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SuffixTree.cpp
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SuffixTree.cpp
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#include "../include/SuffixTree.h"
SuffixTree::SuffixTree(string text) {
this->text = text;
root = NULL;
last_new_node = NULL;
active_node = NULL;
active_edge = -1;
active_length = 0;
remaining_suffix_count = 0;
leaf_end = -1;
root_end = NULL;
split_end = NULL;
size = -1; //Length of input string
size_sub_str = -1;
build_suffix_tree();
index_list.clear();
}
SuffixTree::SuffixTree(string doc, string query) {
this->text = doc+"#"+query+"$";
this->size_sub_str = doc.size();
root = NULL;
last_new_node = NULL;
active_node = NULL;
active_edge = -1;
active_length = 0;
remaining_suffix_count = 0;
leaf_end = -1;
root_end = NULL;
split_end = NULL;
size = -1;
build_suffix_tree();
index_list.clear();
}
SuffixTree::~SuffixTree() {
}
Node* SuffixTree::get_root() {
return root;
}
Node* SuffixTree::new_node(int start, int *end) {
Node *node = new Node(start, end);
node->set_suffix_link(root);
return node;
}
int SuffixTree::edge_length(Node *n) {
return n == root ? 0 : *(n->get_end()) - (n->get_start()) + 1;
}
int SuffixTree::walk_down(Node *currNode) {
if (active_length >= edge_length(currNode)) {
active_edge += edge_length(currNode);
active_length -= edge_length(currNode);
active_node = currNode;
return 1;
}
return 0;
}
void SuffixTree::extend_suffix_tree(int pos) {
leaf_end = pos;
remaining_suffix_count++;
last_new_node = NULL;
while(remaining_suffix_count > 0) {
if (active_length == 0)
active_edge = pos;
if (active_node->get_children(text[active_edge]) == NULL) {
active_node->set_children(text[active_edge], new_node(pos, &leaf_end));
if (last_new_node != NULL) {
last_new_node->set_suffix_link(active_node);
last_new_node = NULL;
}
}
else {
Node *next = active_node->get_children(text[active_edge]);
if (walk_down(next)) {
continue;
}
if (text[next->get_start() + active_length] == text[pos]) {
if(last_new_node != NULL && active_node != root) {
last_new_node->set_suffix_link(active_node);
last_new_node = NULL;
}
active_length++;
break;
}
split_end = new int;
*split_end = next->get_start() + active_length - 1;
Node *split = new_node(next->get_start(), split_end);
active_node->set_children(text[active_edge], split);
split->set_children(text[pos], new_node(pos, &leaf_end));
next->set_start(next->get_start()+active_length);
split->set_children(text[next->get_start()], next);
if (last_new_node != NULL) {
last_new_node->set_suffix_link(split);
}
last_new_node = split;
}
remaining_suffix_count--;
if (active_node == root && active_length > 0) {
active_length--;
active_edge = pos - remaining_suffix_count + 1;
}
else if (active_node != root) {
active_node = active_node->get_suffix_link();
}
}
}
void SuffixTree::set_suffix_index_by_DFS(Node *n, int labelHeight) {
if (n == NULL) return;
int leaf = 1;
int i;
for (i = 0; i < MAX_CHAR; i++) {
if (n->get_children(i) != NULL) {
//Current node is not a leaf as it has outgoing
//edges from it.
leaf = 0;
set_suffix_index_by_DFS(n->get_children(i), labelHeight + edge_length(n->get_children(i)));
}
}
if (leaf == 1) {
n->set_suffix_index(size - labelHeight);
}
}
void SuffixTree::free_suffix_tree_by_post_order(Node *n) {
if (n == NULL)
return;
int i;
for (i = 0; i < MAX_CHAR; i++) {
if (n->get_children(i) != NULL) {
free_suffix_tree_by_post_order(n->get_children(i));
}
}
if (n->get_suffix_index() == -1)
delete (n->get_end());
delete(n);
}
void SuffixTree::build_suffix_tree() {
size = text.size();
int i;
root_end = new int;
*root_end = - 1;
root = new_node(-1, root_end);
active_node = root; //First active_node will be root
for (i=0; i<size; i++)
extend_suffix_tree(i);
int labelHeight = 0;
set_suffix_index_by_DFS(root, labelHeight);
}
int SuffixTree::build_suffix_tree(const 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 SuffixTree::do_traversal_to_count_leaf(Node *n) {
if(n == NULL)
return 0;
if(n->get_suffix_index() > -1) {
index_list.push_back(n->get_suffix_index());
return 1;
}
int count = 0;
int i = 0;
for (i = 0; i < MAX_CHAR; i++)
{
if(n->get_children(i) != NULL)
{
count += do_traversal_to_count_leaf(n->get_children(i));
}
}
return count;
}
int SuffixTree::count_leaf(Node *n) {
if(n == NULL)
return 0;
return do_traversal_to_count_leaf(n);
}
int SuffixTree::do_traversal(Node *n, const char* str, int idx) {
if(n == NULL)
return -1;
int res = -1;
if(n->get_start() != -1) {
res = build_suffix_tree(str, idx, n->get_start(), *(n->get_end()));
if(res == -1)
return -1;
if(res == 1) {
if(n->get_suffix_index() > -1) {
index_list.push_back(n->get_suffix_index());
}
else
count_leaf(n);
return 1;
}
}
idx = idx + edge_length(n);
if(n->get_children(str[idx]) != NULL)
return do_traversal(n->get_children(str[idx]), str, idx);
else
return -1;
}
vector <int> SuffixTree::check_for_sub_string(const char* str) {
index_list.clear();
do_traversal(root, str, 0);
return index_list;
}
#if 1
vector <int> SuffixTree::get_LCS(int *max_height) {
int substring_start_index = 0;
do_traversal(root, 0, max_height, &substring_start_index);
index_list.clear();
if(*max_height == 0) {
return index_list;
}
else {
do_traversal(root, text.substr(substring_start_index, *max_height).c_str(), 0);
}
return index_list;
}
int SuffixTree::do_traversal(Node *n, int label_height, int* max_height, int* substring_start_index) {
if(n == NULL) {
return NULL;
}
int i=0;
int ret = -1;
if(n->get_suffix_index() < 0) {
for (i = 0; i < MAX_CHAR; i++) {
if(n->get_children(i) != NULL) {
ret = do_traversal(n->get_children(i), label_height + edge_length(n->get_children(i)), max_height, substring_start_index);
if(n->get_suffix_index() == -1)
n->set_suffix_index(ret);
else if((n->get_suffix_index() == -2 && ret == -3) || (n->get_suffix_index() == -3 && ret == -2) || n->get_suffix_index() == -4) {
n->set_suffix_index(-4);//Mark node as XY
//Keep track of deepest node
if(*max_height < label_height) {
*max_height = label_height;
*substring_start_index = *(n->get_end()) - label_height + 1;
}
}
}
}
}
else if(n->get_suffix_index() > -1 && n->get_suffix_index() < size_sub_str)//suffix of X
return -2;//Mark node as X
else if(n->get_suffix_index() >= size_sub_str)//suffix of Y
return -3;//Mark node as Y
return n->get_suffix_index();
}
#endif