Module: TraceVisualization::Repetitions

Included in:
Algorithm
Defined in:
lib/trace_visualization/repetitions.rb,
lib/trace_visualization/repetitions_psy.rb,
lib/trace_visualization/repetitions/filter.rb,
lib/trace_visualization/repetitions/context.rb,
lib/trace_visualization/repetitions/concatenation.rb,
lib/trace_visualization/repetitions/incrementation.rb

Defined Under Namespace

Modules: Concatenation, Filter, Incrementation Classes: Context

Class Method Summary collapse

Class Method Details

.char_counter_inc(str, pos, offset) ⇒ Object 



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# File 'lib/trace_visualization/repetitions.rb', line 52

def self.char_counter_inc(str, pos, offset)
  counter = Array.new(256)

  pos.each do |pos|
    if pos + offset - 1 < str.length
      c = str[pos + offset - 1].ord
      counter[c] = [] if counter[c] == nil
      counter[c] << pos        
    end
  end

  counter
end

.decode_psy1_result(result, sa) ⇒ Object 



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# File 'lib/trace_visualization/repetitions_psy.rb', line 77

def self.decode_psy1_result(result, sa)
  repetitions = []

  result.each do |item|
    positions = (item[:i] .. item[:j]).collect { |idx| sa[idx] }
    repetitions << TraceVisualization::Data::Repetition.new(item[:lcp], positions.sort)
  
  end
  
  repetitions
end

.le_letter(l1, l2) ⇒ Object 



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# File 'lib/trace_visualization/repetitions_psy.rb', line 73

def self.le_letter(l1, l2)
  (l1 == TraceVisualization::TERMINATION_CHAR || l1 != l2) ? TraceVisualization::TERMINATION_CHAR : l1
end

.naive(str, l) ⇒ Object

The naive approach to finding repetitions in the string. Time complexity: О(n^2)



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# File 'lib/trace_visualization/repetitions.rb', line 6

def self.naive(str, l)
  result = Array.new(l + 1) { [] }
  result[0] << Array.new(str.length) {|idx| idx + 1 }

  for i in 1 .. l
    result[i - 1].each do |item|
      counter = char_counter_inc(str, item, i - 1)
      counter.each do |positions|
        result[i] << positions if positions != nil && positions.size > 1
      end
    end
  end

  result[l].sort
end

.naive_all(str, p_min) ⇒ Object

The naive approach to finding repetitions in the string. Time complexity: О(n^2)



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# File 'lib/trace_visualization/repetitions.rb', line 24

def self.naive_all(str, p_min)
  result = []

  result << []
  result[0] << Array.new(str.length) {|idx| idx + 1 }

  idx = 1
  while true
    result << []
  
    result[idx - 1].each do |item|
      counter = char_counter_inc(str, item, idx - 1)
      counter.each do |positions|
        if positions != nil && positions.size > 1
          result[idx] << positions
          result[idx - 1].delete_if { |item| item == positions }
        end
      end
    end
  
    break if result.last.size == 0
  
    idx += 1
  end

  result[p_min ... -1] || []
end

.psy1(data, p_min, decode_result = true) ⇒ Object

Computes all the complete nonextendible repeats using PSY1 algorithm

Parameters:

  • data (Array) —

    Array of objects

  • p_min (Integer) —

    The minimum number of positions in which we have repetition

  • decode_result (Boolean) (defaults to: true)

Raises:

  • (ArgumentError) 


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# File 'lib/trace_visualization/repetitions_psy.rb', line 13

def self.psy1(data, p_min, decode_result = true)
  raise ArgumentError, 'Data is empty' if data == nil || data.size == 0
  
  sa  = TraceVisualization::SuffixArray.effective(data)
  lcp = TraceVisualization::LongestCommonPrefix.effective(data, sa, data.size)
  bwt = TraceVisualization::BurrowsWheelerTransform.bwt(data, sa, data.size)
  
  result = psy1_original(lcp, bwt, p_min, data.length)
  result = decode_psy1_result(result, sa) if decode_result
  
  result
end

.psy1_original(_LCP, _BWT, p_min, n) ⇒ Object

PSY1 computes all the complete nonextendible repeats in ‘str’ of length p >= p_min. Complexity: Theta(n)

Article: Fast Optimal Algorithms for Computing All the Repeats is a String by Simon J. Puglisi, William F. Smyth, Munina Yusufu



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# File 'lib/trace_visualization/repetitions_psy.rb', line 32

def self.psy1_original(_LCP, _BWT, p_min, n)
  result = []

  lcp = -1
  lb = 0
  bwt1 = _BWT[0]
        
  _LB = []
  _LB.push(:lcp => lcp, :lb => lb, :bwt => bwt1)
        
  for j in 0 ... n
    lb = j
          
    lcp  = j + 1 < n ? _LCP[j + 1] : -1
    bwt2 = j + 1 < n ? _BWT[j + 1] : TraceVisualization::TERMINATION_CHAR
          
    bwt = le_letter(bwt1, bwt2)
    bwt1 = bwt2
          
    while _LB.last()[:lcp] > lcp
      prev = _LB.pop()
                  
      if prev[:bwt] == TraceVisualization::TERMINATION_CHAR && prev[:lcp] >= p_min
        result.push(:lcp => prev[:lcp], :i => prev[:lb], :j => j)
      end
                  
      lb = prev[:lb]
      _LB.last()[:bwt] = le_letter(prev[:bwt], _LB.last()[:bwt])
      bwt = le_letter(prev[:bwt], bwt)
    end
          
    if _LB.last()[:lcp] == lcp
      _LB.last()[:bwt] = le_letter(_LB.last()[:bwt], bwt)
    else
      _LB.push(:lcp => lcp, :lb => lb, :bwt => bwt)
    end
  end

  result    
end