needleman_wunsch_aligner 1.0.4 → 1.1.0

checksums.yaml

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

@@ -1,3 +1,7 @@
+### 1.1.0
+
+* Changed #compute_score method params: Added row and column index for performance optimizations where I may not want to compute scores for the entire matrix, but only for a narrow band around the diagonal. The width of the band is determined by the maximum expected alignment offset.
+
 ### 1.0.4
 
 * Added overridable methods for `#inspect_alignment`

data/lib/needleman_wunsch_aligner.rb

@@ -28,10 +28,14 @@ class NeedlemanWunschAligner
 
   # This is a basic implementation of the scoring algorithm. See
   # ExampleParagraphAndSentenceAligner for a more complex scoring function.
+  # NOTE: You can use row_index and col_index to improve performance if you know
+  # the maximum offset between left_el and top_el.
   # @param left_el [Object]
   # @param top_el [Object]
+  # @param row_index [Integer] zero based row index, origin is at top.
+  # @param col_index [Integer] zero based column index, origin is to the left.
   # @return [Numeric]
-  def compute_score(left_el, top_el)
+  def compute_score(left_el, top_el, row_index, col_index)
     left_el == top_el ? 1 : -3
   end
 
@@ -155,7 +159,13 @@ protected
         from_top = @score_matrix[row-1][col] + default_gap_penalty
         from_left = @score_matrix[row][col-1] + default_gap_penalty
         # @left_seq and @top_seq are off by 1 because we added cells for gaps in the matrix
-        from_top_left = @score_matrix[row-1][col-1] + compute_score(@left_seq[row-1], @top_seq[col-1])
+        score = compute_score(
+          @left_seq[row-1],
+          @top_seq[col-1],
+          row-1,
+          col-1
+        )
+        from_top_left = @score_matrix[row-1][col-1] + score
 
         # find max score and direction
         max, direction = [from_top_left, '⬉']

data/lib/needleman_wunsch_aligner/example_paragraph_and_sentence_aligner.rb

@@ -14,10 +14,12 @@ class NeedlemanWunschAligner
     #  s/b                            10    -10
     #  s/nil                                10
     #
-    # param left_el [Hash]
-    # param top_el [Hash]
-    # return [Integer]
-    def compute_score(left_el, top_el)
+    # @param left_el [Hash]
+    # @param top_el [Hash]
+    # @param row_index [Integer] zero based row index, origin is at top.
+    # @param col_index [Integer] zero based column index, origin is to the left.
+    # @return [Integer]
+    def compute_score(left_el, top_el, row_index, col_index)
       score = 0
       if left_el[:type] == top_el[:type]
         # Match on type (paragraph vs. sentence)

data/lib/needleman_wunsch_aligner/version.rb

@@ -1,3 +1,3 @@
 class NeedlemanWunschAligner
-  VERSION = "1.0.4"
+  VERSION = "1.1.0"
 end

data/spec/needleman_wunsch_aligner/example_paragraph_and_sentence_aligner_spec.rb

@@ -143,7 +143,7 @@ class NeedlemanWunschAligner
       ].each do |(left_el, right_el, xpect)|
 
         it "handles #{ left_el.inspect }:#{ right_el.inspect }" do
-          aligner.send(:compute_score, left_el, right_el).must_equal(xpect)
+          aligner.send(:compute_score, left_el, right_el, 0, 0).must_equal(xpect)
         end
 
       end

data/spec/needleman_wunsch_aligner_spec.rb

@@ -76,7 +76,7 @@ describe NeedlemanWunschAligner do
     ].each do |(left_el, right_el, xpect)|
 
       it "handles #{ left_el.inspect }:#{ right_el.inspect }" do
-        aligner.send(:compute_score, left_el, right_el).must_equal(xpect)
+        aligner.send(:compute_score, left_el, right_el, 0, 0).must_equal(xpect)
       end
 
     end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: needleman_wunsch_aligner
 version: !ruby/object:Gem::Version
-  version: 1.0.4
+  version: 1.1.0
 platform: ruby
 authors:
 - Jo Hund
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-08-19 00:00:00.000000000 Z
+date: 2016-08-30 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler