# must raise exceptions on overridable methods
require 'spec_helper'
require 'needleman_wunsch_aligner'

describe NeedlemanWunschAligner do

  let(:aligner){ NeedlemanWunschAligner.new([], []) }

  describe "#get_optimal_alignment" do

    [
      [
        [1,2,3],
        [1,2,3],
        [
          [1,2,3],
          [1,2,3]
        ]
      ],
      [
        [1,2,3],
        [2,3,4],
        [
          [  1,2,3,nil],
          [nil,2,3,4]
        ]
      ],
      [
        [2],
        [1,2,3],
        [
          [nil,2,nil],
          [1  ,2,3]
        ]
      ],
      [
        [1,1,1,1],
        [2,2,2,2],
        [
          [nil,nil,nil,nil,1  ,1  ,1  ,1],
          [2  ,2  ,2  ,2  ,nil,nil,nil,nil]
        ]
      ],
      [
        [1,1,1,1],
        [2,2,2,1],
        [
          [nil,nil,nil,1  ,1  ,1  ,1],
          [2  ,2  ,2  ,nil,nil,nil,1]
        ]
      ],
    ].each do |(seq_a, seq_b, optimal_alignment)|

      it "returns the optimal_alignment" do
        a = NeedlemanWunschAligner.new(seq_a, seq_b)
        a.get_optimal_alignment.must_equal(optimal_alignment)
      end

    end

  end

  describe "#compute_score" do

    [
      [1, 1, 1],
      [1, 2, -3],
    ].each do |(left_el, right_el, xpect)|

      it "handles #{ left_el.inspect }:#{ right_el.inspect }" do
        aligner.send(:compute_score, left_el, right_el).must_equal(xpect)
      end

    end
  end

  describe "#default_gap_penalty" do

    it 'returns the expected value' do
      aligner.send(:default_gap_penalty).must_equal(-1)
    end

  end

  describe "#gap_indicator" do

    it 'returns the expected value' do
      aligner.send(:gap_indicator).must_equal(nil)
    end

  end

end