Suffix array and search a substring in a string

Question

I found an implementation of suffix array in Ruby and changed it a bit. Here is what I have:

class SuffixArray
    def initialize(str)
        @string = str
        @suffix_array = []
        (0...str.length).each do |i|
            substring = @string[i...str.length]
            @suffix_array << {:suffix=>substring, :index => i}
        end

        @sorted_suffix_array = @suffix_array.sort {|x,y| x[:suffix] <=> y[:suffix]}
    end

    def print_sorted
      @sorted_suffix_array.each {|item| puts "#{item[:index]}=>#{item[:suffix]}"}
      puts "total=>#{@sorted_suffix_array.size()}"
    end

    def print_unsorted
      @suffix_array.each {|item| puts "#{item[:index]}=>#{item[:suffix]}"}
      puts "total=>#{@suffix_array.size()}"
    end

    def find_substring(substring)
        low = 0
        high = @sorted_suffix_array.length
        while(low <= high) do
            mid = (low + high) / 2
            comparison = @sorted_suffix_array[mid][:suffix]#[0..substring.length]
      if comparison > substring
        high = mid - 1
      elsif comparison < substring
        low = mid + 1
      else 
        return @sorted_suffix_array[mid][:index]
      end
        end
    end

end

It works good but it doesn't find all substrings I want. For example

a = SuffixArray.new("there is a man who likes dogs")
puts a.find_substring("man") #won't be found
puts a.find_substring("who likes dogs") #will be found
puts a.find_substring("o likes dogs") #will be found

How do I change the algorithm to make it find all the substrings I want?

You could maintain the LCP of the suffix array . (Longest common Prefix) - If you search for prefixes of suffixes of the strings in the suffix array- you should find the substrings! - — Arvind
– Arvind, Commented Nov 20, 2012 at 4:52
You shouldn't call it "suffix" anymore if you're looking for arbitrary substrings instead of just suffixes.. — Mark Reed
– Mark Reed, Commented Nov 20, 2012 at 13:02

wye.bee · Accepted Answer · 2012-11-20 06:47:14Z

1

Your code was almost correct. I made some small modifications and it works.

def find_substring(substring)
  low = 0
  high = @sorted_suffix_array.length-1
  while(low <= high) do
    mid = (low + high) / 2
    comparison = @sorted_suffix_array[mid][:suffix][0...substring.length]
    if comparison > substring
      high = mid - 1
    elsif comparison < substring
      low = mid + 1
    else 
      return @sorted_suffix_array[mid][:index]
    end
  end
end

answered Nov 20, 2012 at 6:47

wye.bee

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2 Comments

Alan Coromano Over a year ago

I actually already had that. Why do you use @sorted_suffix_array.length-1 instead of @sorted_suffix_array.length?

wye.bee Over a year ago

When doing a binary search low and high must be valid indices. Check the code on the wikipedia page on the binary search algorithm.

bluetwin · Accepted Answer · 2013-03-29 04:36:42Z

1

For others; reference, Here's one without holding the sub-string in a hash

Gist: https://gist.github.com/bluetwin/5268722

class SuffixArray

  attr_reader :suf, :string

  def initialize(string)
    @string = string
    @suf = (0..string.size-1).sort_by{|i|@string[i..-1]}
  end

  def substring(idx)
    @string[@suf[idx][email protected]]
  end

  def bsearch(str)
    low = 0
    high = @suf.length-1
    found = nil
    while(low <= high) do
      mid = (low + high) / 2
      comp = substring(mid)
      if comp > str
        high = mid - 1
      elsif comp < str
        low = mid + 1
      else
       found = comp
       low = high + 1
      end
    end
    found
  end

end

edited Mar 29, 2013 at 4:36

answered Mar 29, 2013 at 4:27

bluetwin

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