needleman_wunsch_aligner 1.0.2 → 1.0.3

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

@@ -1,3 +1,7 @@
+### 1.0.3
+
+* Improved #inspect_alignment output.
+
 ### 1.0.2
 
 * Memoized computation of optimal alignment for better performance.

data/doc/meta.md

@@ -5,7 +5,7 @@
 * Make and commit code changes.
 * Update `CHANGELOG.md`.
 * Update the gem version in `lib/needleman_wunsch_aligner/version.rb`.
-* Commit version bump and changelog.
+* Commit version bump and changelog with message ‘Bumped version to x.y.z’.
 * Run `rake release`. This will perform the following steps:
     * Build a gem package to e.g. pkg/needleman_wunsch_aligner-1.0.1.gem.
     * Push the `.gem` package to `Rubygems.org`

data/lib/needleman_wunsch_aligner.rb

@@ -54,12 +54,21 @@ class NeedlemanWunschAligner
   def inspect_alignment(col_width = 20)
     aligned_left_seq, aligned_top_seq = get_optimal_alignment
     s = []
-    aligned_left_seq.each_with_index do |ls_el, idx|
-      rs_el = aligned_top_seq[idx]
+    aligned_left_seq.each_with_index do |left_el, idx|
+      top_el = aligned_top_seq[idx]
+      delimiter = if top_el == left_el
+        '=' # match
+      elsif gap_indicator == top_el
+        '-' # delete
+      elsif gap_indicator == left_el
+        '+' # insert
+      else
+        '!' # mismatch
+      end
       s << [
-        ls_el.inspect[0...col_width].rjust(col_width),
-        rs_el.inspect[0...col_width].ljust(col_width),
-      ].join(' | ')
+        left_el.inspect[0...col_width].rjust(col_width),
+        top_el.inspect[0...col_width].ljust(col_width),
+      ].join("  #{ delimiter }  ")
     end
     s.join("\n")
   end

data/lib/needleman_wunsch_aligner/version.rb

@@ -1,3 +1,3 @@
 class NeedlemanWunschAligner
-  VERSION = "1.0.2"
+  VERSION = "1.0.3"
 end

data/spec/needleman_wunsch_aligner_spec.rb

@@ -33,6 +33,14 @@ describe NeedlemanWunschAligner do
           [1  ,2,3]
         ]
       ],
+      [
+        [1],
+        [1,2,3],
+        [
+          [1,nil,nil],
+          [1,2  ,3]
+        ]
+      ],
       [
         [1,1,1,1],
         [2,2,2,2],
@@ -94,19 +102,19 @@ describe NeedlemanWunschAligner do
 
     it 'prints the alignment' do
       aligner.inspect_alignment.must_equal([
-        '                   1 | nil                 ',
-        '                   2 | 2                   ',
-        '                   3 | 3                   ',
-        '                 nil | 4                   ',
+        '                   1  -  nil                 ',
+        '                   2  =  2                   ',
+        '                   3  =  3                   ',
+        '                 nil  +  4                   ',
       ].join("\n"))
     end
 
     it 'adjusts the column width' do
       aligner.inspect_alignment(4).must_equal([
-        '   1 | nil ',
-        '   2 | 2   ',
-        '   3 | 3   ',
-        ' nil | 4   ',
+        '   1  -  nil ',
+        '   2  =  2   ',
+        '   3  =  3   ',
+        ' nil  +  4   ',
       ].join("\n"))
     end
 

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: needleman_wunsch_aligner
 version: !ruby/object:Gem::Version
-  version: 1.0.2
+  version: 1.0.3
 platform: ruby
 authors:
 - Jo Hund