Java Program to Implement Suffix Array

A Suffix Array is a fundamental data structure used in string processing and computational biology. It represents an array of all suffixes of a given string, sorted lexicographically. Suffix arrays find applications in pattern matching, substring search, text compression, and bioinformatics, among others.

Organization of Suffix Array

A suffix array is essentially an array of integers, each representing the starting index of a suffix in the original string. The array is sorted in lexicographical order, so it provides an efficient way to search for substrings within the string. Here's an illustration:

Let's take an example string "banana":

The corresponding suffix array for "banana" would be: [ 5 , 3 , 1 , 0 , 4 , 2 ]

Implementation of Suffix Array

The implementation of a suffix array can be done efficiently using various algorithms such as the Manber-Myers algorithm, the Skew algorithm, or the SA-IS algorithm. Here's a simplified explanation of how it can be implemented:

• Construct Suffixes : Generate all suffixes of the given string.
• Sort Suffixes : Sort the generated suffixes lexicographically.
• Construct Suffix Array : Create an array that stores the indices of the sorted suffixes.

Basic Operations and Complexity

Program to Implement Suffix Array

Below is the Program to Implement Suffix Array:

// Java Program to Implement Suffix Array
import java.util.*;

// Driver Class
class SuffixArray {
      public static int[] constructSuffixArray(String text) {
        // Get the length of the input text
        int n = text.length();
    
        // Create an array of Integer objects to store indices
        Integer[] helper = new Integer[n];
    
        // Initialize the array with indices from 0 to n-1
        for (int i = 0; i < n; i++)
            helper[i] = i;

        // Sort the array of indices based on the suffixes
        Arrays.sort(sa, (a, b) -> text.substring(a)
                    .compareTo(text.substring(b)));
    
        // Convert the Integer array to an int array
        int[] suffixArray = new int[n];
        for (int i = 0; i < n; i++)
              suffixArray[i] = helper[i];

        return suffixArray;
    }

      public static void main(String[] args) {
        // Example input text
        String text = "banana$";

        // Construct the suffix array
        int[] suffixArray = constructSuffixArray(text);

        // Print the suffix array
        System.out.println("Suffix Array for \"" + text
                           + "\": " + Arrays.toString(suffixArray));
    }
}

Output

Applications of Suffix Array

• Pattern Matching: Efficiently find occurrences of substrings within a text.
• Substring Search: Quickly locate substrings within large texts.
• Bioinformatics: Analyze DNA sequences for patterns and mutations.
• Text Compression: Used in algorithms like Burrows-Wheeler Transform.