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`)