README.md in needleman_wunsch_aligner-1.0.0 vs README.md in needleman_wunsch_aligner-1.0.1
- old
+ new
@@ -1,6 +1,6 @@
-# NeedlemanWunschAligner
+# Needleman Wunsch Aligner
This gem finds the optimal alignment of two sequences of any kind of Ruby Objects. You can implement sophisticated scoring functions, using any of the Objects’ attributes.
The [Needleman-Wunsch algorithm](https://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm) is typically used in bioinformatics to align protein or nucleotide sequences, however it works really well for any kind of sequence. I have used this gem to align paragraphs and sentences of pairs of bilingual texts.
@@ -48,29 +48,29 @@
aligner.get_optimal_alignment
# => [[1, 2, 3, nil], [nil, 2, 3, 4]]
Inspect the alignment:
- aligner.print_alignment
+ puts aligner.inspect_alignment
# => 1 | nil
2 | 2
3 | 3
nil | 4
Inspect the score table:
- aligner.print_as_table(:score)
+ puts aligner.inspect_matrix(:score)
# => 2 3 4
0 -1 -2 -3
1 -1 -2 -3 -4
2 -2 0 -1 -2
3 -3 -1 1 0
Inspect the traceback table:
- aligner.print_as_table(:traceback)
+ puts aligner.inspect_matrix(:traceback)
# => 2 3 4
x ← ← ←
1 ↑ ↑ ↑ ↑
2 ↑ ⬉ ← ←
3 ↑ ↑ ⬉ ←
@@ -92,5 +92,21 @@
1. Fork it ( https://github.com/jhund/needleman_wunsch_aligner/fork )
2. Create your feature branch (`git checkout -b my-new-feature`)
3. Commit your changes (`git commit -am 'Add some feature'`)
4. Push to the branch (`git push origin my-new-feature`)
5. Create a new Pull Request
+
+### Resources
+
+* [Source code (github)](https://github.com/jhund/needleman_wunsch_aligner)
+* [Issues](https://github.com/jhund/needleman_wunsch_aligner/issues)
+* [Rubygems.org](http://rubygems.org/gems/needleman_wunsch_aligner)
+
+[](https://travis-ci.org/jhund/needleman_wunsch_aligner)
+
+### License
+
+[MIT licensed](https://github.com/jhund/needleman_wunsch_aligner/blob/master/LICENSE.txt).
+
+### Copyright
+
+Copyright (c) 2015 Jo Hund. See [(MIT) LICENSE](https://github.com/jhund/needleman_wunsch_aligner/blob/master/LICENSE.txt) for details.