Suffix Tree Application 1 Substring Check (original) (raw)

`// A C program for substring check using Ukkonen's Suffix // Tree Construction #include <bits/stdc++.h> using namespace std; #define MAX_CHAR 256

struct SuffixTreeNode { struct SuffixTreeNode* children[MAX_CHAR];

// pointer to other node via suffix link
struct SuffixTreeNode* suffixLink;

/*(start, end) interval specifies the edge, by which the
 node is connected to its parent node. Each edge will
 connect two nodes,  one parent and one child, and
 (start, end) interval of a given edge  will be stored
 in the child node. Let's say there are two nods A and B
 connected by an edge with indices (5, 8) then this
 indices (5, 8) will be stored in node B. */
int start;
int* end;

/*for leaf nodes, it stores the index of suffix for
  the path  from root to leaf*/
int suffixIndex;

};

typedef struct SuffixTreeNode Node;

char text[100]; // Input string Node* root = NULL; // Pointer to root node

/lastNewNode will point to newly created internal node, waiting for it's suffix link to be set, which might get a new suffix link (other than root) in next extension of same phase. lastNewNode will be set to NULL when last newly created internal node (if there is any) got it's suffix link reset to new internal node created in next extension of same phase. / Node lastNewNode = NULL; Node activeNode = NULL;

/activeEdge is represented as an input string character index (not the character itself)/ int activeEdge = -1; int activeLength = 0;

// remainingSuffixCount tells how many suffixes yet to // be added in tree int remainingSuffixCount = 0; int leafEnd = -1; int* rootEnd = NULL; int* splitEnd = NULL; int size = -1; // Length of input string

Node* newNode(int start, int* end) { Node* node = (Node*)malloc(sizeof(Node)); int i; for (i = 0; i < MAX_CHAR; i++) node->children[i] = NULL;

/*For root node, suffixLink will be set to NULL
For internal nodes, suffixLink will be set to root
by default in  current extension and may change in
next extension*/
node->suffixLink = root;
node->start = start;
node->end = end;

/*suffixIndex will be set to -1 by default and
  actual suffix index will be set later for leaves
  at the end of all phases*/
node->suffixIndex = -1;
return node;

}

int edgeLength(Node* n) { if (n == root) return 0; return *(n->end) - (n->start) + 1; }

int walkDown(Node* currNode) { /activePoint change for walk down (APCFWD) using Skip/Count Trick (Trick 1). If activeLength is greater than current edge length, set next internal node as activeNode and adjust activeEdge and activeLength accordingly to represent same activePoint/ if (activeLength >= edgeLength(currNode)) { activeEdge += edgeLength(currNode); activeLength -= edgeLength(currNode); activeNode = currNode; return 1; } return 0; }

void extendSuffixTree(int pos) { /Extension Rule 1, this takes care of extending all leaves created so far in tree/ leafEnd = pos;

/*Increment remainingSuffixCount indicating that a
new suffix added to the list of suffixes yet to be
added in tree*/
remainingSuffixCount++;

/*set lastNewNode to NULL while starting a new phase,
 indicating there is no internal node waiting for
 it's suffix link reset in current phase*/
lastNewNode = NULL;

// Add all suffixes (yet to be added) one by one in tree
while (remainingSuffixCount > 0) {

    if (activeLength == 0)
        activeEdge = pos; // APCFALZ

    // There is no outgoing edge starting with
    // activeEdge from activeNode
    if (activeNode->children[text[activeEdge]]
        == NULL) {
        // Extension Rule 2 (A new leaf edge gets
        // created)
        activeNode->children[text[activeEdge]]
            = newNode(pos, &leafEnd);

        /*A new leaf edge is created in above line
         starting from  an existing node (the current
         activeNode), and if there is any internal node
         waiting for it's suffix link get reset, point
         the suffix link from that last internal node to
         current activeNode. Then set lastNewNode to
         NULL indicating no more node waiting for suffix
         link reset.*/
        if (lastNewNode != NULL) {
            lastNewNode->suffixLink = activeNode;
            lastNewNode = NULL;
        }
    }
    // There is an outgoing edge starting with
    // activeEdge from activeNode
    else {
        // Get the next node at the end of edge starting
        // with activeEdge
        Node* next
            = activeNode->children[text[activeEdge]];
        if (walkDown(next)) // Do walkdown
        {
            // Start from next node (the new activeNode)
            continue;
        }
        /*Extension Rule 3 (current character being
          processed is already on the edge)*/
        if (text[next->start + activeLength]
            == text[pos]) {
            // If a newly created node waiting for it's
            // suffix link to be set, then set suffix
            // link of that waiting node to current
            // active node
            if (lastNewNode != NULL
                && activeNode != root) {
                lastNewNode->suffixLink = activeNode;
                lastNewNode = NULL;
            }

            // APCFER3
            activeLength++;
            /*STOP all further processing in this phase
            and move on to next phase*/
            break;
        }

        /*We will be here when activePoint is in the
        middle of the edge being traversed and current
        character being processed is not  on the edge
        (we fall off the tree). In this case, we add a
        new internal node and a new leaf edge going out
        of that new node. This is Extension Rule 2,
        where a new leaf edge and a new internal node
        get created*/
        splitEnd = (int*)malloc(sizeof(int));
        *splitEnd = next->start + activeLength - 1;

        // New internal node
        Node* split = newNode(next->start, splitEnd);
        activeNode->children[text[activeEdge]] = split;

        // New leaf coming out of new internal node
        split->children[text[pos]]
            = newNode(pos, &leafEnd);
        next->start += activeLength;
        split->children[text[next->start]] = next;

        /*We got a new internal node here. If there is
          any internal node created in last extensions
          of same phase which is still waiting for it's
          suffix link reset, do it now.*/
        if (lastNewNode != NULL) {
            /*suffixLink of lastNewNode points to
              current newly created internal node*/
            lastNewNode->suffixLink = split;
        }

        /*Make the current newly created internal node
          waiting for it's suffix link reset (which is
          pointing to root at present). If we come
          across any other internal node (existing or
          newly created) in next extension of same
          phase, when a new leaf edge gets added (i.e.
          when Extension Rule 2 applies is any of the
          next extension of same phase) at that point,
          suffixLink of this node will point to that
          internal node.*/
        lastNewNode = split;
    }

    /* One suffix got added in tree, decrement the count
      of suffixes yet to be added.*/
    remainingSuffixCount--;
    if (activeNode == root
        && activeLength > 0) // APCFER2C1
    {
        activeLength--;
        activeEdge = pos - remainingSuffixCount + 1;
    }
    else if (activeNode != root) // APCFER2C2
    {
        activeNode = activeNode->suffixLink;
    }
}

}

void print(int i, int j) { int k; for (k = i; k <= j; k++) printf("%c", text[k]); }

// Print the suffix tree as well along with setting suffix // index So tree will be printed in DFS manner Each edge // along with it's suffix index will be printed void setSuffixIndexByDFS(Node* n, int labelHeight) { if (n == NULL) return;

if (n->start != -1) // A non-root node
{
    // Print the label on edge from parent to current
    // node Uncomment below line to print suffix tree
    // print(n->start, *(n->end));
}
int leaf = 1;
int i;
for (i = 0; i < MAX_CHAR; i++) {
    if (n->children[i] != NULL) {
        // Uncomment below two lines to print suffix
        // index
        // if (leaf == 1 && n->start != -1)
        //   printf(" [%d]\n", n->suffixIndex);

        // Current node is not a leaf as it has outgoing
        // edges from it.
        leaf = 0;
        setSuffixIndexByDFS(
            n->children[i],
            labelHeight + edgeLength(n->children[i]));
    }
}
if (leaf == 1) {
    n->suffixIndex = size - labelHeight;
    // Uncomment below line to print suffix index
    // printf(" [%d]\n", n->suffixIndex);
}

}

void freeSuffixTreeByPostOrder(Node* n) { if (n == NULL) return; int i; for (i = 0; i < MAX_CHAR; i++) { if (n->children[i] != NULL) { freeSuffixTreeByPostOrder(n->children[i]); } } if (n->suffixIndex == -1) free(n->end); free(n); }

/Build the suffix tree and print the edge labels along with suffixIndex. suffixIndex for leaf edges will be >= 0 and for non-leaf edges will be -1/ void buildSuffixTree() { size = strlen(text); int i; rootEnd = (int*)malloc(sizeof(int)); *rootEnd = -1;

/*Root is a special node with start and end indices as
-1, as it has no parent from where an edge comes to
root*/
root = newNode(-1, rootEnd);

activeNode = root; // First activeNode will be root
for (i = 0; i < size; i++)
    extendSuffixTree(i);
int labelHeight = 0;
setSuffixIndexByDFS(root, labelHeight);

}

int traverseEdge(char* str, int idx, int start, int end) { int k = 0; // Traverse the edge with character by character // matching for (k = start; k <= end && str[idx] != '\0'; k++, idx++) { if (text[k] != str[idx]) return -1; // mo match } if (str[idx] == '\0') return 1; // match return 0; // more characters yet to match }

int doTraversal(Node* n, char* str, int idx) { if (n == NULL) { return -1; // no match } int res = -1; // If node n is not root node, then traverse edge // from node n's parent to node n. if (n->start != -1) { res = traverseEdge(str, idx, n->start, *(n->end)); if (res != 0) return res; // match (res = 1) or no match (res // = -1) } // Get the character index to search idx = idx + edgeLength(n); // If there is an edge from node n going out // with current character str[idx], traverse that edge if (n->children[str[idx]] != NULL) return doTraversal(n->children[str[idx]], str, idx); else return -1; // no match }

void checkForSubString(char* str) { int res = doTraversal(root, str, 0); if (res == 1) printf("Pattern <%s> is a Substring\n", str); else printf("Pattern <%s> is NOT a Substring\n", str); }

// driver program to test above functions int main(int argc, char* argv[]) { strcpy(text, "THIS IS A TEST TEXT$"); buildSuffixTree();

checkForSubString("TEST");
checkForSubString("A");
checkForSubString(" ");
checkForSubString("IS A");
checkForSubString(" IS A ");
checkForSubString("TEST1");
checkForSubString("THIS IS GOOD");
checkForSubString("TES");
checkForSubString("TESA");
checkForSubString("ISB");

// Free the dynamically allocated memory
freeSuffixTreeByPostOrder(root);

return 0;

}

`// A C program for substring check using Ukkonen's Suffix // Tree Construction #include <stdio.h> #include <stdlib.h> #include <string.h> #define MAX_CHAR 256