Class: SmithWaterman

Inherits:
Object
  • Object
show all
Includes:
Singleton
Defined in:
lib/smith-waterman.rb

Instance Method Summary collapse

Instance Method Details

#alignment(target, input) ⇒ Object 



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# File 'lib/smith-waterman.rb', line 10

def alignment(target,input)
  alignments = [] * 2
  alignments[0] = alignment_local(target,input)
  alignments[1] = alignment_local(target,aside_sequence(input))
  alignments[1].aside = true

  # TODO: wholeLengthI, wholeLengthJを設定する
  # a[1].startJ = a[1].wholeLengthJ -a[1].startJ -1;
  # a[1].endJ = a[1].wholeLengthJ -a[1].endJ-1;
  return max(alignments)
end

#alignment_local(target, input) ⇒ Object 



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# File 'lib/smith-waterman.rb', line 22

def alignment_local(target,input)
  raise "input is nil or empty" if input.nil? || input.empty?
  raise "target is nil or empty" if target.nil? || target.empty?

  # 行列の初期化

  matrix = Array.new(target.length) { Array.new(input.length,0) }
  maxScore = 0; maxI = 0; maxJ = 0
  target.length.times do |i|
    ci = target[i] # 検索対象文字
    input.length.times do |j|
      cj = input[j] # 検索文字
      candidates = [0] * 4
      candidates[0] = 0 # 未使用(常に0)
      if i > 0 && j > 0
        candidates[1] = matrix[i-1][j-1] + s(ci,cj)
      else
        candidates[1] = s(ci,cj)
      end

      if i > 0
        candidates[2] = matrix[i-1][j] - 1
      end
      if j > 0
        candidates[3] = matrix[i][j-1] - 1
      end
      matrix[i][j] = candidates.max
      # スコアの最大点を記憶
      if matrix[i][j] >= maxScore
        maxScore = matrix[i][j]
        maxI = i
        maxJ = j
      end
    end
    puts ci+" "+matrix[i].join(" ") if ENV["DEBUG"]      
  end
  puts "maxScore=#{maxScore} maxI=#{maxI} maxJ=#{maxJ}" if ENV["DEBUG"]

  a = Alignment.new
  a.endI = maxI
  a.endJ = maxJ
  i = maxI; j = maxJ; bufI = target[i]; bufJ = input[j]
  while i > 0 && j > 0 do
    dst = [] * 3
    dst[0] = matrix[i-1][j-1]
    dst[1] = matrix[i-1][j] if i > 0
    dst[2] = matrix[i][j-1] if j > 0
    break if dst.max == 0 # 行き先がなければ終了
    case dst.index(dst.max)
    when 0
      i -= 1
      j -= 1
      bufI += target[i]
      bufJ += input[j]
    when 1
      i -= 1
      bufI += target[i]
      bufJ += Alignment::BLANK        
    when 2
      j -= 1
      bufI += Alignment::BLANK
      bufJ += input[j]
    end
  end
  a.alignmentI = bufI.reverse
  a.alignmentJ = bufJ.reverse
  a.startI = i
  a.startJ = j

  # スコアはここでは求めない(Java版ではここで決定していた)
  return a
end