needleman_wunsch_aligner 1.0.1 → 1.0.2

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@@ -1,7 +1,7 @@
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data/CHANGELOG.md

@@ -1,3 +1,7 @@
+### 1.0.2
+
+* Memoized computation of optimal alignment for better performance.
+
 ### 1.0.1
 
 * Added travis CI integration.

data/lib/needleman_wunsch_aligner.rb

@@ -20,8 +20,10 @@ class NeedlemanWunschAligner
 
   # Returns two arrays that represent the optimal alignment.
   def get_optimal_alignment
-    construct_score_matrix_and_traceback_matrix
-    compute_optimal_alignment
+    @get_optimal_alignment ||= (
+      construct_score_matrix_and_traceback_matrix
+      compute_optimal_alignment
+    )
   end
 
   # This is a basic implementation of the scoring algorithm. See
@@ -67,7 +69,7 @@ class NeedlemanWunschAligner
   # @param col_width [Integer, optional], defaults to 3
   # @return [String]
   def inspect_matrix(which_matrix, col_width = 3)
-    get_optimal_alignment  if @score_matrix.nil?
+    get_optimal_alignment  # make sure we have computed the matrices
     the_matrix = case which_matrix
     when :traceback
       @traceback_matrix
@@ -140,21 +142,22 @@ protected
     left = Array.new
     top = Array.new
     while row > 0 or col > 0
-      if @traceback_matrix[row][col] == '⬉'
+      case @traceback_matrix[row][col]
+      when '⬉'
         left.push(@left_seq[row-1])
         top.push(@top_seq[col-1])
         row -= 1
         col -= 1
-      elsif @traceback_matrix[row][col] == '←'
+      when '←'
         left.push(gap_indicator)
         top.push @top_seq[col-1]
         col -= 1
-      elsif @traceback_matrix[row][col] == '↑'
+      when '↑'
         left.push @left_seq[row-1]
         top.push(gap_indicator)
         row -= 1
       else
-        puts "something strange happened" # this shouldn't happen
+        raise "Handle this"
       end
     end
     [left.reverse, top.reverse]

data/lib/needleman_wunsch_aligner/version.rb

@@ -1,3 +1,3 @@
 class NeedlemanWunschAligner
-  VERSION = "1.0.1"
+  VERSION = "1.0.2"
 end

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: needleman_wunsch_aligner
 version: !ruby/object:Gem::Version
-  version: 1.0.1
+  version: 1.0.2
 platform: ruby
 authors:
 - Jo Hund