needleman_wunsch_aligner 1.0.0 → 1.0.1

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data/.gitignore

@@ -9,7 +9,6 @@ Gemfile.lock
 InstalledFiles
 _yardoc
 coverage
-doc/
 lib/bundler/man
 pkg
 rdoc

data/.travis.yml

@@ -0,0 +1,7 @@
+language: ruby
+
+script: "bundle exec rake test"
+
+rvm:
+  - 1.9.3
+  - 2.2.1

data/CHANGELOG.md

@@ -0,0 +1,11 @@
+### 1.0.1
+
+* Added travis CI integration.
+* Fixed UTF-8 encoding issues for Ruby 1.9.
+* Added minitest Gem for Ruby 2.2.
+* Updated documentation.
+* Changed return value of inspect methods.
+
+# 1.0.0
+
+Initial release

data/README.md

@@ -1,4 +1,4 @@
-# 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.
 
@@ -50,7 +50,7 @@ Instantiate a new aligner with the two sequences and compute the optimal alignme
 
 Inspect the alignment:
 
-    aligner.print_alignment
+    puts aligner.inspect_alignment
 
     # =>   1 | nil
            2 | 2
@@ -59,7 +59,7 @@ Inspect the alignment:
 
 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
@@ -68,7 +68,7 @@ Inspect the score table:
 
 Inspect the traceback table:
 
-    aligner.print_as_table(:traceback)
+    puts aligner.inspect_matrix(:traceback)
     # =>            2   3   4
                 x   ←   ←   ←
             1   ↑   ↑   ↑   ↑
@@ -94,3 +94,19 @@ example.
 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)
+
+[![Build Status](https://travis-ci.org/jhund/needleman_wunsch_aligner.svg?branch=master)](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.

data/doc/meta.md

@@ -0,0 +1,19 @@
+# Gem meta info
+
+## Release a new version
+
+* Make and commit code changes.
+* Update `CHANGELOG.md`.
+* Update the gem version in `lib/needleman_wunsch_aligner/version.rb`.
+* Commit version bump and changelog.
+* 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`
+    * Add and push a tag like “v1.0.1” to git.
+    * Push commits to the git remote.
+
+## Run tests
+
+    rake test
+
+Also every push to github will trigger a test run at travis CI.

data/lib/needleman_wunsch_aligner/example_paragraph_and_sentence_aligner.rb

@@ -1,3 +1,5 @@
+# -*- coding: utf-8 -*-
+
 class NeedlemanWunschAligner
   class ExampleParagraphAndSentenceAligner < NeedlemanWunschAligner
 

data/lib/needleman_wunsch_aligner/version.rb

@@ -1,3 +1,3 @@
 class NeedlemanWunschAligner
-  VERSION = "1.0.0"
+  VERSION = "1.0.1"
 end

data/lib/needleman_wunsch_aligner.rb

@@ -1,3 +1,6 @@
+# -*- coding: utf-8 -*-
+
+require "needleman_wunsch_aligner/example_paragraph_and_sentence_aligner"
 require "needleman_wunsch_aligner/version"
 
 # Finds the optimal alignment of two sequences using the Needleman-Wunsch algorithm.
@@ -43,24 +46,27 @@ class NeedlemanWunschAligner
     nil
   end
 
-  # Prints the optimal alignment.
+  # Returns a string representation of the optimal alignment in two columns.
   # @param col_width [Integer, optional] max width of each col in chars
-  def print_alignment(col_width = 20)
+  # @return [String]
+  def inspect_alignment(col_width = 20)
     aligned_left_seq, aligned_top_seq = get_optimal_alignment
-    puts
+    s = []
     aligned_left_seq.each_with_index do |ls_el, idx|
       rs_el = aligned_top_seq[idx]
-      puts [
-        ls_el.inspect[0..col_width].rjust(col_width),
-        rs_el.inspect[0..col_width].ljust(col_width),
+      s << [
+        ls_el.inspect[0...col_width].rjust(col_width),
+        rs_el.inspect[0...col_width].ljust(col_width),
       ].join(' | ')
     end
+    s.join("\n")
   end
 
-  # Prints either the score or the traceback matrix as table.
+  # Returns string representation of either the score or the traceback matrix.
   # @param which_matrix [Symbol] one of :traceback or :score
   # @param col_width [Integer, optional], defaults to 3
-  def print_as_table(which_matrix, col_width = 3)
+  # @return [String]
+  def inspect_matrix(which_matrix, col_width = 3)
     get_optimal_alignment  if @score_matrix.nil?
     the_matrix = case which_matrix
     when :traceback
@@ -71,27 +77,29 @@ class NeedlemanWunschAligner
       raise "Handle this: #{ which_matrix.inspect }"
     end
 
-    puts
-    puts 'left_seq = ' + @left_seq.join
-    puts 'top_seq = ' + @top_seq.join
-    puts
-    print ' ' * 2 * col_width
-
-    # Print header row
-    @top_seq.each_index { |e| print(@top_seq[e].to_s.rjust(col_width)) }
+    s = ''
+    s << 'left_seq = ' + @left_seq.join + "\n"
+    s << 'top_seq = ' + @top_seq.join + "\n"
+    s <<  "\n"
+    # Header row
+    s << ' ' * 2 * col_width
+    @top_seq.each_index { |e| s << @top_seq[e].to_s.rjust(col_width) }
+    s << "\n"
 
-    puts ''
     traverse_score_matrix do |row, col|
       if 0 == col and 0 == row
         # first column in first row
-        print ' '.rjust(col_width)
+        s << ' '.rjust(col_width)
       elsif 0 == col
         # first col in subsequent rows
-        print @left_seq[row - 1].to_s.rjust(col_width)
+        s << @left_seq[row - 1].to_s.rjust(col_width)
       end
-      print the_matrix[row][col].to_s.rjust(col_width)
-      puts '' if col == the_matrix[row].length - 1
+      # subsequent cells
+      s << the_matrix[row][col].to_s.rjust(col_width)
+      # finalize row
+      s << "\n" if col == the_matrix[row].length - 1
     end
+    s
   end
 
 protected

data/needleman_wunsch_aligner.gemspec

@@ -19,4 +19,5 @@ Gem::Specification.new do |spec|
 
   spec.add_development_dependency "bundler", "~> 1.6"
   spec.add_development_dependency "rake"
+  spec.add_development_dependency "minitest"
 end

data/spec/needleman_wunsch_aligner/example_paragraph_and_sentence_aligner_spec.rb

@@ -1,7 +1,6 @@
-require 'spec_helper'
-require 'needleman_wunsch_aligner'
-require 'needleman_wunsch_aligner/example_paragraph_and_sentence_aligner'
-require 'pp'
+# -*- coding: utf-8 -*-
+
+require_relative '../spec_helper'
 
 class NeedlemanWunschAligner
 

data/spec/needleman_wunsch_aligner_spec.rb

@@ -1,10 +1,10 @@
-# must raise exceptions on overridable methods
-require 'spec_helper'
-require 'needleman_wunsch_aligner'
+# -*- coding: utf-8 -*-
+
+require_relative './spec_helper'
 
 describe NeedlemanWunschAligner do
 
-  let(:aligner){ NeedlemanWunschAligner.new([], []) }
+  let(:aligner){ NeedlemanWunschAligner.new([1,2,3], [2,3,4]) }
 
   describe "#get_optimal_alignment" do
 
@@ -90,4 +90,26 @@ describe NeedlemanWunschAligner do
 
   end
 
+  describe "#inspect_alignment" do
+
+    it 'prints the alignment' do
+      aligner.inspect_alignment.must_equal([
+        '                   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   ',
+      ].join("\n"))
+    end
+
+  end
+
 end

data/spec/spec_helper.rb

@@ -1,6 +1,5 @@
-ENV["RAILS_ENV"] = "test"
+# -*- coding: utf-8 -*-
+
 require 'bundler/setup'
 require 'minitest/autorun'
 require 'needleman_wunsch_aligner'
-
-#MiniTest::Unit.autorun

metadata

@@ -1,7 +1,7 @@
 --- !ruby/object:Gem::Specification
 name: needleman_wunsch_aligner
 version: !ruby/object:Gem::Version
-  version: 1.0.0
+  version: 1.0.1
 platform: ruby
 authors:
 - Jo Hund
@@ -38,6 +38,20 @@ dependencies:
     - - '>='
       - !ruby/object:Gem::Version
         version: '0'
+- !ruby/object:Gem::Dependency
+  name: minitest
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
 description: 
 email:
 - jhund@clearcove.ca
@@ -46,10 +60,13 @@ extensions: []
 extra_rdoc_files: []
 files:
 - .gitignore
+- .travis.yml
+- CHANGELOG.md
 - Gemfile
 - LICENSE.txt
 - README.md
 - Rakefile
+- doc/meta.md
 - lib/needleman_wunsch_aligner.rb
 - lib/needleman_wunsch_aligner/example_paragraph_and_sentence_aligner.rb
 - lib/needleman_wunsch_aligner/version.rb