programming-examples/java/Data_Structures/SuffixTree.java

import java.util.Random;

// See http://codeforces.ru/blog/entry/16780 for description
public class SuffixTree {
	static final String ALPHABET = "abcdefghijklmnopqrstuvwxyz0123456789\1\2";

	public static class Node {
		int begin;
		int end;
		int depth; // distance in characters from root to this node
		Node parent;
		Node[] children;
		Node suffixLink;

		Node(int begin, int end, int depth, Node parent) {
			this.begin = begin;
			this.end = end;
			this.parent = parent;
			this.depth = depth;
			children = new Node[ALPHABET.length()];
		}
	}

	public static Node buildSuffixTree(CharSequence s) {
		int n = s.length();
		byte[] a = new byte[n];
		for (int i = 0; i < n; i++) a[i] = (byte) ALPHABET.indexOf(s.charAt(i));
		Node root = new Node(0, 0, 0, null);
		Node node = root;
		for (int i = 0, tail = 0; i < n; i++, tail++) {
			Node last = null;
			while (tail >= 0) {
				Node ch = node.children[a[i - tail]];
				while (ch != null && tail >= ch.end - ch.begin) {
					tail -= ch.end - ch.begin;
					node = ch;
					ch = ch.children[a[i - tail]];
				}
				if (ch == null) {
					node.children[a[i]] = new Node(i, n, node.depth + node.end - node.begin, node);
					if (last != null) last.suffixLink = node;
					last = null;
				} else {
					byte afterTail = a[ch.begin + tail];
					if (afterTail == a[i]) {
						if (last != null) last.suffixLink = node;
						break;
					} else {
						Node splitNode = new Node(ch.begin, ch.begin + tail, node.depth + node.end - node.begin, node);
						splitNode.children[a[i]] = new Node(i, n, ch.depth + tail, splitNode);
						splitNode.children[afterTail] = ch;
						ch.begin += tail;
						ch.depth += tail;
						ch.parent = splitNode;
						node.children[a[i - tail]] = splitNode;
						if (last != null) last.suffixLink = splitNode;
						last = splitNode;
					}
				}
				if (node == root) {
					--tail;
				} else {
					node = node.suffixLink;
				}
			}
		}
		return root;
	}

	// random test
	public static void main(String[] args) {
		Random rnd = new Random(1);
		for (int step = 0; step < 100_000; step++) {
			int n1 = rnd.nextInt(10);
			int n2 = rnd.nextInt(10);
			String s1 = getRandomString(n1, rnd);
			String s2 = getRandomString(n2, rnd);
			// build generalized suffix tree
			String s = s1 + '\1' + s2 + '\2';
			Node tree = buildSuffixTree(s);
			lcsLength = 0;
			lcsBeginIndex = 0;
			// find longest common substring
			lcs(tree, s1.length(), s1.length() + s2.length() + 1);
			int res2 = slowLcs(s1, s2);
			if (lcsLength != res2) {
				System.err.println(s.substring(lcsBeginIndex - 1, lcsBeginIndex + lcsLength - 1));
				System.err.println(s1);
				System.err.println(s2);
				System.err.println(lcsLength + " " + res2);
				throw new RuntimeException();
			}
		}
	}

	static int lcsLength;
	static int lcsBeginIndex;

	// traverse suffix tree to find longest common substring
	public static int lcs(Node node, int i1, int i2) {
		if (node.begin <= i1 && i1 < node.end) {
			return 1;
		}
		if (node.begin <= i2 && i2 < node.end) {
			return 2;
		}
		int mask = 0;
		for (char f = 0; f < ALPHABET.length(); f++) {
			if (node.children[f] != null) {
				mask |= lcs(node.children[f], i1, i2);
			}
		}
		if (mask == 3) {
			int curLength = node.depth + node.end - node.begin;
			if (lcsLength < curLength) {
				lcsLength = curLength;
				lcsBeginIndex = node.begin;
			}
		}
		return mask;
	}

	static int slowLcs(String a, String b) {
		int[][] lcs = new int[a.length()][b.length()];
		int res = 0;
		for (int i = 0; i < a.length(); i++) {
			for (int j = 0; j < b.length(); j++) {
				if (a.charAt(i) == b.charAt(j))
					lcs[i][j] = 1 + (i > 0 && j > 0 ? lcs[i - 1][j - 1] : 0);
				res = Math.max(res, lcs[i][j]);
			}
		}
		return res;
	}

	static String getRandomString(int n, Random rnd) {
		return rnd.ints(n, 0, 3).mapToObj(i -> String.valueOf((char) (i + 'a'))).reduce("", (a, b) -> a + b);
	}
}