Class: Bioroebe::SmithWaterman

Inherits:
Object
  • Object
show all
Defined in:
lib/bioroebe/string_matching/smith_waterman.rb

Overview

Bioroebe::SmithWaterman

Constant Summary collapse

MATCH_COST =
#

MATCH_COST

First, define the match, mismatch and gap costs.

#
2
MISMATCH_COST =
#

MISMATCH_COST

#
-1
GAP_COST =
#

GAP_COST

#
-4
SCORE_INSERT =
#

SCORE_INSERT

#
0
SCORE_DELETE =
#

SCORE_DELETE

#
-1
SCORE_MISS = 
-1
SCORE_MATCH = 
2

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(stra, strb, opts = {}) ⇒ SmithWaterman

#

initialize

Provide the two strings as input.

#


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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 57

def initialize(
    stra, strb, opts = {}
  )
  @str_a  = stra
  @str_b  = strb
  @str_a_arr = stra.unpack('U*')
  @str_b_arr = strb.unpack('U*')
  @m      = str_a.length + 1
  @n      = str_b.length + 1
  @mat    = Matrix.new(m, n)
  @config = opts
end

Instance Attribute Details

#config ⇒ Object (readonly)

Returns the value of attribute config.



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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 50

def config
  @config
end

#m ⇒ Object (readonly)

Returns the value of attribute m.



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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 47

def m
  @m
end

#mat ⇒ Object (readonly)

Returns the value of attribute mat.



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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 49

def mat
  @mat
end

#n ⇒ Object (readonly)

Returns the value of attribute n.



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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 48

def n
  @n
end

#str_a ⇒ Object (readonly)

Returns the value of attribute str_a.



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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 43

def str_a
  @str_a
end

#str_a_arr ⇒ Object (readonly)

Returns the value of attribute str_a_arr.



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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 45

def str_a_arr
  @str_a_arr
end

#str_b ⇒ Object (readonly)

Returns the value of attribute str_b.



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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 44

def str_b
  @str_b
end

#str_b_arr ⇒ Object (readonly)

Returns the value of attribute str_b_arr.



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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 46

def str_b_arr
  @str_b_arr
end

Instance Method Details

#alignment_inspect ⇒ Object

#

alignment_inspect

#


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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 82

def alignment_inspect
  la = '... '.dup
  lb = '... '.dup

  alignment.each_with_index { |pos, i|
    next if i == 0
    case alignment[i-1][2]
    # === :down
    when :down
      la << [ str_a_arr[pos[0]-1] ].pack('U*')
      lb << '-'
    # === :right
    when :right
      la << '-'
      lb << [ str_b_arr[pos[1]-1] ].pack('U*')
    else
      la << [ str_a_arr[pos[0]-1] ].pack('U*')
      lb << [ str_b_arr[pos[1]-1] ].pack('U*')
    end
  }
  "#{la} ...\n#{lb} ..."    
end

#do_perform_the_alignment ⇒ Object

#

do_perform_the_alignment

#


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# File 'lib/bioroebe/string_matching/smith_waterman.rb', line 73

def do_perform_the_alignment
  do_iterate_over_the_cells
  find_optimal_path
  return alignment
end