needleman_wunsch_aligner 1.0.3 → 1.0.4

checksums.yaml

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

@@ -1,3 +1,7 @@
+### 1.0.4
+
+* Added overridable methods for `#inspect_alignment`
+
 ### 1.0.3
 
 * Improved #inspect_alignment output.

data/README.md

@@ -12,18 +12,8 @@ Given two sequences
 The algorithm will find the optimal alignment based on a scoring function you specify:
 
     GCATG-CU
-    =+==!-=!
     G-ATTACA
 
-Meaning of the symbols:
-
-    = Match
-    ! Mismatch
-    + Insert
-    - Deletion
-
-Insert and Deletion are usually grouped together as `IndDel`.
-
 ## Installation
 
 Add this line to your application's Gemfile:
@@ -52,10 +42,10 @@ Inspect the alignment:
 
     puts aligner.inspect_alignment
 
-    # =>   1 | nil
-           2 | 2
-           3 | 3
-         nil | 4
+    # =>   1 - nil
+           2 = 2
+           3 = 3
+         nil + 4
 
 Inspect the score table:
 
@@ -69,11 +59,11 @@ Inspect the score table:
 Inspect the traceback table:
 
     puts aligner.inspect_matrix(:traceback)
-    # =>            2   3   4
-                x   ←   ←   ←
-            1   ↑   ↑   ↑   ↑
-            2   ↑   ⬉   ←   ←
-            3   ↑   ↑   ⬉   ←
+    # =>  2  3  4
+       x  ←  ←  ←
+    1  ↑  ↑  ↑  ↑
+    2  ↑  ⬉  ←  ←
+    3  ↑  ↑  ⬉  ←
 
 ## Customization
 
@@ -87,6 +77,11 @@ sophisticated ones by subclassing the `NeedlemanWunschAligner` class and overrid
 Please see `NeedlemanWunschAligner::ExampleParagraphAndSentenceAligner` for an
 example.
 
+You can also override these methods which are related to `#inspect_alignment`:
+
+* `element_for_inspection_display`
+* `elements_are_equal_for_inspection`
+
 ## Contributing
 
 1. Fork it ( https://github.com/jhund/needleman_wunsch_aligner/fork )

data/lib/needleman_wunsch_aligner.rb

@@ -56,7 +56,7 @@ class NeedlemanWunschAligner
     s = []
     aligned_left_seq.each_with_index do |left_el, idx|
       top_el = aligned_top_seq[idx]
-      delimiter = if top_el == left_el
+      delimiter = if elements_are_equal_for_inspection(top_el, left_el)
         '=' # match
       elsif gap_indicator == top_el
         '-' # delete
@@ -66,8 +66,8 @@ class NeedlemanWunschAligner
         '!' # mismatch
       end
       s << [
-        left_el.inspect[0...col_width].rjust(col_width),
-        top_el.inspect[0...col_width].ljust(col_width),
+        element_for_inspection_display(left_el, col_width).rjust(col_width),
+        element_for_inspection_display(top_el, col_width).ljust(col_width),
       ].join("  #{ delimiter }  ")
     end
     s.join("\n")
@@ -113,6 +113,29 @@ class NeedlemanWunschAligner
     s
   end
 
+  # Transforms element to an object that can be used for display when inspecting
+  # an alignment
+  # @params element [Object]
+  # @return [Object]
+  def element_for_inspection_display(element, col_width = nil)
+    r = case element
+    when String
+      element
+    else
+      element.inspect
+    end
+    col_width ? r[0...col_width] : r
+  end
+
+  # Returns true if top_el and left_el are considered equal for inspection
+  # purposes
+  # @params top_el [Object]
+  # @params left_el [Object]
+  # @return [Boolean]
+  def elements_are_equal_for_inspection(top_el, left_el)
+    top_el == left_el
+  end
+
 protected
 
   def construct_score_matrix_and_traceback_matrix

data/lib/needleman_wunsch_aligner/version.rb

@@ -1,3 +1,3 @@
 class NeedlemanWunschAligner
-  VERSION = "1.0.3"
+  VERSION = "1.0.4"
 end

data/spec/needleman_wunsch_aligner_spec.rb

@@ -80,6 +80,7 @@ describe NeedlemanWunschAligner do
       end
 
     end
+
   end
 
   describe "#default_gap_penalty" do
@@ -118,6 +119,52 @@ describe NeedlemanWunschAligner do
       ].join("\n"))
     end
 
+    it 'uses #element_for_inspection_display' do
+      def aligner.element_for_inspection_display(element, col_width)
+        'override'
+      end
+
+      aligner.inspect_alignment(8).must_equal([
+        'override  -  override',
+        'override  =  override',
+        'override  =  override',
+        'override  +  override',
+      ].join("\n"))
+    end
+
+    it 'uses #elements_are_equal_for_inspection' do
+      def aligner.elements_are_equal_for_inspection(top_el, left_el)
+        false
+      end
+
+      aligner.inspect_alignment(4).must_equal([
+        '   1  -  nil ',
+        '   2  !  2   ',
+        '   3  !  3   ',
+        ' nil  +  4   ',
+      ].join("\n"))
+    end
+
+  end
+
+  describe "#element_for_inspection_display" do
+
+    it 'returns the expected value' do
+      aligner.element_for_inspection_display('hello', 3).must_equal('hel')
+    end
+
+  end
+
+  describe "#elements_are_equal_for_inspection" do
+
+    it 'returns true if equal' do
+      aligner.elements_are_equal_for_inspection('hello', 'hello').must_equal(true)
+    end
+
+    it 'returns false if not equal' do
+      aligner.elements_are_equal_for_inspection('hello', 'heller').must_equal(false)
+    end
+
   end
 
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: needleman_wunsch_aligner
 version: !ruby/object:Gem::Version
-  version: 1.0.3
+  version: 1.0.4
 platform: ruby
 authors:
 - Jo Hund
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2015-07-24 00:00:00.000000000 Z
+date: 2015-08-19 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: bundler