README.md in needleman_wunsch_aligner-1.0.3 vs README.md in needleman_wunsch_aligner-1.0.4

- old
+ new

@@ -10,22 +10,12 @@ seq2 = 'GATTACA' 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: gem 'needleman_wunsch_aligner' @@ -50,14 +40,14 @@ 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: puts aligner.inspect_matrix(:score) # => 2 3 4 @@ -67,15 +57,15 @@ 3 -3 -1 1 0 Inspect the traceback table: puts aligner.inspect_matrix(:traceback) - # => 2 3 4 - x ← ← ← - 1 ↑ ↑ ↑ ↑ - 2 ↑ ⬉ ← ← - 3 ↑ ↑ ⬉ ← + # => 2 3 4 + x ← ← ← + 1 ↑ ↑ ↑ ↑ + 2 ↑ ⬉ ← ← + 3 ↑ ↑ ⬉ ← ## Customization The gem comes with a very basic scoring function. You can implement much more sophisticated ones by subclassing the `NeedlemanWunschAligner` class and overriding the following instance methods: @@ -84,9 +74,14 @@ * `default_gap_penalty` * `gap_indicator` 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 ) 2. Create your feature branch (`git checkout -b my-new-feature`)