align 0.0.2

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color
+--format nested
+-b

data/Gemfile

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+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "rspec", "~> 2.3.0"
+  gem "yard", "~> 0.6.0"
+  # kramdown provides pure-ruby markdown for yard.
+  gem "kramdown", "~> 0.13"
+  # Code coverage the way I like.
+  gem 'simplecov', '>= 0.4.0'
+  gem "bundler", "~> 1.0.0"
+  gem "jeweler", "~> 1.5.2"
+end

data/LICENSE.txt

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+Copyright (c) 2011 Michael Ryan
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# align
+align provides implementations of global and local alignment algorithms. 
+This library was created as it seemed that the Ruby landscape seemed to lack 
+implementations of the [Needleman-Wunsch](http://en.wikipedia.org/wiki/Needleman%E2%80%93Wunsch_algorithm) 
+and [Smith–Waterman](http://en.wikipedia.org/wiki/Smith-Waterman_algorithm) 
+algorithms. These algorithms are most often associated with the field of 
+[Bioinformatics](http://en.wikipedia.org/wiki/Bioinformatics), and allow for 
+an efficient mechanisms for aligning protein and nucleotide sequences.
+
+The goal of this library is to provide implementations of algorithms
+in a way that they might be used to align anything from simple strings to 
+complicated objects. As time goes on, I'll be sure to make an effort to provide
+examples of how this may be done.
+
+## Contributing to align
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it
+* Fork the project
+* Start a feature/bugfix branch
+* Commit and push until you are happy with your contribution
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+## Copyright
+
+Copyright (c) 2011 Michael Ryan. See LICENSE.txt for further details.
+

data/Rakefile

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+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "align"
+  gem.homepage = "http://github.com/justfalter/align"
+  gem.license = "MIT"
+  gem.summary = %Q{Provides sequence alignment algorithms}
+  gem.description = %Q{Provides sequence alignment algorithms}
+  gem.email = "falter@gmail.com"
+  gem.authors = ["Mike Ryan"]
+  # Include your dependencies below. Runtime dependencies are required when using your gem,
+  # and development dependencies are only needed for development (ie running rake tasks, tests, etc)
+  #  gem.add_runtime_dependency 'jabber4r', '> 0.1'
+  #  gem.add_development_dependency 'rspec', '> 1.2.3'
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec/core'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec) do |spec|
+  spec.pattern = FileList['spec/**/*_spec.rb']
+end
+
+desc "Runs specs with coverage via Simplecov"
+task :coverage do
+  ENV['COVERAGE'] = "true"
+  Rake::Task[:spec].invoke
+end
+
+task :default => :spec
+
+require 'yard'
+YARD::Rake::YardocTask.new

data/VERSION

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+0.0.2

data/lib/align.rb

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+require 'align/needleman_wunsch'
+require 'align/smith_waterman'

data/lib/align/basic_scoring.rb

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+module Align
+  # Basic Scoring interface
+  class BasicScoring
+    # @param [Numeric] align_match Price for alignment.
+    # @param [Numeric] align_mismatch Penalty for misalignment
+    # @param [Numeric] gap_penalty Gap penalty for insert/delete
+    def initialize(align_match, align_mismatch, gap_penalty)
+      @align_match = align_match
+      @align_mismatch = align_mismatch
+      @gap_penalty = gap_penalty
+    end
+
+    def score_align(a,b)
+      (a == b) ? @align_match : @align_mismatch
+    end
+
+    def score_insert(a)
+      @gap_penalty
+    end
+
+    def score_delete(a)
+      @gap_penalty
+    end
+  end
+end

data/lib/align/needleman_wunsch.rb

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+require 'align/basic_scoring'
+require 'align/pairwise_algorithm'
+
+module Align
+  # Align two sequences via [NeedlemanWunsch.align]
+  # References:
+  # [http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html]
+  class NeedlemanWunsch < PairwiseAlgorithm
+    attr_reader :cols, :rows, :matrix
+
+    # Default scoring for 
+    SCORING_DEFAULT = Align::BasicScoring.new(1,0,0)
+    SCORING_ALT1    = Align::BasicScoring.new(1,-1,-1)
+
+    # @param [#[], #size] seq1 The first sequence
+    # @param [#[], #size] seq2 The second sequence
+    # @param [Hash] opts Options
+    # @option opts [NeedlemanWunschScoring] :scoring (NeedlemanWunschScoring) An instance of a scoring object.
+    # @option opts [Object] :skip_obj (nil) An object to shove into the gaps of
+    #  the aligned sequences
+    def initialize(seq1, seq2, opts = {})
+      super(seq1, seq2, opts[:scoring] || SCORING_DEFAULT)
+
+      @rows = @seq1.size + 1
+      @cols = @seq2.size + 1
+
+      @skip_obj = opts[:skip_obj] || nil
+
+      @matrix = Array.new(@rows) do 
+        Array.new(@cols)
+      end
+
+      fill()
+    end
+
+    def score
+      @matrix[@rows-1][@cols-1]
+    end
+
+    # Fills the matrix with the alignment map.
+    def fill
+      @matrix[0][0] = 0
+      # Set up the first column on each row.
+      1.upto(@rows-1) {|i| @matrix[i][0] = @matrix[i-1][0] + @scoring.score_delete(@seq1[i])}
+      # Set up the first row 
+      1.upto(@cols-1) {|j| @matrix[0][j] = @matrix[0][j-1] + @scoring.score_insert(@seq2[j])}
+
+      1.upto(@rows-1) do |i|
+        prv_row = @matrix[i-1]
+        cur_row = @matrix[i]
+
+        1.upto(@cols-1) do |j|
+          
+          seq1_obj = @seq1[i-1]
+          seq2_obj = @seq2[j-1]
+
+          # Calculate the score.
+          score_align = prv_row[j-1] + @scoring.score_align(seq1_obj, seq2_obj)
+          score_delete = prv_row[j] + @scoring.score_delete(seq1_obj)
+          score_insert = cur_row[j-1] + @scoring.score_insert(seq2_obj)
+          max = max3(score_align, score_delete, score_insert)
+
+          @matrix[i][j] = max
+        end
+      end
+    end # fill
+
+    # Traces backward, finding the alignment.
+    # @yield [i,j,step] 
+    # @yieldparam i [Integer] The location in sequence one
+    # @yieldparam j [Integer] The location in sequence two
+    # @yieldparam step [Integer] The direction we took
+    def traceback
+      i = @rows - 1
+      j = @cols - 1
+
+      while (i > 0 && j > 0)
+        score = @matrix[i][j]
+
+        seq1_obj = @seq1[i-1]
+        seq2_obj = @seq2[j-1]
+
+        score_align = @matrix[i-1][j-1] + @scoring.score_align(seq1_obj, seq2_obj)
+        score_delete = @matrix[i-1][j] + @scoring.score_delete(seq1_obj)
+        score_insert = @matrix[i][j-1] + @scoring.score_insert(seq2_obj)
+
+        flags = 0
+        need_select = false
+
+        if score == score_align
+          flags = :align
+          i-=1
+          j-=1
+        elsif score == score_delete
+          flags = :delete
+          i-=1
+        else
+          flags = :insert
+          j-=1
+        end
+
+        yield(i,j,flags) 
+      end # while
+
+      while i > 0
+        i-=1
+        yield(i,j,:delete) 
+      end
+
+      while j > 0
+        j-=1
+        yield(i,j,:insert) 
+      end
+    end # traceback
+
+    # Like traceback, but returns an array of the traceback instead of 
+    # yielding blocks.
+    def traceback_array
+      trace = []
+      traceback do |i,j,flags|
+        trace << [i,j,flags]
+      end
+      trace
+    end # traceback_array
+
+    # Returns the sequences in aligned arrays. Gaps are filled with :skip_obj
+    # @return Two arrays containing the sequences, and their elements.
+    def align
+      alignment_1 = []
+      alignment_2 = []
+
+      traceback do |i, j, flags|
+        seq1_val = seq2_val = @skip_obj
+        case flags
+        when :align
+          seq1_val = @seq1[i]
+          seq2_val = @seq2[j]
+        when :insert
+          seq2_val = @seq2[j]
+        when :delete
+          seq1_val = @seq1[i]
+        end
+        alignment_1.unshift seq1_val
+        alignment_2.unshift seq2_val
+      end
+
+      [alignment_1, alignment_2]
+    end
+
+    # Aligns two sequences together.
+    # @param see (#initialize)
+    def self.align(seq1, seq2, opts = {})
+      self.new(seq1, seq2, opts).align
+    end
+
+  end
+end

data/lib/align/pairwise_algorithm.rb

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+module Align
+  # Provides a base for algorithms that align two sequences.
+  class PairwiseAlgorithm
+    attr_reader :seq1, :seq2, :scoring
+
+    def initialize(seq1, seq2, scoring)
+      @seq1 = seq1
+      @seq2 = seq2
+      @scoring = scoring
+    end
+
+    # Max of 2
+    def max2(a,b)
+      a >= b ? a : b
+    end
+
+    # Determines the maximum value of three variables. 3-4 times faster than
+    # [a,b,c].max.
+    def max3(a,b,c)
+      (a >= b) ? ((a >= c)? a : c) : ((b >= c)? b : c)
+    end
+
+    # Returns the max of 4 integers
+    def max4(a,b,c,d)
+      x = a >= b ? a : b
+      y = c >= d ? c : d
+      (x >= y) ? x : y
+    end
+
+
+
+    # Returns the sequences in aligned arrays. Gaps are filled with :skip_obj
+    # @return Two arrays containing the sequences, and their elements.
+    def align
+      raise NotImplementedError.new("#{self.class}#align")
+    end
+  end
+end

data/lib/align/smith_waterman.rb

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+require 'align/basic_scoring'
+require 'align/pairwise_algorithm'
+
+module Align
+  # Align two sequences via [SmithWaterman.align]
+  # References:
+  # [http://www.avatar.se/molbioinfo2001/dynprog/dynamic.html]
+  class SmithWaterman < PairwiseAlgorithm
+    attr_reader :cols, :rows, :matrix, :max_score, :max_row, :max_col
+
+    # Default scoring for 
+    SCORING_DEFAULT = BasicScoring.new(2,-1,-3)
+
+    # @param [#[], #size] seq1 The first sequence
+    # @param [#[], #size] seq2 The second sequence
+    # @param [Hash] opts Options
+    # @option opts [SmithWatermanScoring] :scoring (SmithWatermanScoring) An instance of a scoring object.
+    # @option opts [Object] :skip_obj (nil) An object to shove into the gaps of
+    #  the aligned sequences
+    def initialize(seq1, seq2, opts = {})
+      super(seq1, seq2, opts[:scoring] || SCORING_DEFAULT)
+
+      @max_score = nil
+      @max_row = nil
+      @max_col = nil
+
+      @rows = @seq1.size + 1
+      @cols = @seq2.size + 1
+
+      @skip_obj = opts[:skip_obj] || nil
+
+      @matrix = Array.new(@rows) do 
+        Array.new(@cols)
+      end
+
+      fill()
+    end
+
+    # Fills the matrix with the alignment map.
+    def fill
+      @matrix[0][0] = 0
+      # Set up the first column on each row.
+      1.upto(@rows-1) {|i| @matrix[i][0] = 0}
+      # Set up the first row 
+      1.upto(@cols-1) {|j| @matrix[0][j] = 0}
+
+      1.upto(@rows-1) do |i|
+        prv_row = @matrix[i-1]
+        cur_row = @matrix[i]
+
+        1.upto(@cols-1) do |j|
+          
+          seq1_obj = @seq1[i-1]
+          seq2_obj = @seq2[j-1]
+
+          # Calculate the score.
+          score_align = prv_row[j-1] + @scoring.score_align(seq1_obj, seq2_obj)
+          score_delete = prv_row[j] + @scoring.score_delete(seq1_obj)
+          score_insert = cur_row[j-1] + @scoring.score_insert(seq2_obj)
+          max = max4(score_align, score_delete, score_insert, 0)
+
+          if @max_score.nil? || max >= @max_score
+            @max_score = max
+            @max_row = i
+            @max_col = j
+          end
+
+          @matrix[i][j] = max
+        end
+      end
+    end # fill
+
+    # Traces backward, finding the alignment.
+    # @param [Integer] i The row to traceback from
+    # @param [Integer] j The column to traceback from
+    # @yield [i,j,step] 
+    # @yieldparam i [Integer] The location in sequence one
+    # @yieldparam j [Integer] The location in sequence two
+    # @yieldparam step [Integer] The direction we took
+    def traceback(i = @max_row, j = @max_col)
+
+      while (i > 0 && j > 0) && @matrix[i][j] > 0
+        score = @matrix[i][j]
+
+        seq1_obj = @seq1[i-1]
+        seq2_obj = @seq2[j-1]
+
+        score_align = @matrix[i-1][j-1] + @scoring.score_align(seq1_obj, seq2_obj)
+        score_delete = @matrix[i-1][j] + @scoring.score_delete(seq1_obj)
+        score_insert = @matrix[i][j-1] + @scoring.score_insert(seq2_obj)
+
+        flags = 0
+        need_select = false
+
+        if score == score_align
+          flags = :align
+          i-=1
+          j-=1
+        elsif score == score_delete
+          flags = :delete
+          i-=1
+        else
+          flags = :insert
+          j-=1
+        end
+
+        yield(i,j,flags) 
+      end # while
+
+    end # traceback
+
+    # Like traceback, but returns an array of the traceback instead of 
+    # yielding blocks.
+    # @param [Integer] r The row to traceback from
+    # @param [Integer] c The column to traceback from
+    def traceback_array(r = @max_row, c = @max_col)
+      trace = []
+      traceback(r,c) do |i,j,flags|
+        trace << [i,j,flags]
+      end
+      trace
+    end # traceback_array
+
+    # Returns the sequences in aligned arrays. Gaps are filled with :skip_obj
+    # @return Two arrays containing the sequences, and their elements.
+    # @param [Integer] r The row to traceback from
+    # @param [Integer] c The column to traceback from
+    def align(r = @max_row, c = @max_col)
+      alignment_1 = []
+      alignment_2 = []
+
+      traceback(r,c) do |i, j, flags|
+        seq1_val = seq2_val = @skip_obj
+        case flags
+        when :align
+          seq1_val = @seq1[i]
+          seq2_val = @seq2[j]
+        when :insert
+          seq2_val = @seq2[j]
+        when :delete
+          seq1_val = @seq1[i]
+        end
+        alignment_1.unshift seq1_val
+        alignment_2.unshift seq2_val
+      end
+
+      [alignment_1, alignment_2]
+    end
+
+    # Aligns two sequences together.
+    # @param see (#initialize)
+    def self.align(seq1, seq2, opts = {})
+      self.new(seq1, seq2, opts).align
+    end
+
+  end
+end

data/spec/needleman_wunsch_spec.rb

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+require_relative 'spec_helper'
+require 'align/needleman_wunsch'
+
+shared_examples_for "a needleman-wunsch alignment algorithm" do
+  examples = [ 
+    ['bcefg', 'abcdef', '-bc-efg', 'abcdef-'],
+    ['GAATTCAGTTA', 'GGATCGA', 'GAATTCAGTTA', 'GGA-TC-G--A']
+  ]
+
+  examples.each do |seq1, seq2, exp1, exp2|
+    context "when aligning '#{seq1}' and '#{seq2}'" do
+      before :each do
+        @opts[:skip_obj] = "-"
+        @align1, @align2 = @klass.align(seq1, seq2, @opts)
+      end
+      
+      it "should align 1 as '#{exp1}'" do
+        @align1.join('').should == exp1
+      end
+      it "should align 2 as '#{exp2}'" do
+        @align2.join('').should == exp2
+      end
+    end
+
+    context "when aligning '#{seq2}' and '#{seq1}'" do
+      before :each do
+        @opts[:skip_obj] = "-"
+        @align1, @align2 = @klass.align(seq2, seq1, @opts)
+      end
+      
+      it "should align 1 as '#{exp2}'" do
+        @align1.join('').should == exp2
+      end
+      it "should align 2 as '#{exp1}'" do
+        @align2.join('').should == exp1
+      end
+    end
+
+  end
+
+  context "with two similar sequences" do
+    before :each do
+      @seq1 = "GAATTCAGTTA"
+      @seq2 = "GGATCGA"
+      @nw = @klass.new(@seq1, @seq2, @opts)
+    end
+
+    # Actual matrix
+    #     #0 1 2 3 4 5 6 7 8 9 A B 
+    #     #- G A A T T C A G T T A
+    # 0 - [0,0,0,0,0,0,0,0,0,0,0,0]
+    # 1 G [0,1,1,1,1,1,1,1,1,1,1,1]
+    # 2 G [0,1,1,1,1,1,1,1,2,2,2,2]
+    # 3 A [0,1,2,2,2,2,2,2,2,2,2,3]
+    # 4 T [0,1,2,2,3,3,3,3,3,3,3,3]
+    # 5 C [0,1,2,2,3,3,4,4,4,4,4,4]
+    # 6 G [0,1,2,2,3,3,4,4,5,5,5,5]
+    # 7 A [0,1,2,3,3,3,4,5,5,5,5,6]
+
+    # Actual matrix
+    #     #0 1 2 3 4 5 6 7 8 9 A B 
+    #     #- G A A T T C A G T T A
+    # 0 - [0,0,0,0,0,0,0,0,0,0,0,0]
+    # 1 G [0,X,1,1,1,1,1,1,1,1,1,1]
+    # 2 G [0,1,X,1,1,1,1,1,2,2,2,2]
+    # 3 A [0,1,2,X,X,2,2,2,2,2,2,3]
+    # 4 T [0,1,2,2,3,X,3,3,3,3,3,3]
+    # 5 C [0,1,2,2,3,3,X,X,4,4,4,4]
+    # 6 G [0,1,2,2,3,3,4,4,X,X,X,5]
+    # 7 A [0,1,2,3,3,3,4,5,5,5,5,X]
+
+    subject {@nw}
+    its(:rows) { should == @seq1.size + 1}
+    its(:cols) { should == @seq2.size + 1}
+
+    it "should use the score for the lower, right" do
+      @nw.score.should == @score
+    end
+
+#    it "should have a properly built score matrix" do
+#      @nw.matrix.should == 
+#        [
+#        [0,0,0,0,0,0,0,0],
+#        [0,1,1,1,1,1,1,1],
+#        [0,1,1,2,2,2,2,2],
+#        [0,1,1,2,2,2,2,3],
+#        [0,1,1,2,3,3,3,3],
+#        [0,1,1,2,3,3,3,3],
+#        [0,1,1,2,3,4,4,4],
+#        [0,1,1,2,3,4,4,5],
+#        [0,1,2,2,3,4,5,5],
+#        [0,1,2,2,3,4,5,5],
+#        [0,1,2,2,3,4,5,5],
+#        [0,1,2,3,3,4,5,6],
+#      ]
+#    end
+
+    it "should be possible to return the proper traceback" do
+      @nw.traceback_array.should == [
+        [10,6, :align],
+        [9,6, :delete],
+        [8,6, :delete],
+        [7,5, :align],
+        [6,5, :delete],
+        [5,4, :align],
+        [4,3, :align],
+        [3,3, :delete],
+        [2,2, :align],
+        [1,1, :align],
+        [0,0, :align]
+      ]
+    end
+
+    it "should be possible to construct the proper traceback via yield" do
+      traceback = []
+      @nw.traceback do |i,j, last_move|
+        traceback << [i,j, last_move]
+      end
+      traceback.should == [
+        [10,6, :align],
+        [9,6, :delete],
+        [8,6, :delete],
+        [7,5, :align],
+        [6,5, :delete],
+        [5,4, :align],
+        [4,3, :align],
+        [3,3, :delete],
+        [2,2, :align],
+        [1,1, :align],
+        [0,0, :align]
+      ]
+    end
+  end # "with two similar sequences"
+end
+
+describe Align::NeedlemanWunsch do
+  before :each do
+    @klass = Align::NeedlemanWunsch
+    @opts = {}
+    @score = 6
+  end
+  context "by default" do
+    it_should_behave_like "a needleman-wunsch alignment algorithm" 
+  end
+
+  context "using SCORING_ALT1" do
+    before :each do
+      @klass = Align::NeedlemanWunsch
+      @opts[:scoring] = Align::NeedlemanWunsch::SCORING_ALT1
+      @score = 1
+    end
+
+    it_should_behave_like "a needleman-wunsch alignment algorithm" 
+  end
+end
+

data/spec/pairwise_algorithm_spec.rb

@@ -0,0 +1,38 @@
+require_relative 'spec_helper'
+require 'align/pairwise_algorithm'
+require 'align/basic_scoring'
+
+describe Align::PairwiseAlgorithm do
+  before :each do
+    @seq1 = "GAATTCAGTTA"
+    @seq2 = "GGATCGA"
+    @scoring = Align::BasicScoring.new(1,-1,-1)
+  end
+  subject {Align::PairwiseAlgorithm.new(@seq1, @seq2, @scoring)}
+  its(:seq1) {should == @seq1}
+  its(:seq2) {should == @seq2}
+  its(:scoring) {should == @scoring}
+  describe :align do
+    it "should raise a NotImplementedError" do
+      lambda {subject.align}.should raise_error(NotImplementedError)
+    end
+  end
+
+  it "#max2 should find the max amongst two numbers" do
+    [1,2].permutation.each do |a,b|
+      subject.max2(a,b).should == 2
+    end
+  end
+
+  it "#max3 should find the max amongst three numbers" do
+    [1,2,3].permutation.each do |a,b,c|
+      subject.max3(a,b,c).should == 3
+    end
+  end
+
+  it "#max4 should find the max amongst four numbers" do
+    [1,2,3,4].permutation.each do |a,b,c,d|
+      subject.max4(a,b,c,d).should == 4
+    end
+  end
+end

data/spec/smith_waterman_spec.rb

@@ -0,0 +1,78 @@
+require_relative 'spec_helper'
+require 'align/smith_waterman'
+require 'benchmark'
+
+describe Align::SmithWaterman do
+  before :each do
+    @klass = Align::SmithWaterman
+    @opts = {}
+  end
+
+  examples = [ 
+    ['CAGCCUCGCUUAG', 'AAUGCCAUUGACGG', 'GCC-UCG', 'GCCAUUG'],
+    ['AAUGCCAUUGACGG', 'CAGCCUCGCUUAG', 'GCCAUUG', 'GCC-UCG'],
+    ['ACACACTA', 'AGCACACA', 'CACAC', 'CACAC']
+  ]
+
+  examples.each do |seq1, seq2, exp1, exp2|
+    context "when aligning '#{seq1}' and '#{seq2}'" do
+      before :each do
+        @opts[:skip_obj] = "-"
+        @align1, @align2 = @klass.align(seq1, seq2, @opts)
+      end
+      
+      it "should align 1 as '#{exp1}'" do
+        @align1.join('').should == exp1
+      end
+      it "should align 2 as '#{exp2}'" do
+        @align2.join('').should == exp2
+      end
+    end
+  end
+
+  context "with two similar sequences" do
+    before :each do
+      @seq1 = "CAGCCUCGCUUAG"
+      @seq2 = "AAUGCCAUUGACGG"
+      @nw = @klass.new(@seq1, @seq2, @opts)
+    end
+
+    subject {@nw}
+    its(:rows) { should == @seq1.size + 1}
+    its(:cols) { should == @seq2.size + 1}
+    its(:max_score) { should == 6 }
+    its(:max_row) {should == 8 }
+    its(:max_col) {should == 10}
+
+    it "should be possible to return the proper traceback" do
+      @nw.traceback_array.should == 
+      [
+        [7, 9, :align],
+        [6, 8, :align],
+        [5, 7, :align],
+        [5, 6, :insert],
+        [4, 5, :align],
+        [3, 4, :align],
+        [2, 3, :align]
+      ]
+    end
+
+    it "should be possible to construct the proper traceback via yield" do
+      traceback = []
+      @nw.traceback do |i,j, last_move|
+        traceback << [i,j, last_move]
+      end
+      traceback.should == 
+      [
+        [7, 9, :align],
+        [6, 8, :align],
+        [5, 7, :align],
+        [5, 6, :insert],
+        [4, 5, :align],
+        [3, 4, :align],
+        [2, 3, :align]
+      ]
+    end
+  end # "with two similar sequences"
+
+end

data/spec/spec_helper.rb

@@ -0,0 +1,22 @@
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+
+if ENV['COVERAGE'] 
+  require 'simplecov'
+  SimpleCov.start do
+    add_filter '/spec/'
+    add_filter '/.bundle/'
+  end
+end
+
+require 'rspec'
+require 'align'
+
+
+# Requires supporting files with custom matchers and macros, etc,
+# in ./support/ and its subdirectories.
+Dir["#{File.dirname(__FILE__)}/support/**/*.rb"].each {|f| require f}
+
+RSpec.configure do |config|
+  
+end

metadata

@@ -0,0 +1,143 @@
+--- !ruby/object:Gem::Specification 
+name: align
+version: !ruby/object:Gem::Version 
+  prerelease: 
+  version: 0.0.2
+platform: ruby
+authors: 
+- Mike Ryan
+autorequire: 
+bindir: bin
+cert_chain: []
+
+date: 2011-04-25 00:00:00 -05:00
+default_executable: 
+dependencies: 
+- !ruby/object:Gem::Dependency 
+  name: rspec
+  requirement: &id001 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 2.3.0
+  type: :development
+  prerelease: false
+  version_requirements: *id001
+- !ruby/object:Gem::Dependency 
+  name: yard
+  requirement: &id002 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 0.6.0
+  type: :development
+  prerelease: false
+  version_requirements: *id002
+- !ruby/object:Gem::Dependency 
+  name: kramdown
+  requirement: &id003 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: "0.13"
+  type: :development
+  prerelease: false
+  version_requirements: *id003
+- !ruby/object:Gem::Dependency 
+  name: simplecov
+  requirement: &id004 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ">="
+      - !ruby/object:Gem::Version 
+        version: 0.4.0
+  type: :development
+  prerelease: false
+  version_requirements: *id004
+- !ruby/object:Gem::Dependency 
+  name: bundler
+  requirement: &id005 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.0.0
+  type: :development
+  prerelease: false
+  version_requirements: *id005
+- !ruby/object:Gem::Dependency 
+  name: jeweler
+  requirement: &id006 !ruby/object:Gem::Requirement 
+    none: false
+    requirements: 
+    - - ~>
+      - !ruby/object:Gem::Version 
+        version: 1.5.2
+  type: :development
+  prerelease: false
+  version_requirements: *id006
+description: Provides sequence alignment algorithms
+email: falter@gmail.com
+executables: []
+
+extensions: []
+
+extra_rdoc_files: 
+- LICENSE.txt
+- README.md
+files: 
+- .document
+- .rspec
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- VERSION
+- lib/align.rb
+- lib/align/basic_scoring.rb
+- lib/align/needleman_wunsch.rb
+- lib/align/pairwise_algorithm.rb
+- lib/align/smith_waterman.rb
+- spec/needleman_wunsch_spec.rb
+- spec/pairwise_algorithm_spec.rb
+- spec/smith_waterman_spec.rb
+- spec/spec_helper.rb
+has_rdoc: true
+homepage: http://github.com/justfalter/align
+licenses: 
+- MIT
+post_install_message: 
+rdoc_options: []
+
+require_paths: 
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      hash: 2168051897343409579
+      segments: 
+      - 0
+      version: "0"
+required_rubygems_version: !ruby/object:Gem::Requirement 
+  none: false
+  requirements: 
+  - - ">="
+    - !ruby/object:Gem::Version 
+      version: "0"
+requirements: []
+
+rubyforge_project: 
+rubygems_version: 1.6.0
+signing_key: 
+specification_version: 3
+summary: Provides sequence alignment algorithms
+test_files: 
+- spec/needleman_wunsch_spec.rb
+- spec/pairwise_algorithm_spec.rb
+- spec/smith_waterman_spec.rb
+- spec/spec_helper.rb