert(m.q_beg + q_gaps, "-" * diff.abs)
           q_gaps += diff.abs
         elsif diff > 0
-          @s_entry.seq.insert(match.s_beg + s_gaps, "-" * diff.abs)
+          @s_entry.seq.insert(m.s_beg + s_gaps, "-" * diff.abs)
           s_gaps += diff.abs
         end
       end
diff --git a/code_ruby/test/maasha/test_math_aux.rb b/code_ruby/test/maasha/test_math_aux.rb
index 1cc3790..29a0fac 100755
--- a/code_ruby/test/maasha/test_math_aux.rb
+++ b/code_ruby/test/maasha/test_math_aux.rb
@@ -38,3 +38,4 @@ class MathTest < Test::Unit::TestCase
     assert_equal(1.5, Math.dist_point2line( 3, 3, 0, 4.5, 5, 4.5))
   end
 end
+