Merge branch 'ZhangYou0122-master' into develop

Makefile

@@ -68,8 +68,9 @@ PROGRAMS =  m_based_demo \
 			bubble_sort_demo \
 			selection_sort_demo	\
 			8queue_demo \
-			palindrome_demo	\
-			suffix_array_demo
+			palindrome_demo \
+			suffix_array_demo \
+			suffix_tree_demo
 
 all: $(PROGRAMS)
 

include/suffix_tree.h

@@ -0,0 +1,310 @@
+#include <string>
+//#include <tr1/unordered_map>
+#include <limits>
+#include <map>
+#include <vector>
+#include <iostream>
+#include <stdexcept>
+
+using std::vector;
+using std::string;
+using std::map;
+using std::make_pair;
+using std::cout;
+using std::endl;
+using std::out_of_range;
+using std::ostream;
+//typedef tr1::unordered_map map;
+
+// TODO: upgrade it to process trace. Rule: char-->elem  string-->elem_list
+class SuffixTree
+{
+public:
+	// active point is initialized as (root, None, 0), remainder initialized as 1
+	SuffixTree(string str):test_str(str), pos(0), root(test_str), active_point(&root, 0, 0), remainder(0), ls() {}
+	int construct(void);
+
+	// return -1 if no such sub exist, return the beginning postion of this substring in thr original string if it exist
+	int search(string sub);
+
+	// return the length of the longest prefix of sub which can be matched in suffix tree
+	template <class Iterator>
+	Iterator inc_search(Iterator sub)
+	{
+		typedef typename Iterator::value_type T;	// extract real type
+
+		Iterator result = sub;
+		Node* node = &root;
+		Edge* edge = NULL;
+		int pos = 0;	// the iter's pos at edge
+		int edge_len = -1;
+		bool flag = true;
+
+
+		while (flag) {
+			if (edge == NULL) {
+				edge = node->find_edge(*result);	
+				if (edge == NULL) {
+					flag = false;
+				}
+				else {
+					result++;
+					pos = 1; // the second element of the edge
+					edge_len = edge->length();
+				}
+			}
+			else {
+				if (pos >= edge_len) {
+					node = edge->endpoint;
+					edge = NULL;
+					edge_len = 0;
+				}
+				else {
+					if (*result == (*edge)[pos]) {
+						result++;
+						pos++;
+					}
+					else
+						flag = false;
+				}
+			}
+		}
+
+		return result;
+	}
+
+	int print_tree(void);
+private:
+	string test_str;
+
+	struct Node;
+	typedef struct Node Node;
+
+	struct Edge{
+		// the begin and end pos of this edge, note that INT_MAX stands for #(the changing end pos of this entire string)
+		int begin, end;
+		// Is there a better way to find test_str?
+		string& test_node_str;
+
+		Node * endpoint;
+
+		Edge(int b, int e, string& str):
+			test_node_str(str) 
+		{
+			begin = b;
+			end = e;
+			endpoint = NULL;
+			//std::cout << "Edge initialized" << std::endl;
+		}
+
+		void change_edge(int b, int e)
+		{
+			begin = b;
+			end = e;
+		}
+
+		int length(void) 
+		{
+
+			if (end > test_node_str.size())
+				return test_node_str.size() - begin;
+			else
+				return end - begin + 1; 
+		}
+
+		// needed by map
+		friend bool operator<(const Edge& me, const Edge& other)
+		{
+			return me.begin < other.begin;
+		}
+
+		char operator[](int i)
+		{
+			i += begin;
+			if (i > end)
+				throw out_of_range("Edge [] out of range.");
+
+			return test_node_str[i];
+		}
+
+		friend ostream& operator<<(ostream& os, Edge& edge)
+		{
+			int end = edge.test_node_str.size()-1;
+			if (end >= edge.end)
+				end = edge.end;
+
+			char c;
+			for (int i=edge.begin; i<=end; i++) {
+				c = edge.test_node_str[i];
+				os << c;
+			}
+			if (end != edge.end)
+				os << '#';
+
+			return os;
+		}
+
+		bool is_none(void) { return begin == 0 && end == 0; }
+	};
+	typedef struct Edge Edge;
+
+	struct Node{
+		string& test_node_str;
+		map<int, int> testmap;
+		map<Edge*, bool> edges;
+		// find the edge quicky by storing the leading char of this edge
+		map<char, Edge*> findedges;
+		Node* suffix_link;
+
+		friend class LinkState;
+
+		Node(string& str) : 
+			test_node_str(str), suffix_link(NULL) { edges.clear(); findedges.clear(); }
+
+		void add_edge(Edge* edge) { 
+			if (edge->endpoint == NULL)
+				edge->endpoint = new Node(test_node_str);
+			make_pair(edge, true);
+			edges.insert(make_pair(edge, true)); 
+			findedges.insert(make_pair(test_node_str[edge->begin], edge));
+			//cout << "edge added. Now we have " << edges.size() << "edges." << endl;
+		}
+
+		void del_edge(Edge* edge) {
+			map<Edge*, bool>::iterator iter = edges.find(edge);
+
+			if (iter == edges.end())
+				throw out_of_range("edge don't exit");
+			else {
+				// note we should erase the findedges too
+				edges.erase(edge);
+				//cout << "delete" << (*edge)[0] << endl;
+				findedges.erase((*edge)[0]);
+				//cout << "edge deleted. Now we have " << edges.size() << "edges." << endl;
+			}
+
+		}
+
+		// find edge by the first char
+		Edge* find_edge(char c)
+		{
+			//cout << "finding edge";
+			map<char, Edge*>::iterator iter = findedges.find(c);
+			//cout << "founded?" << endl;
+			if (iter != findedges.end()) 
+				return iter->second;
+			else
+				return NULL;
+		}
+
+		bool isleaf() { return edges.empty(); }
+
+		bool operator==(Node& other)
+		{
+			return (this) == (&other);
+		}
+
+		friend ostream& operator<<(ostream& os, Node& node)
+		{
+			map<Edge*, bool>::iterator iter;
+			map<char, Edge*>::iterator iter_f;
+
+			for (iter=node.edges.begin(); iter!=node.edges.end(); ++iter)
+				os << iter->first << '\t';
+			os << endl;
+
+			for (iter_f=node.findedges.begin(); iter_f!=node.findedges.end(); ++iter_f)
+				os << iter_f->first << "-->" << iter_f->second << endl;
+
+			return os;
+		}
+	};
+	//typedef struct Node Node;
+
+	class ActivePoint{
+	public:
+		Node* active_node;
+		char active_edge;
+		int active_length;
+
+		ActivePoint(Node* node, char edge, int length): 
+			active_node(node), active_edge(edge), active_length(length) { std::cout << "ActivePoint initialized" << std::endl; }
+	};
+
+	Node root;
+	ActivePoint active_point;
+
+	Node* get_active_node(void) { return active_point.active_node; }
+	void set_active_node(Node* node) { active_point.active_node = node; cout << "Active node set as " << node << endl; }
+	char get_active_edge(void) { return active_point.active_edge; }
+	void set_active_edge(char edge) { active_point.active_edge = edge; }
+	int get_active_length(void) { return active_point.active_length; }
+	void set_active_length(int len) { active_point.active_length = len; }
+	void inc_active_len() { active_point.active_length++; }
+	void dec_active_len() { active_point.active_length--; }
+
+	// how many suffixes is to be inserted?
+	int remainder;
+	// how many characters inserted?
+	int pos;
+	char get_ele(int i) { return test_str[i]; }
+	// insert a char from pos to suffix tree
+	int insert();
+	int insert_rule1();
+	int insert_rule3();
+	int print_node(Node* node, int level);
+
+
+	Node* seperate_edge(Node * node, Edge* edge, int rule);
+
+	// check if we can change active node
+	void check_an(void)
+	{
+		Node* node = get_active_node();
+		Edge* edge = node->find_edge(get_active_edge());
+
+		if (edge == NULL)
+			return;
+
+		int edge_size = edge->end - edge->begin + 1;
+
+		// update
+		if (edge_size == get_active_length()) {
+			set_active_node(edge->endpoint);
+			set_active_edge(0);
+			set_active_length(0);
+		}
+	}
+
+	// this class indicate when shall we insert a suffix link
+	// ls should be a singleton
+	class LinkState
+	{
+		bool first;
+
+		Node* prev, *curr;
+
+	public:
+		LinkState() : first(true), prev(NULL), curr(NULL) {}
+
+		void ins_link(Node* node)
+		{
+			prev = curr;
+			curr = node;
+
+			if (!first) {
+				prev->suffix_link = curr;
+				cout << "Suffix link added from prev " << prev << " to curr " << curr << endl;
+			}
+
+			first = false;
+		}
+
+		void clear(void)
+		{
+			first = true;
+			prev = curr = NULL;
+		}
+	};
+	LinkState ls;
+};