304 lines
11 KiB
Java
304 lines
11 KiB
Java
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/*This is a Java Program to implement Suffix Tree. A suffix tree is a compressed trie containing all the suffixes of the given text as their keys and positions in the text as their values. Suffix tree allows a particularly fast implementation of many important string operations. The construction of such a tree for the string S takes time and space linear in the length of S. Once constructed, several operations can be performed quickly, for instance locating a substring in S, locating a substring if a certain number of mistakes are allowed, locating matches for a regular expression pattern etc. Suffix trees also provided one of the first linear-time solutions for the longest common substring problem. These speedups come at a cost: storing a string’s suffix tree typically requires significantly more space than storing the string itself. This program is based on Mark Nelson’s implementation of Ukkonen’s algorithm.*/
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/*
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* Java Program to Implement Suffix Tree
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*/
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import java.io.*;
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/** Class Node **/
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class Node
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{
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public int suffix_node;
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public static int Count = 1;
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/** Constructor **/
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public Node()
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{
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suffix_node = -1;
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}
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}
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/** Class Suffix Tree **/
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class SuffixTree
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{
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private static final int MAX_LENGTH = 1000;
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private static final int HASH_TABLE_SIZE = 2179;
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private char[] T = new char[ MAX_LENGTH ];
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private int N;
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private Edge[] Edges ;
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private Node[] Nodes ;
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private Suffix active;
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/** Class Suffix **/
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class Suffix
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{
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public int origin_node;
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public int first_char_index;
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public int last_char_index;
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/** Constructor **/
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public Suffix(int node, int start, int stop )
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{
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origin_node = node ;
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first_char_index = start ;
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last_char_index = stop;
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}
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/** Function Implicit **/
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public boolean Implicit()
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{
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return first_char_index > last_char_index;
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}
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/** Function Explicit **/
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public boolean Explicit()
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{
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return first_char_index > last_char_index;
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}
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/** Function Canonize()
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* A suffix in the tree is denoted by a Suffix structure
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* that denotes its last character. The canonical
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* representation of a suffix for this algorithm requires
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* that the origin_node by the closest node to the end
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* of the tree. To force this to be true, we have to
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* slide down every edge in our current path until we
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* reach the final node
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**/
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public void Canonize()
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{
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if (!Explicit() )
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{
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Edge edge = Find( origin_node, T[ first_char_index ] );
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int edge_span = edge.last_char_index - edge.first_char_index;
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while ( edge_span <= ( last_char_index - first_char_index ) )
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{
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first_char_index = first_char_index + edge_span + 1;
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origin_node = edge.end_node;
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if ( first_char_index <= last_char_index )
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{
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edge = Find( edge.end_node, T[ first_char_index ] );
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edge_span = edge.last_char_index - edge.first_char_index;
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}
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}
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}
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}
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}
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/** Class Edge **/
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class Edge
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{
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public int first_char_index;
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public int last_char_index;
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public int end_node;
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public int start_node;
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/** Constructor **/
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public Edge()
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{
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start_node = -1;
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}
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/** Constructor **/
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public Edge( int init_first, int init_last, int parent_node )
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{
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first_char_index = init_first;
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last_char_index = init_last;
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start_node = parent_node;
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end_node = Node.Count++;
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}
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/** function Insert ()
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* A given edge gets a copy of itself inserted into the table
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* with this function. It uses a linear probe technique, which
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* means in the case of a collision, we just step forward through
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* the table until we find the first unused slot.
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**/
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public void Insert()
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{
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int i = Hash( start_node, T[ first_char_index ] );
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while ( Edges[ i ].start_node != -1 )
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i = ++i % HASH_TABLE_SIZE;
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Edges[ i ] = this;
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}
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/** function SplitEdge ()
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* This function is called
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* to split an edge at the point defined by the Suffix argument
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**/
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public int SplitEdge( Suffix s )
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{
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Remove();
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Edge new_edge = new Edge( first_char_index, first_char_index + s.last_char_index - s.first_char_index, s.origin_node );
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new_edge.Insert();
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Nodes[ new_edge.end_node ].suffix_node = s.origin_node;
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first_char_index += s.last_char_index - s.first_char_index + 1;
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start_node = new_edge.end_node;
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Insert();
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return new_edge.end_node;
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}
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/** function Remove ()
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* This function is called to remove an edge from hash table
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**/
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public void Remove()
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{
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int i = Hash( start_node, T[ first_char_index ] );
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while ( Edges[ i ].start_node != start_node ||
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Edges[ i ].first_char_index != first_char_index )
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i = ++i % HASH_TABLE_SIZE;
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for ( ; ; )
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{
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Edges[ i ].start_node = -1;
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int j = i;
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for ( ; ; )
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{
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i = ++i % HASH_TABLE_SIZE;
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if ( Edges[ i ].start_node == -1 )
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return;
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int r = Hash( Edges[ i ].start_node, T[ Edges[ i ].first_char_index ] );
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if ( i >= r && r > j )
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continue;
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if ( r > j && j > i )
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continue;
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if ( j > i && i >= r )
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continue;
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break;
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}
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Edges[ j ] = Edges[ i ];
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}
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}
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}
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/** Constructor */
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public SuffixTree()
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{
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Edges = new Edge[ HASH_TABLE_SIZE ];
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for (int i = 0; i < HASH_TABLE_SIZE; i++)
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Edges[i] = new Edge();
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Nodes = new Node[ MAX_LENGTH * 2 ];
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for (int i = 0; i < MAX_LENGTH * 2 ; i++)
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Nodes[i] = new Node();
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active = new Suffix( 0, 0, -1 );
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}
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/** Function Find() - function to find an edge **/
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public Edge Find( int node, int c )
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{
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int i = Hash( node, c );
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for ( ; ; )
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{
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if ( Edges[ i ].start_node == node )
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if ( c == T[ Edges[ i ].first_char_index ] )
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return Edges[ i ];
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if ( Edges[ i ].start_node == -1 )
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return Edges[ i ];
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i = ++i % HASH_TABLE_SIZE;
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}
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}
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/** Function Hash() - edges are inserted into the hash table using this hashing function **/
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public static int Hash( int node, int c )
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{
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return (( node << 8 ) + c ) % HASH_TABLE_SIZE;
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}
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/** Function AddPrefix() - called repetitively, once for each of the prefixes of the input string **/
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public void AddPrefix( Suffix active, int last_char_index )
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{
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int parent_node;
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int last_parent_node = -1;
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for ( ; ; )
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{
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Edge edge;
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parent_node = active.origin_node;
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if ( active.Explicit() )
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{
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edge = Find( active.origin_node, T[ last_char_index ] );
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if ( edge.start_node != -1 )
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break;
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}
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else
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{
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edge = Find( active.origin_node, T[ active.first_char_index ] );
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int span = active.last_char_index - active.first_char_index;
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if ( T[ edge.first_char_index + span + 1 ] == T[ last_char_index ] )
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break;
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parent_node = edge.SplitEdge( active );
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}
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Edge new_edge = new Edge( last_char_index, N, parent_node );
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new_edge.Insert();
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if ( last_parent_node > 0 )
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Nodes[ last_parent_node ].suffix_node = parent_node;
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last_parent_node = parent_node;
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if ( active.origin_node == 0 )
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active.first_char_index++;
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else
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active.origin_node = Nodes[ active.origin_node ].suffix_node;
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active.Canonize();
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}
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if ( last_parent_node > 0 )
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Nodes[ last_parent_node ].suffix_node = parent_node;
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active.last_char_index++;
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active.Canonize();
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}
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/** Function to print all contents and details of suffix tree **/
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public void dump_edges(int current_n )
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{
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System.out.println(" Start End Suf First Last String\n");
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for ( int j = 0 ; j < HASH_TABLE_SIZE ; j++ )
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{
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Edge s = Edges[j];
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if ( s.start_node == -1 )
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continue;
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System.out.printf("%5d %5d %3d %5d %6d ", s.start_node, s.end_node, Nodes[ s.end_node ].suffix_node, s.first_char_index, s.last_char_index);
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int top;
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if ( current_n > s.last_char_index )
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top = s.last_char_index;
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else
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top = current_n;
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for ( int l = s.first_char_index ; l <= top; l++)
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System.out.print( T[ l ]);
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System.out.println();
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}
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}
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/** Main Function **/
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public static void main(String[] args) throws IOException
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{
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BufferedReader br = new BufferedReader(new InputStreamReader(System.in));
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System.out.println("Suffix Tree Test\n");
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System.out.println("Enter string\n");
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String str = br.readLine();
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/** Construct Suffix Tree **/
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SuffixTree st = new SuffixTree();
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st.T = str.toCharArray();
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st.N = st.T.length - 1;
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for (int i = 0 ; i <= st.N ; i++ )
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st.AddPrefix( st.active, i );
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st.dump_edges( st.N );
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}
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}
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/*
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Suffix Tree Test
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Enter string
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Start End Suf First Last String
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0 2 -1 1 9 anfoundry
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0 9 -1 7 9 dry
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0 4 -1 3 9 foundry
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0 7 0 2 2 n
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0 5 -1 4 9 oundry
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0 10 -1 8 9 ry
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0 1 -1 0 9 sanfoundry
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0 6 -1 5 9 undry
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0 11 -1 9 9 y
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7 8 -1 7 9 dry
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7 3 -1 3 9 foundry
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