Cosmetic changes

README.md

@@ -22,7 +22,7 @@ An ANSI C Compiler (e.g. GNU GCC)
 
 ## API
 
-**gsacak.h**
+**gsacak.h** (the same for gsais.h)
 
 ```c
 /** @brief Computes the suffix array SA (LCP, DA) of T^cat in s[0..n-1]
@@ -66,8 +66,8 @@ int gsacak_int(uint_t *s, uint_t *SA, int_t *LCP, int_t *DA, uint_t n, uint_t k)
 **Compilation:**
 
 ```sh
-gcc -c sacak-lcp.c experiments/external/malloc_count.c
-gcc test.c -o test sacak-lcp.o malloc_count.o -ldl
+gcc -c gsacak.c experiments/external/malloc_count/malloc_count.c
+gcc test.c -o test gsacak.o malloc_count.o -ldl
 ```
 
 **Run a test:**
@@ -80,7 +80,7 @@ gcc test.c -o test sacak-lcp.o malloc_count.o -ldl
 
 ```c
 sizeof(int_t) = 4 bytes
-sum = 18
+N = 18
 Text = banana$anaba$anan$#
 i	SA	DA	LCP	BWT	suffixes
 0	18	3	0	$	#
@@ -136,7 +136,7 @@ Please, if you use this tool in an academic setting cite the following paper:
 
 \[1\] Louza, F. A., Gog, S., Telles, G. P., Induced Suffix Sorting for String Collections. In Proc. DCC, pp. 43-58, 2016, [IEEE](http://ieeexplore.ieee.org/document/7786148/).
 
-\[2\] Louza, F. A., Gog, S., and Telles, G. P., Inducing enhanced suffix arrays for string collections. Theor. Comput. Sci., pages 1–34.
+\[2\] Louza, F. A., Gog, S., Telles, G. P., Inducing enhanced suffix arrays for string collections. Theor. Comput. Sci., (to appear), pages 1-34.
 
 \[3\] Nong G., Zhang S., Chan W. H., Two efficient algorithms for linear time suffix array construction, IEEE Trans. Comput., vol. 60, no. 10, pp. 1471–1484, 2011
 

experiments/Makefile

@@ -30,7 +30,7 @@ LIBOBJ = \
 	lib/lcp_array.o\
 	lib/document_array.o\
 	external/malloc_count/malloc_count.o\
-	src/gsais.o\
+	../gsais.o\
 	../gsacak.o
 
 

experiments/README.md

@@ -17,7 +17,9 @@ make
 
 --
 
-**Settings:**
+**Settings**
+
+**SA:**
 
 MODE parameter specifies which algorithm is called by main.c:
 
@@ -32,7 +34,7 @@ SAIS\* and SACA-K\* are versions that receive an integer alphabet as input.
 
 --
 
-**LCP-array:**
+**SA and LCP:**
 
 MODE parameter:
 
@@ -51,7 +53,7 @@ make run MODE=6 LCP_COMPUTE=1
 
 --
 
-**Document-array:**
+**SA and DA:**
 
 MODE parameter:
 
@@ -80,6 +82,20 @@ SDV=1 uses a sparse bitvector.
 
 --
 
+**SA, LCP and DA:**
+
+MODE parameter:
+
+* 11:  gSAIS+LCP+DA
+* 12:  gSACA-K+LCP+DA
+
+```sh
+make run MODE=11
+make run MODE=12
+```
+
+--
+
 **Validate:**
 
 One can check if the output produced is correct:

experiments/main.c

@@ -18,7 +18,7 @@
 #include "lib/lcp_array.h"
 #include "lib/document_array.h"
 #include "external/malloc_count/malloc_count.h"
-#include "src/gsais.h"
+#include "../gsais.h"
 #include "../gsacak.h"
 
 #ifndef DEBUG
@@ -51,9 +51,9 @@ clock_t c_start=0, c_total=0;
 	sscanf(argv[7], "%u", &VALIDATE);
 	sscanf(argv[8], "%u", &OUTPUT);
 
-	if(MODE==7 || MODE==8 || MODE==11) LCP_COMPUTE=1;
-	if(MODE==9 || MODE==10 || MODE==11) DA_COMPUTE=1;
-	if(MODE>11) return 1;
+	if(MODE==7 || MODE==8  || MODE==11 || MODE==12) LCP_COMPUTE=1;
+	if(MODE==9 || MODE==10 || MODE==11 || MODE==12) DA_COMPUTE=1;
+	if(MODE>12) return 1;
 
 	file_chdir(c_dir);
 
@@ -124,7 +124,8 @@ clock_t c_start=0, c_total=0;
 
 	switch(MODE){
 		case 1: printf("## SAIS (int) ##\n");
-			depth = SAIS((int_t*)str_int, SA, n, 256+k, sizeof(int_t), 0);
+			//depth = SAIS((int_t*)str_int, SA, n, 256+k, sizeof(int_t), 0);
+			depth = sais_int((int_t*)str_int, (uint_t*)SA, n, 256+k);
 			break;
 
 		case 2: printf("## SACA_K (int) ##\n"); 
@@ -133,7 +134,8 @@ clock_t c_start=0, c_total=0;
 			break;
 
 		case 3: printf("## SAIS (char) ##\n");
-			depth = SAIS((int_t*)str, SA, n, 256, sizeof(char), 0);
+			//depth = SAIS((int_t*)str, SA, n, 256, sizeof(char), 0);
+			depth = sais(str, (uint_t*)SA, n);
 			break;
 
 		case 4: printf("## SACA_K (char) ##\n"); 
@@ -142,7 +144,8 @@ clock_t c_start=0, c_total=0;
 			break;
 
 		case 5: printf("## gSAIS ##\n"); 
-			depth = gSAIS((unsigned char*)str, SA, n, 256, sizeof(char), 0, 1);//separator=1
+			//depth = gSAIS((unsigned char*)str, SA, n, 256, sizeof(char), 0, 1);//separator=1
+			depth = gsais((unsigned char*)str, (uint_t*)SA, NULL, NULL, n);
 			break;
 
  		case 6: printf("## gSACA_K ##\n"); 
@@ -151,7 +154,8 @@ clock_t c_start=0, c_total=0;
 			break;
 
  		case 7: printf("## gSAIS+LCP ##\n"); 
-			depth = gSAIS_LCP((unsigned char*)str, SA, LCP, n, 256, sizeof(char), 0, 1);//separator=1
+			//depth = gSAIS_LCP((unsigned char*)str, SA, LCP, n, 256, sizeof(char), 0, 1);//separator=1
+			depth = gsais((unsigned char*)str, (uint_t*)SA, LCP, NULL, n);
 			break;
 
  		case 8: printf("## gSACA_K+LCP ##\n"); 
@@ -160,14 +164,20 @@ clock_t c_start=0, c_total=0;
 			break;
 
  		case 9: printf("## gSAIS+DA ##\n"); 
-			depth = gSAIS_DA((unsigned char*)str, SA, DA, n, 256, sizeof(char), 0, 1);//separator=1
+			//depth = gSAIS_DA((unsigned char*)str, SA, DA, n, 256, sizeof(char), 0, 1);//separator=1
+			depth = gsais((unsigned char*)str, (uint_t*)SA, NULL, DA, n);
 			break;
 
  		case 10: printf("## gSACA_K+DA ##\n"); 
 			//depth = gSACA_K_DA((unsigned char*)str, (uint_t*)SA, DA, n, 256, sizeof(char), 0, 1);//separator=1
 			depth = gsacak((unsigned char*)str, (uint_t*)SA, NULL, DA, n);
 			break;
- 		case 11: printf("## gSACA_K+LCP+DA ##\n"); 
+
+ 		case 11: printf("## gSAIS+LCP+DA ##\n"); 
+			depth = gsais((unsigned char*)str, (uint_t*)SA, LCP, DA, n);
+			break;
+
+ 		case 12: printf("## gSACA_K+LCP+DA ##\n"); 
 			depth = gsacak((unsigned char*)str, (uint_t*)SA, LCP, DA, n);
 			break;
 
@@ -177,7 +187,7 @@ clock_t c_start=0, c_total=0;
 	fprintf(stderr,"%.6lf\n", time_stop(t_start, c_start));
 
 	//LCP array
-	if(LCP_COMPUTE && (MODE!=7 && MODE!=8 && MODE!=11)){
+	if(LCP_COMPUTE && (MODE!=7 && MODE!=8 && MODE!=11 && MODE!=12)){
 		time_start(&t_start, &c_start);
 		if(MODE==1 || MODE==2)
 			lcp_PHI_int((int_t*)str_int, SA, LCP, n, sizeof(int_t));
@@ -188,7 +198,7 @@ clock_t c_start=0, c_total=0;
 	}
 
 	//Document array
-	if(DA_COMPUTE && (MODE!=9 && MODE!=10 && MODE!=11)){
+	if(DA_COMPUTE && (MODE!=9 && MODE!=10 && MODE!=11 && MODE!=12)){
 		time_start(&t_start, &c_start);
 		if(MODE==1 || MODE==2)
 			document_array_LF_int((int_t*)str_int, SA, DA, n, 256+k, sizeof(int_t), 1, k);