code update

git-svn-id: http://biopieces.googlecode.com/svn/trunk@1354 74ccb610-7750-0410-82ae-013aeee3265d

diff --git a/bp_bin/plot_scores b/bp_bin/plot_scores
index af37cc2a4639db430114b30ebd3429213c93a29b..95570958c8837cae0fcb943d2050a3afc7223773 100755 (executable)
--- a/bp_bin/plot_scores
+++ b/bp_bin/plot_scores
@@ -20,14 +20,6 @@
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<
 
-# This program is part of the Biopieces framework (www.biopieces.org).
-
-use warnings;
-use strict;
-use Maasha::Biopieces;
-use Maasha::Fastq;
-use Maasha::Plot;
-
 # Plot a histogram of mean sequence quality scores.
 
 # >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>><<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<

diff --git a/code_ruby/Maasha/lib/patternmatcher.rb b/code_ruby/Maasha/lib/patternmatcher.rb
index 6d9db38da4712a625ea1fb97e9f40a9c2a9135e6..19a0250453caa89c33cd3b0ec946bb2dc8cdacd3 100644 (file)
--- a/code_ruby/Maasha/lib/patternmatcher.rb
+++ b/code_ruby/Maasha/lib/patternmatcher.rb
@@ -139,28 +139,31 @@ module PatternMatcher
 
   # Method to update the score vector.
   def vector_update
-    new_vector = @vector.dup
+    new_vector    = []
+    new_vector[0] = Score.new
 
     (0 ... @pattern.length).each do |i|
+      score_diag = @vector[i]
+      score_up   = new_vector[i]  # insertion
+      score_left = @vector[i + 1] # deletion
+
       if match?(@seq[@pos], @pattern[i])
-        new_vector[i + 1] = @vector[i].dup
-        new_vector[i + 1].matches += 1
+        new_score = score_diag.dup
+        new_score.matches += 1
       else
-        mismatch  = @vector[i].dup
-        insertion = new_vector[i].dup
-        deletion  = @vector[i + 1].dup
-
-        if deletion?(mismatch, insertion, deletion)
-          deletion.deletions += 1
-          new_vector[i + 1] = deletion
-        elsif mismatch?(mismatch, insertion, deletion)
-          mismatch.mismatches += 1
-          new_vector[i + 1] = mismatch
-        elsif insertion?(mismatch, insertion, deletion)
-          insertion.insertions += 1
-          new_vector[i + 1] = insertion
+        if deletion?(score_diag, score_up, score_left)
+          new_score = score_left.dup
+          new_score.deletions += 1
+        elsif mismatch?(score_diag, score_up, score_left)
+          new_score = score_diag.dup
+          new_score.mismatches += 1
+        elsif insertion?(score_diag, score_up, score_left)
+          new_score = score_up.dup
+          new_score.insertions += 1
         end
       end
+
+      new_vector[i + 1] = new_score
     end
 
     @vector = new_vector