Suffix Trees: Java Code as Separate Classes

In this post - Suffix Trees: Java Code as Separate Classes.
Download java source code.

Please refer previous posts about Suffix Trees:

• Suffix Trees: Refactored Java Code
• Suffix Trees: Java Ukkonen's Algorithm

Class diagram:

contains and indexOf functions:

public boolean contains(String str) {
    return indexOf(str) >= 0;
}
   public int indexOf(String str) {
    if (str.length() == 0)
        return -1;
   
    int index = -1;
    Node node = root;
   
    int i = 0;
    while (i<str.length()) {
        if ((node == null) || (i == text.length()))
            return -1;
   
        Edge edge = node.findEdge(str.charAt(i));
        if (edge == null)
            return -1;
   
        index = edge.getBeginIndex()-i;
        i++;
   
        for(int j=edge.getBeginIndex()+1; j<=edge.getEndIndex(); j++) {
            if (i == str.length())
                break;
            if (text.charAt(j) != str.charAt(i))
                return -1;
            i++;
        }
        node = edge.getEndNode();
    }
    return index;
}

Future plans:

• Generalized Suffix Tree;
• Longest Common SubString;

More information about Suffix Trees Use Cases you can find in:

• Suffix Trees and Applications
• Algorithms on strings, trees, and sequences: computer science and computational biology