Update README.md

README.md

@@ -1,11 +1,11 @@
 # gsa-is
 
-gSAIS and gSACA-K are suffix array construction algorithms for string collections. 
+gSAIS and gSACA-K are suffix array (SA) construction algorithms for string collections. 
 
 ## Introduction
 
 gSAIS and gSACA-K [1, 2] extend the linear-time suffix sorting algorithms SAIS
-[3] and SACA-K [4] to compute the suffix array for a string collection,
+[3] and SACA-K [4] to compute SA for string collections,
 maintaining their theoretical bounds and improving their practical performance.
 
 Moreover, gSAIS and gSACA-K can also compute the LCP-array (LCP) and the
@@ -28,7 +28,7 @@ An ANSI C Compiler (e.g. GNU GCC)
 /** @brief Computes the suffix array SA (LCP, DA) of T^cat in s[0..n-1]
  *
  *  @param s    input concatenated string, using separators s[i]=1 and with s[n-1]=0
- *  @param SA   suffix array 
+ *  @param SA   Suffix array 
  *  @param LCP  LCP array 
  *  @param DA   Document array
  *  @param n    string length
@@ -39,8 +39,8 @@ int gsacak(unsigned char *s, uint_t *SA, int_t *LCP, int_t *DA, uint_t n);
 
 /** @brief Computes the suffix array SA (LCP, DA) of T^cat in s[0..n-1]
  *
- *  @param s    input concatenated string, with s[n-1]=0
- *  @param SA   suffix array 
+ *  @param s    input concatenated string, using separators s[i]=1 and with s[n-1]=0
+ *  @param SA   Suffix array 
  *  @param LCP  LCP array 
  *  @param DA   Document array
  *  @param n    string length
@@ -151,4 +151,4 @@ Please, if you use this tool in an academic setting cite the following paper:
 
 ## Thanks
 
-Thanks to [Giovanni Manzini](https://github.com/giovmanz) and [Giovanna Rosone](https://github.com/giovannarosone) by helpful suggestions and debugging.
+Thanks to [Giovanni Manzini](https://github.com/giovmanz), [Giovanna Rosone](https://github.com/giovannarosone) and René de R. Sacramento by helpful suggestions and debugging.

gsacak.h

@@ -1,3 +1,5 @@
+// vim: noai:ts=2:sw=2
+
 /* 
  * Authors: Felipe A. Louza, Simon Gog, Guilherme P. Telles
  * contact: [email protected]
@@ -92,19 +94,25 @@ int sacak_int(int_text *s, uint_t *SA, uint_t n, uint_t k);
 /** @brief Computes the suffix array SA (LCP, DA) of T^cat in s[0..n-1]
  *
  *  @param s		input concatenated string, using separators s[i]=1 and with s[n-1]=0
- *  @param SA		suffix array 
+ *  @param SA		Suffix array 
  *  @param LCP	LCP array 
  *  @param DA		Document array
- *  @param n	string length
+ *  @param n		String length
  *  
  *  @return depth of the recursive calls.
  */
 int gsacak(unsigned char *s, uint_t *SA, int_t *LCP, int_da *DA, uint_t n);
 
 /** @brief Computes the suffix array SA (LCP, DA) of T^cat in s[0..n-1]
  *
- *  @param s    input concatenated string, with s[n-1]=0
- *  @param K	alphabet size
+ *  @param s		input concatenated string, using separators s[i]=1 and with s[n-1]=0
+ *  @param SA		Suffix array 
+ *  @param LCP	LCP array 
+ *  @param DA		Document array
+ *  @param n		String length
+ *  @param K		Alphabet size
+ *
+ *  @return depth of the recursive calls.
  */
 int gsacak_int(int_text *s, uint_t *SA, int_t *LCP, int_da *DA, uint_t n, uint_t k);
 

gsais.h

@@ -1,3 +1,5 @@
+// vim: noai:ts=2:sw=2
+
 /* 
  * Authors: Felipe A. Louza, Simon Gog, Guilherme P. Telles
  * contact: [email protected]
@@ -75,9 +77,9 @@ typedef uint_t int_da;
 /** @brief computes the suffix array of string s[0..n-1] 
  *
  *  @param s	input string with s[n-1]=0
- *  @param SA 	suffix array 
+ *  @param SA suffix array 
  *  @param n	string length
- *  @return -1 if an error occured, otherwise the depth of the recursive calls.
+ *  @return		-1 if an error occured, otherwise the depth of the recursive calls.
  */
 int sais(unsigned char *s, uint_t *SA, uint_t n);
 
@@ -91,20 +93,27 @@ int sais_int(int_text *s, uint_t *SA, uint_t n, uint_t k);
 
 /** @brief Computes the suffix array SA (LCP, DA) of T^cat in s[0..n-1]
  *
- *  @param s    input concatenated string, using separators s[i]=1 and with s[n-1]=0
- *  @param SA 	suffix array 
- *  @param LCP 	LCP array 
- *  @param DA 	Document array
- *  @param n	string length
- *  
+ *  @param s		input concatenated string, using separators s[i]=1 and with s[n-1]=0
+ *  @param SA		Suffix array 
+ *  @param LCP	LCP array 
+ *  @param DA		Document array
+ *  @param n		String length
+ *  @param K		alphabet size
+ *
  *  @return depth of the recursive calls.
  */
 int gsais(unsigned char *s, uint_t *SA, int_t *LCP, int_da *DA, uint_t n);
 
 /** @brief Computes the suffix array SA (LCP, DA) of T^cat in s[0..n-1]
  *
- *  @param s    input concatenated string, with s[n-1]=0
- *  @param K	alphabet size
+ *  @param s		input concatenated string, using separators s[i]=1 and with s[n-1]=0
+ *  @param SA		Suffix array 
+ *  @param LCP	LCP array 
+ *  @param DA		Document array
+ *  @param n		String length
+ *  @param K		Alphabet size
+ *
+ *  @return depth of the recursive calls.
  */
 int gsais_int(int_text *s, uint_t *SA, int_t *LCP, int_da *DA, uint_t n, uint_t k);
 

test.c

@@ -5,15 +5,21 @@
 #include "gsacak.h"
 #include "experiments/external/malloc_count/malloc_count.h" //memory counter
 
+#ifndef DEBUG
+	#define DEBUG 0
+#endif
+
 int main(int argc, char *argv[]){
 
-	printf("sizeof(int_t) = %zu bytes\n", sizeof(int_t));
+	#if DEBUG
+		printf("sizeof(int_t) = %zu bytes\n", sizeof(int_t));
+	#endif
+
 	unsigned char *Text;
 	uint_t n=0;
 
 	// intput data
 	if(argc>=2){
-
 		//concatenate all strings s_1, s_2, .., s_d in s_1$s_2$..%s_d$#
 		int i = 2, sum=0;
 		for(; i<= argc; i++){
@@ -31,33 +37,18 @@ int main(int argc, char *argv[]){
 		printf("N = %d\n", n);
 	}
 	else{
-		unsigned char *S[3] = {"banana", "anaba", "anan"};
-		//unsigned char *S[3] = {"a", "", "c"};
-		int i, sum=0;
-		for(i=0; i< 3; i++){
-			sum += strlen((S[i]))+1;
-		}
-		n = sum+1;
-		Text = malloc(n*sizeof(unsigned char));
-		sum=0;
-		for(i=0; i< 3; i++){
-			sscanf(S[i], "%s", &Text[sum]);
-			sum += strlen((S[i]))+1;
-			Text[sum-1]=1;//separator
-		}
-		Text[n-1]=0;
-		printf("N = %d\n", n);
+		fprintf(stderr, "Please, insert at least one string.\n");
+		exit(-1);
 	}	
 
 	int i, j;
-	printf("Text = ");
+	printf("T^{cat} = ");
 	for(i=0;i<n-1;i++){
 		if(Text[i]==1) printf("$");
 		else printf("%c", Text[i]);
 	}
 	printf("#\n");
 
-/**/
 	// allocate
 	uint_t *SA = (uint_t *)malloc(n * sizeof(uint_t));
 	int_t *LCP = (int_t *)malloc(n * sizeof(int_t));
@@ -79,7 +70,6 @@ int main(int argc, char *argv[]){
 	    printf("#\n");
 	}
 
-
 	// deallocate
 	free(SA);
 	free(DA);