README updated

Makefile

@@ -18,13 +18,13 @@ LIBOBJ = \
 	lib/file.o\
 	lib/suffix_array.o\
 	external/malloc_count/malloc_count.o\
-	gsais.o\
-	gsaca-k.o
+	src/gsais.o\
+	src/gsaca-k.o
 
 all: compile
 
 clean:
-	\rm lib/*.o *.o external/*.o gsais -v
+	\rm lib/*.o src/*.o external/*.o gsais -v
 
 compile: main.c ${LIBOBJ} 
 	$(CC) $(CFLAGS) $(LFLAGS) -o gsais main.c ${LIBOBJ}

README.md

@@ -1,8 +1,8 @@
 #gsa-is
 
-This code is an implementation of gSAIS and gSACA-K, which are modifications of
-SAIS [1] and SACA-K [2] to compute the generalized suffix array,
-maintaining their theoretical bounds and improving their practical performance.
+This code is an implementation of gSAIS and gSACA-K [1], which extend the
+linear­time suffix sorting algorithms SAIS [2] and SACA-K [3] to compute the
+generalized suffix array.
 
 Overall, SACA-K's time-space trade-off is Pareto optimal compared to the all
 other algorithms in the experiments.
@@ -315,8 +315,10 @@ MODE parameter specifies which algorithm is called by main.c:
 
 ##references
 
-\[1\] G. Nong, S. Zhang, and W. H. Chan, “Two efficient algorithms for linear time suffix array construction,” IEEE Trans. Comput., vol. 60, no. 10, pp. 1471–1484, 2011
+\[1\] Louza, F. A., Gog, S., Telles, G. P, "Induced Suffix Sorting for String Collections", submitted to DCC, 2016.
 
-\[2\] Nong, G. Practical linear-time O(1)-workspace suffix sorting for constant alphabets,” ACM Trans. Inform. Syst., vol. 31, no. 3, pp. 1–15, 2013
+\[2\] 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
+
+\[3\] Nong, G., "Practical linear-time O(1)-workspace suffix sorting for constant alphabets", ACM Trans. Inform. Syst., vol. 31, no. 3, pp. 1–15, 2013
 
 

main.c

@@ -15,8 +15,8 @@
 #include "lib/file.h"
 #include "lib/suffix_array.h"
 #include "external/malloc_count/malloc_count.h"
-#include "gsais.h"
-#include "gsaca-k.h"
+#include "src/gsais.h"
+#include "src/gsaca-k.h"
 
 #define DEBUG 0
 

src/gsaca-k.h

@@ -0,0 +1,32 @@
+/* 
+ * Authors: Felipe A. Louza, Simon Gog, Guilherme P. Telles
+ * contact: [email protected]
+ * 01/09/2015
+ */
+
+/* 
+ * This code is a modification of SACA-K algorithm by G. Nong, which can be
+ * retrieved at: http://code.google.com/p/ge-nong/ 
+ *
+ * Our version of SACA-K, called gSACA-K, maintain the theoretical bounds of the
+ * original algorithm to construct the generalized suffix array.
+ *
+ */
+
+#ifndef GSACA_K_H
+#define GSACA_K_H
+
+#include <stdlib.h>
+#include <stdio.h>
+
+#include "../lib/utils.h"
+
+int_t SACA_K(int_t *s, uint_t *SA,
+  uint_t n, unsigned int K,
+  uint_t m, int cs, int level);
+
+int_t gSACA_K(unsigned char *s, uint_t *SA,
+  uint_t n, unsigned int K,
+  uint_t m, int cs, int level, unsigned char separator);
+
+#endif

gsais.h → src/gsais.h

@@ -1,7 +1,17 @@
-// This is (a modification of) SA-IS algorithm, which can be retrieved at:
-// http://code.google.com/p/ge-nong/ 
-// Our version of SAIS, called gSAIS, maintain the theoretical bounds of the
-// original algorithm to construct the generalized suffix array.
+/* 
+ * Authors: Felipe A. Louza, Simon Gog, Guilherme P. Telles
+ * contact: [email protected]
+ * 01/09/2015
+ */
+
+/* 
+ * This code is a modification of SA-IS algorithm by G. Nong, which can be
+ * retrieved at: http://code.google.com/p/ge-nong/ 
+ *
+ * Our version of SA-IS, called gSA-IS, maintain the theoretical bounds of the
+ * original algorithm to construct the generalized suffix array.
+ *
+ */
 
 #ifndef GSAIS_H
 #define GSAIS_H
@@ -11,7 +21,7 @@
 #include <memory.h>
 #include <time.h>
 
-#include "lib/utils.h"
+#include "../lib/utils.h"
 
 #define tget(i) ( (t[(i)/8]&mask[(i)%8]) ? 1 : 0 )
 #define tset(i, b) t[(i)/8]=(b) ? (mask[(i)%8]|t[(i)/8]) : ((~mask[(i)%8])&t[(i)/8])