add kmp algorithms

Author: xtaci

Makefile

@@ -51,7 +51,8 @@ PROGRAMS =  m_based \
 			simhash_demo \
 			imath_demo \
 			random_demo \
-			k-means_demo
+			k-means_demo \
+			kmp_demo
 
 all: $(PROGRAMS)
 

include/kmp.h

@@ -0,0 +1,86 @@
+/*******************************************************************************
+ * ALGORITHM IMPLEMENTAIONS
+ *
+ *  /\  |  _   _  ._ o _|_ |_  ._ _   _ 
+ * /--\ | (_| (_) |  |  |_ | | | | | _> 
+ *         _|                      
+ *
+ * KNUTH-MORRIS-PRATT ALGORITHMS
+ *
+ * Features:
+ * Complexity is O(n + k), where n is the target string length, 
+ * and k is the pattern length
+ *
+ * http://en.wikipedia.org/wiki/Knuth%E2%80%93Morris%E2%80%93Pratt_algorithm
+ *
+ ******************************************************************************/
+
+#ifndef __KMP_H__
+#define __KMP_H__
+#include <string.h>
+
+namespace alg {
+	static void kmp_table(const char *W, int * T, int len);
+	/**
+	 * S -> the text to be searched
+	 * W -> the word to search 
+	 * return the position where W is found S
+	 */
+	static int kmp_search(const char * S, const char * W) {
+		int LEN_S = strlen(S);
+		int LEN_W = strlen(W);
+
+		int m = 0;
+		int i = 0;
+		int * T = new int[LEN_W];
+		
+		kmp_table(W,T, LEN_W);
+
+		while (m+i < LEN_S) {
+			if (W[i] == S[m+i]) {
+				if (i == LEN_W -1) {
+					return m;
+				}
+				i++;
+			} else {
+				m = m+i-T[i];
+				if (T[i] > -1) {
+					i = T[i];
+				} else {
+					i = 0;
+				}
+			}
+		}
+		return -1;
+	}
+
+	/**
+	 * build a table for the word to be searched  
+	 * eg:
+	 * i		0 	1 	2 	3 	4 	5 	6
+	 * W[i] 	A 	B 	C 	D 	A 	B 	D
+	 * T[i] 	-1 	0 	0 	0 	0 	1 	2
+	 */
+	static void kmp_table(const char *W, int * T, int len) {
+		int pos = 2; // the current position we are computing in T 
+		int cnd = 0; // the next character of the current candidate substring
+		T[0] = -1;
+		T[1] = 0;
+
+		while (pos < len) {
+			// first case: the substring continues
+			if (W[pos-1] == W[cnd]) {
+				cnd++;
+				T[pos] = cnd;
+				pos++;
+			} else if (cnd >0) { // second case: it doesn't, but we can fall back
+				cnd = T[cnd];
+			} else { // third case: we have run out of candidates.  Note cnd = 0
+				T[pos] = 0;
+				pos++;
+			}
+		}
+	}
+}
+
+#endif //

src/kmp_demo.cpp

@@ -0,0 +1,39 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <time.h>
+
+#include "kmp.h"
+using namespace alg;
+int main(void)
+{
+	srand(time(NULL));
+	char * S = (char*)malloc(10000);
+	char * W = (char*)malloc(6);
+
+	memset(S,0, 10000);
+	memset(W,0, 10);
+
+	// random genrate a pattern for A, G, C,T
+	const char P[] = {'A', 'G','C','T'};
+
+	for (int i=0;i<10000;i++) {
+		int k = rand()%4;
+		S[i] = P[k];
+	}
+
+	for (int i=0;i<6;i++) {
+		int k = rand()%4;
+		W[i] = P[k];
+	}
+
+	// do a search for W from S
+	int pos = kmp_search(S, W);
+
+	printf("text:\n%s\n", S);
+	if (pos > 0) {
+		printf("found %s from text, pos %d\n", W, pos);
+	} else {
+		printf("cannot found %s from text\n", W);
+	}
+}