1 文本格式

// A C program to implement Ukkonen's Suffix Tree Construction
// And then build generalized suffix tree
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#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. Lets 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 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] == NULL)
        {
            //Extension Rule 2 (A new leaf edge gets created)
            activeNode->children] =
                                        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];
            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 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] = split;

            //New leaf coming out of new internal node
            split->children] = newNode(pos, &leafEnd);
            next->start += activeLength;
            split->children] = 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 && text[k] != '#'; k++)
        printf("%c", text[k]);
    if(k<=j)
        printf("#");
}

//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
        print(n->start, *(n->end));
    }
    int leaf = 1;
    int i;
    for (i = 0; i < MAX_CHAR; i++)
    {
        if (n->children[i] != NULL)
        {
            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)
    {
        for(i= n->start; i<= *(n->end); i++)
        {
            if(text[i] == '#') //Trim unwanted characters
            {
                n->end = (int*) malloc(sizeof(int));
                *(n->end) = i;
            }
        }
        n->suffixIndex = size - labelHeight;
        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);

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

// driver program to test above functions
int main(int argc, char *argv[])
{
// strcpy(text, "xabxac#abcabxabcd$"); buildSuffixTree();
    strcpy(text, "xabxa#babxba$"); buildSuffixTree();
    return 0;
}

2 代码格式

// A C program to implement Ukkonen's Suffix Tree Construction
// And then build generalized suffix tree
#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#define MAX_CHAR 256struct SuffixTreeNode {struct SuffixTreeNode *children[MAX_CHAR];//pointer to other node via suffix linkstruct SuffixTreeNode *suffixLink;/*(start, end) interval specifies the edge, by which thenode is connected to its parent node. Each edge willconnect two nodes, one parent and one child, and(start, end) interval of a given edge will be storedin the child node. Lets say there are two nods A and Bconnected by an edge with indices (5, 8) then thisindices (5, 8) will be stored in node B. */int start;int *end;/*for leaf nodes, it stores the index of suffix forthe 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 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 stringNode *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 NULLFor internal nodes, suffixLink will be set to rootby default in current extension and may change innext extension*/node->suffixLink = root;node->start = start;node->end = end;/*suffixIndex will be set to -1 by default andactual suffix index will be set later for leavesat 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) usingSkip/Count Trick (Trick 1). If activeLength is greaterthan current edge length, set next internal node asactiveNode and adjust activeEdge and activeLengthaccordingly 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 allleaves created so far in tree*/leafEnd = pos;/*Increment remainingSuffixCount indicating that anew suffix added to the list of suffixes yet to beadded in tree*/remainingSuffixCount++;/*set lastNewNode to NULL while starting a new phase,indicating there is no internal node waiting forit's suffix link reset in current phase*/lastNewNode = NULL;//Add all suffixes (yet to be added) one by one in treewhile(remainingSuffixCount > 0) {if (activeLength == 0)activeEdge = pos; //APCFALZ// There is no outgoing edge starting with// activeEdge from activeNodeif (activeNode->children] == NULL){//Extension Rule 2 (A new leaf edge gets created)activeNode->children] =newNode(pos, &leafEnd);/*A new leaf edge is created in above line startingfrom an existing node (the current activeNode), andif there is any internal node waiting for it's suffixlink get reset, point the suffix link from that lastinternal node to current activeNode. Then set lastNewNodeto NULL indicating no more node waiting for suffix linkreset.*/if (lastNewNode != NULL){lastNewNode->suffixLink = activeNode;lastNewNode = NULL;}}// There is an outgoing edge starting with activeEdge// from activeNodeelse{// Get the next node at the end of edge starting// with activeEdgeNode *next = activeNode->children];if (walkDown(next))//Do walkdown{//Start from next node (the new activeNode)continue;}/*Extension Rule 3 (current character being processedis 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 nodeif(lastNewNode != NULL && activeNode != root){lastNewNode->suffixLink = activeNode;lastNewNode = NULL;}//APCFER3activeLength++;/*STOP all further processing in this phaseand move on to next phase*/break;}/*We will be here when activePoint is in middle ofthe edge being traversed and current characterbeing processed is not on the edge (we fall offthe tree). In this case, we add a new internal nodeand a new leaf edge going out of that new node. Thisis Extension Rule 2, where a new leaf edge and a newinternal node get created*/splitEnd = (int*) malloc(sizeof(int));*splitEnd = next->start + activeLength - 1;//New internal nodeNode *split = newNode(next->start, splitEnd);activeNode->children] = split;//New leaf coming out of new internal nodesplit->children] = newNode(pos, &leafEnd);next->start += activeLength;split->children] = next;/*We got a new internal node here. If there is anyinternal node created in last extensions of samephase which is still waiting for it's suffix linkreset, do it now.*/if (lastNewNode != NULL){/*suffixLink of lastNewNode points to current newlycreated internal node*/lastNewNode->suffixLink = split;}/*Make the current newly created internal node waitingfor it's suffix link reset (which is pointing to rootat present). If we come across any other internal node(existing or newly created) in next extension of samephase, when a new leaf edge gets added (i.e. whenExtension Rule 2 applies is any of the next extensionof same phase) at that point, suffixLink of this nodewill point to that internal node.*/lastNewNode = split;}/* One suffix got added in tree, decrement the count ofsuffixes 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 && text[k] != '#'; k++)printf("%c", text[k]);if(k<=j)printf("#");
}//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 nodeprint(n->start, *(n->end));}int leaf = 1;int i;for (i = 0; i < MAX_CHAR; i++){if (n->children[i] != NULL){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){for(i= n->start; i<= *(n->end); i++){if(text[i] == '#') //Trim unwanted characters{n->end = (int*) malloc(sizeof(int));*(n->end) = i;}}n->suffixIndex = size - labelHeight;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 rootfor (i=0; i<size; i++)extendSuffixTree(i);int labelHeight = 0;setSuffixIndexByDFS(root, labelHeight);//Free the dynamically allocated memoryfreeSuffixTreeByPostOrder(root);
}// driver program to test above functions
int main(int argc, char *argv[])
{
// strcpy(text, "xabxac#abcabxabcd$"); buildSuffixTree();strcpy(text, "xabxa#babxba$"); buildSuffixTree();return 0;
}