如何找到最长的公共 substring

Question

What is the best available algorithm to search the longest common substring? Strings contains 16000+ characters and alphabet is ACDT.

1. Boyer–Moore–Horspool - time taken is very high
2. Rabin-Karp - worst than 1st one
3. Suffix tree - 2d array memory overflow

Any other methods or modifications? Actually I want to calculate the average common substring of two genomes.

Answer 1

Gnomes or genomes?!

See here . Dynamic programming may be the route to take?

Also note that the first two algorithms you've listed are for string searching.

Answer 2

public class LongestCommonSubS {
    public static void main(String[] args) throws IOException {
        String str1 = "Koushikpaul";
        String str2 = "asdfgoushqwertikpauzxcv";
        StringBuilder sub1 = new StringBuilder();
        for (int i = 0; i < str1.length(); i++) {
            StringBuilder sub2 = new StringBuilder();
            int k = 0;
            for (int j = 0; j < str2.length() & (i + k) < str1.length(); j++) {
                if (str1.charAt(i + k) == str2.charAt(j)) {
                    sub2.append(str2.charAt(j));
                    k++;
                } else if (k > 0 & str1.charAt(i + k) != str2.charAt(j))break;
            }
            if (sub2.length() > sub1.length())sub1 = sub2;
        }
        System.out.println(sub1);
    }
}