Module: TraceVisualization::SuffixArray

Defined in:
lib/trace_visualization/suffix_array.rb

Class Method Summary collapse

Class Method Details

.effective(str) ⇒ Object 



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# File 'lib/trace_visualization/suffix_array.rb', line 22

def self.effective(str)
  n = str.length
  s = []

  if str.instance_of? String
    str.each_char { |c| s << c.ord }
  elsif str.instance_of? Array
    str.each { |c| s << c.ord }
  else
    s = str
  end

  3.times { s << 0 }

  suffix_array = Array.new(n + 3, 0)

  effective_linear(s, suffix_array, n, s.max + 1)

  3.times { s.pop }

  suffix_array[0 ... -3]
end

.effective_linear(s, suffix_array, n, alphabet_size) ⇒ Object

by Juha Karkkainen, Peter Sanders and Stefan Burkhardt



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# File 'lib/trace_visualization/suffix_array.rb', line 48

def self.effective_linear(s, suffix_array, n, alphabet_size)
n0 = (n + 2) / 3
n1 = (n + 1) / 3
n2 = n / 3
n02 = n0 + n2
		
  s12 = Array.new(n02 + 3, 0)
  sa12 = Array.new(n02 + 3, 0)
  s0 = Array.new(n0, 0)
  sa0 = Array.new(n0, 0)

# Generate positions of mod 1 and mod 2 suffixes
# the "+(n0-n1)" adds a dummy mod 1 suffix if n%3 == 1
  i = j = 0
  while (i < n + (n0 - n1))
    if i % 3 != 0
      s12[j] = i
      j += 1
    end
    i += 1
  end

# LSB radix sort the mod 1 and mod 2 triples
radix_pass(s12, sa12, s[2 ... s.length], n02, alphabet_size)
radix_pass(sa12, s12, s[1 ... s.length], n02, alphabet_size)
radix_pass(s12, sa12, s, n02, alphabet_size)

# Find lexicographic names of triples
name, c0, c1, c2 = 0, -1, -1, -1
  for i in 0 ... n02
	if (s[sa12[i]] != c0 || s[sa12[i] + 1] != c1 || s[sa12[i] + 2] != c2)
		name += 1
		c0 = s[sa12[i]]
		c1 = s[sa12[i] + 1]
		c2 = s[sa12[i] + 2]
    end
			
	if (sa12[i] % 3 == 1) 
		s12[sa12[i]/3] = name      # Left half
    else
		s12[sa12[i]/3 + n0] = name # Right half
    end
  end

# Recurse if names are not yet unique
if name < n02
	effective_linear(s12, sa12, n02, name)
			
	# Store unique names in s12 using the suffix array
    for i in 0 ... n02
		s12[sa12[i]] = i + 1
    end
  else
	# Generate the suffix array of s12 directly
    for i in 0 ... n02
		sa12[s12[i] - 1] = i
    end
  end

# Stably sort the mod 0 suffixes from sa12 by their first character
  i, j = 0, 0
  while i < n02
    if sa12[i] < n0
      s0[j] = 3 * sa12[i]
      j += 1
    end
    i += 1
  end
radix_pass(s0, sa0, s, n0, alphabet_size)

# Merge sorted sa0 suffixes and sorted sa12 suffixes
  p, t, k = 0, n0 - n1, 0

  while k < n
	# Pos of current offset 12 suffix
	i = get_i(n0, sa12, t)
  
	# Pos of current offset 0 suffix
	j = sa0[p]
  
    # Different compares for mod 1 and mod 2 suffixes
	if (sa12[t] < n0 ? leq_pairs(s[i], s12[sa12[t] + n0], s[j], s12[j/3]) : leq_triples(s[i], s[i + 1], s12[sa12[t] - n0 + 1], s[j], s[j + 1], s12[j/3 + n0]))
		suffix_array[k] = i
		t += 1
		if t == n02
			# Done: only sa0 suffixes left
        k += 1
        while p < n0
          suffix_array[k] = sa0[p]
          p += 1
          k += 1
        end
      end
    else
		suffix_array[k] = j
		p += 1;
		if p == n0
			# Done: only sa12 suffixes left
        k += 1
        while t < n02
          suffix_array[k] = get_i(n0, sa12, t)
          t += 1
          k += 1
        end				
      end
    end
  
    k += 1
  end

end

.naive(str) ⇒ Object 



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# File 'lib/trace_visualization/suffix_array.rb', line 3

def self.naive(str)
  n = str.length

  tmp    = Array.new(n)
  result = Array.new(n)

  for i in 0 ... n
    tmp[i] = [str[i .. -1], i]
  end

  tmp.sort! { |x, y| x[0] <=> y[0] }    

  for i in 0 ... n
    result[i] = tmp[i][1]
  end

  result
end