Suffix Array

Pattern Searching AlgorithmsAlgorithmsData Structure

From a given string, we can get all possible suffixes. After sorting the suffixes in lexicographical order, we can get the suffix array. Suffix arrays can also be formed using suffix trees. By using the DFS traversal of suffix trees, we can get suffix arrays. Suffix arrays are helpful to find suffixes in linear time. We can also find substrings using suffix array by using binary search type procedure.

The time complexity is O(m log n)

Input and Output

Main String: “BANANA”, Pattern: “NAN”
Pattern found at position: 2


fillSuffixArray (text, suffArray)

Input: The main string

Output: The array of suffixes

   n := text Length
   define suffix array as allSuffix of size n

   for i := 0 to n-1, do
      allSuffix[i].index := i
      allSuffix[i].suff := substring of text from (i to end)

   sort the allSuffix array
   store indexes of all suffix array in suffArray.

suffixArraySearch (text, pattern, suffArray)

Input: The main string, the pattern and the suffix array

Output − the location where patterns are found

   patLen := size of pattern
   strLen := size of text
   left := 0
   right := strLen -1

   while left <= right, do
      mid := left + (right - left)/2
      tempStr := substring of text from suffArray[mid] to end
      result := compare tempStr and pattern upto pattern length.

      if result = 0, then
         print the location
      if res < 0, then
         right := mid – 1
         left := mid +1


using namespace std;

struct suffix {
   int index;
   string suff;

int strCompare(string st1, string st2, int n) {
   int i = 0;
   while(n--) {
      if(st1[i] != st2[i])
         return st1[i] - st2[i];
   return 0;

bool comp(suffix suff1, suffix suff2) {     //compare two strings for sorting
      return true;
   return false;

void fillSuffixArray(string mainString, int suffArr[]) {
   int n = mainString.size();
   suffix allSuffix[n];    //array to hold all suffixes

   for(int i = 0; i<n; i++) {
      allSuffix[i].index = i;
      allSuffix[i].suff = mainString.substr(i);    //from ith position to end

   sort(allSuffix, allSuffix+n, comp);
   for(int i = 0; i<n; i++)
      suffArr[i] = allSuffix[i].index;    //indexes of all sorted suffix

void suffixArraySearch(string mainString, string pattern, int suffArr[], int array[], int *index) {
   int patLen = pattern.size();
   int strLen = mainString.size();
   int left = 0, right = strLen - 1;    //left and right for binary search

   while(left <= right) {
      int mid = left + (right - left)/2;
      string tempStr = mainString.substr(suffArr[mid]);
      int result = strCompare(pattern,tempStr, patLen);
      if(result == 0) {    //the pattern is found
        array[(*index)] = suffArr[mid];

      if(result < 0)
         right = mid -1;
         left = mid +1;

int main() {
   string mainString = "BANANA";
   string pattern = "NAN";
   int locArray[mainString.size()];
   int index = -1;

   int suffArr[mainString.size()];
   fillSuffixArray(mainString,  suffArr);
   suffixArraySearch(mainString, pattern, suffArr, locArray, &index);
   for(int i = 0; i <= index; i++) {
      cout << "Pattern found at position: " << locArray[i]<<endl;


Pattern found at position: 2
Published on 09-Jul-2018 15:12:11