View source for Talk:Ukkonen’s suffix tree construction

This isn't the easiest of tasks and I suspect that most of us will prefer to translate the C code rather than start from scratch.
 
Unfortunately, the C code [https://www.geeksforgeeks.org/suffix-tree-application-3-longest-repeated-substring/ here] which is the most relevant for completing this task doesn't compile due to the index of the 'children' array being missing in a number of places.

Luckily, I found a C++ translation of most of this code [https://github.com/ganesh-k13/suffix-tree/blob/master/src/SuffixTree.cpp on GitHub] and this has enabled me to fill in the gaps in the C code so that it now compiles and produces the desired results. Here's the final version:

<lang C>// A C program to implement Ukkonen's Suffix Tree Construction 
// And then find Longest Repeated Substring 
#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 represeted 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[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 existng 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 curent 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[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); 
} 
  
void doTraversal(Node *n, int labelHeight, int* maxHeight,  
int* substringStartIndex) 
{ 
    if(n == NULL) 
    { 
        return; 
    } 
    int i=0; 
    if(n->suffixIndex == -1) //If it is internal node 
    { 
        for (i = 0; i < MAX_CHAR; i++) 
        { 
            if(n->children[i] != NULL) 
            { 
                doTraversal(n->children[i], labelHeight + 
                                edgeLength(n->children[i]), maxHeight, 
                                 substringStartIndex); 
            } 
        } 
    } 
    else if(n->suffixIndex > -1 &&  
                (*maxHeight < labelHeight - edgeLength(n))) 
    { 
        *maxHeight = labelHeight - edgeLength(n); 
        *substringStartIndex = n->suffixIndex; 
    } 
} 
  
void getLongestRepeatedSubstring() 
{ 
    int maxHeight = 0; 
    int substringStartIndex = 0; 
    doTraversal(root, 0, &maxHeight, &substringStartIndex); 
//    printf("maxHeight %d, substringStartIndex %d\n", maxHeight, 
//           substringStartIndex); 
    printf("Longest Repeated Substring in %s is: ", text); 
    int k; 
    for (k=0; k<maxHeight; k++) 
        printf("%c", text[k + substringStartIndex]); 
    if(k == 0) 
        printf("No repeated substring"); 
    printf("\n"); 
} 
   
// driver program to test above functions 
int main(int argc, char *argv[]) 
{ 
    strcpy(text, "GEEKSFORGEEKS$");  
    buildSuffixTree();     
    getLongestRepeatedSubstring(); 
    //Free the dynamically allocated memory 
    freeSuffixTreeByPostOrder(root); 
  
    strcpy(text, "AAAAAAAAAA$");  
    buildSuffixTree();     
    getLongestRepeatedSubstring(); 
    //Free the dynamically allocated memory 
    freeSuffixTreeByPostOrder(root); 
  
    strcpy(text, "ABCDEFG$");  
    buildSuffixTree();     
    getLongestRepeatedSubstring(); 
    //Free the dynamically allocated memory   
    freeSuffixTreeByPostOrder(root); 
  
    strcpy(text, "ABABABA$");  
    buildSuffixTree();     
    getLongestRepeatedSubstring(); 
    //Free the dynamically allocated memory 
    freeSuffixTreeByPostOrder(root); 
  
    strcpy(text, "ATCGATCGA$");  
    buildSuffixTree();     
    getLongestRepeatedSubstring(); 
    //Free the dynamically allocated memory 
    freeSuffixTreeByPostOrder(root); 
  
    strcpy(text, "banana$");  
    buildSuffixTree();     
    getLongestRepeatedSubstring(); 
    //Free the dynamically allocated memory 
    freeSuffixTreeByPostOrder(root); 
  
    strcpy(text, "abcpqrabpqpq$");  
    buildSuffixTree();     
    getLongestRepeatedSubstring(); 
    //Free the dynamically allocated memory 
    freeSuffixTreeByPostOrder(root); 
  
    strcpy(text, "pqrpqpqabab$");  
    buildSuffixTree();     
    getLongestRepeatedSubstring(); 
    //Free the dynamically allocated memory 
    freeSuffixTreeByPostOrder(root); 
  
    return 0; 
}</lang> 
--[[User:PureFox|PureFox]] ([[User talk:PureFox|talk]]) 00:46, 25 April 2019 (UTC)

:This should be on the main page under <nowiki>=={{header|C}}=={{incomplete|C|Pi part missing}}</nowiki> [?] --[[User:Petelomax|Pete Lomax]] ([[User talk:Petelomax|talk]]) 12:04, 2 August 2020 (UTC)
::I put it on here rather than the main page because neither Nigel (the task author) nor myself wrote it and I didn't want it to look as though we had. It is presumably the copyright of the original author and/or the GeeksForGeeks site.

::I thought twice about even putting it on here but I decided to do so as a lot more people know C than Go and I didn't really think anyone would mind if I just filled in the missing bits.--[[User:PureFox|PureFox]] ([[User talk:PureFox|talk]]) 12:54, 2 August 2020 (UTC)

::: "copyright": I added a comment/link to the geeksforgeeks page, more as a common courtesy thing than expecting there be any reasonable objection. "didn't want it to look as though": a simple comment/link would explain that best. I get your reservations: when I first penned that comment I began with "Shouldn't this be on the main page" before realising that either it should, or it shouldn't be on this site at all... (of course it should). --[[User:Petelomax|Pete Lomax]] ([[User talk:Petelomax|talk]]) 23:37, 2 August 2020 (UTC)