Ok, so I took the code from here and adapted it to keep track of and print the longest repeated substring. Just run it using JUnit.
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import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.junit.Test;
public class SuffixTree {
@Test
public void sampleUsage() {
AbstractSuffixTree tree = new SimpleSuffixTree(
"LLLLLLLLAATAALLLLALLLLLLAATAALLLATLLLLLAATAALLAALLLLLAATAALL");
System.out.println("Longest repeating substring "
+ tree.best.printResult() + " repetitions=" + tree.best.visits
+ " length=" + tree.best.stringDepth);
}
}
abstract class AbstractSuffixTree {
SuffixTreeNode best;
String text = null;
SuffixTreeNode root = null;
int inputAlphabetSize = -1;
AbstractSuffixTree(String text) {
if (text.length() > 0 && text.charAt(text.length() - 1) == '$') {
this.text = text;
} else {
this.text = text + "$";
}
}
}
class SimpleSuffixTree extends AbstractSuffixTree {
public SimpleSuffixTree(String text) {
super(text);
constructTree();
}
private void constructTree() {
super.root = new SuffixTreeNode(this);
best = root;
char[] s = super.text.toCharArray();
for (int i = 0; i < s.length; i++) {
List<String> suffixList = new ArrayList<String>();
for (int k = i; k < s.length; k++) {
suffixList.add(s[k] + "");
}
super.root.addSuffix(suffixList, i + 1);
}
}
}
class CompactSuffixTree extends AbstractSuffixTree {
public CompactSuffixTree(SimpleSuffixTree simpleSuffixTree) {
super(simpleSuffixTree.text);
super.root = compactNodes(simpleSuffixTree.root, 0);
super.best = simpleSuffixTree.best;
}
private SuffixTreeNode compactNodes(SuffixTreeNode node, int nodeDepth) {
node.nodeDepth = nodeDepth;
for (SuffixTreeNode child : node.children) {
while (child.children.size() == 1) {
SuffixTreeNode grandchild = child.children.iterator().next();
child.incomingEdge.label += ", "
+ grandchild.incomingEdge.label;
child.stringDepth += grandchild.incomingEdge.label.length();
child.children = grandchild.children;
// for (SuffixTreeNode grandchild : child.children)
grandchild.parent = node;
}
child = compactNodes(child, nodeDepth + 1);
}
return node;
}
}
class SuffixTreeNode {
AbstractSuffixTree tree;
SuffixTreeEdge incomingEdge = null;
int nodeDepth = -1;
int label = -1;
Collection<SuffixTreeNode> children = null;
SuffixTreeNode parent = null;
int stringDepth;
int id = 0;
public static int c;
public int visits = 1;
public SuffixTreeNode(AbstractSuffixTree tree, SuffixTreeNode parent,
String incomingLabel, int depth, int label, int id) {
children = new ArrayList<SuffixTreeNode>();
incomingEdge = new SuffixTreeEdge(incomingLabel, label);
nodeDepth = depth;
this.label = label;
this.parent = parent;
stringDepth = parent.stringDepth + incomingLabel.length();
this.id = id;
this.tree = tree;
}
public SuffixTreeNode(AbstractSuffixTree tree) {
children = new ArrayList<SuffixTreeNode>();
nodeDepth = 0;
label = 0;
this.tree = tree;
}
public void addSuffix(List<String> suffix, int pathIndex) {
SuffixTreeNode insertAt = this;
insertAt = search(this, suffix);
insert(insertAt, suffix, pathIndex);
}
private SuffixTreeNode search(SuffixTreeNode startNode, List<String> suffix) {
if (suffix.isEmpty()) {
throw new IllegalArgumentException(
"Empty suffix. Probably no valid simple suffix tree exists for the input.");
}
Collection<SuffixTreeNode> children = startNode.children;
for (SuffixTreeNode child : children) {
if (child.incomingEdge.label.equals(suffix.get(0))) {
suffix.remove(0);
child.visits++;
if (child.visits > 1
&& child.stringDepth > tree.best.stringDepth) {
tree.best = child;
}
if (suffix.isEmpty()) {
return child;
}
return search(child, suffix);
}
}
return startNode;
}
private void insert(SuffixTreeNode insertAt, List<String> suffix,
int pathIndex) {
for (String x : suffix) {
SuffixTreeNode child = new SuffixTreeNode(tree, insertAt, x,
insertAt.nodeDepth + 1, pathIndex, id);
insertAt.children.add(child);
insertAt = child;
}
}
public String toString() {
StringBuilder result = new StringBuilder();
String incomingLabel = this.isRoot() ? "" : this.incomingEdge.label;
for (int i = 1; i <= this.nodeDepth; i++)
result.append("\t");
if (this.isRoot()) {
c = 1;
this.id = 1;
} else {
this.id = c;
result.append(this.parent.id + " -> ");
result.append(this.id + "[label=\"" + incomingLabel + "\"]" + "("
+ visits + "," + (stringDepth) + ")" + ";\n");
}
for (SuffixTreeNode child : children) {
c++;
child.id = c;
result.append(child.toString());
}
return result.toString();
}
public String printResult() {
if (parent == null) {
return "";
} else {
return this.parent.printResult() + this.incomingEdge.label;
}
}
public boolean isRoot() {
return this.parent == null;
}
public boolean isLeaf() {
return children.size() == 0;
}
}
class SuffixTreeEdge {
String label = null;
@SuppressWarnings("unused")
private int branchIndex = -1;
public SuffixTreeEdge(String label, int branchIndex) {
this.label = label;
this.branchIndex = branchIndex;
}
}
Output:
Longest repeating substring
LLLLLLAATAALLL repetitions=2 length=14
EDIT: response to your comments.
Currently I simply keep track of the longest repeating SuffixTreeNode (it's a field in AbstractSuffixTree). You could modify this so it keeps track of a SortedQueue of nodes, ordered by their stringDepth.
