Merge branch 'master' into doc_list_idx

CMakeLists.txt

@@ -41,3 +41,11 @@ add_subdirectory(lib)
 
 configure_file("${CMAKE_CURRENT_SOURCE_DIR}/Make.helper.cmake" 
 		       "${CMAKE_CURRENT_SOURCE_DIR}/Make.helper" @ONLY)	
+
+## Add 'uninstall' target ##
+CONFIGURE_FILE(
+  "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/cmake_uninstall.cmake.in"
+  "${CMAKE_CURRENT_BINARY_DIR}/CMakeModules/cmake_uninstall.cmake"
+  IMMEDIATE @ONLY)
+ADD_CUSTOM_TARGET(uninstall
+  "${CMAKE_COMMAND}" -P "${CMAKE_CURRENT_BINARY_DIR}/CMakeModules/cmake_uninstall.cmake")

benchmark/indexing_count/Makefile

@@ -27,7 +27,7 @@ TIME_FILES  = $(foreach IDX_ID,$(IDX_IDS),\
 					 $(foreach COMPILE_ID,$(COMPILE_IDS),results/$(TC_ID).$(IDX_ID).$(COMPILE_ID))))
 COMP_FILES  = $(addsuffix .z.info,$(TC_PATHS))
 
-all: $(BUILD_EXECS) $(QUERY_EXECS) pattern
+all: $(BUILD_EXECS) $(QUERY_EXECS) $(INFO_EXECS)
 
 info: $(INFO_EXECS) $(INFO_FILES) 
 	cd ../../examples; make json2html.x
@@ -116,9 +116,13 @@ $(BIN_DIR)/info_%: $(SRC_DIR)/info.cpp index.config
 
 include ../Make.download
 
+clean-build:
+	@echo "Remove executables"
+	@rm -f $(QUERY_EXECS) $(BUILD_EXECS) $(INFO_EXECS)
+
 clean:
 	@echo "Remove executables and indexes"
-	@rm -f $(QUERY_EXECS) $(LOCATE_EXECS) $(BUILD_EXECS) $(INFO_EXECS) \
+	@rm -f $(QUERY_EXECS) $(BUILD_EXECS) $(INFO_EXECS) \
 		   $(INFO_FILES) $(INDEXES) $(BIN_DIR)/genpatterns
 
 cleanresults: 

benchmark/indexing_count/src/info.cpp

@@ -11,7 +11,6 @@ using namespace std;
 
 int main(int argc, char* argv[])
 {
-    char* filename;
     if (argc < 2)  {
         cout << "./" << argv[0] << " index_file " << endl;
         return 1;

benchmark/indexing_count/src/run_queries_sdsl.cpp

@@ -54,7 +54,7 @@ int main(int argc, char* argv[])
     querytype = *argv[2];
 
     CSA_TYPE csa;
-    fprintf(stderr, "# File = %s\n",(string(argv[1]) + "." + string(SUF)).c_str());
+    fprintf(stderr, "# File = %s\n",(string(filename) + "." + string(SUF)).c_str());
     fprintf(stderr, "# program = %s\n",string(SUF).c_str());
     Load_time = getTime();
     load_from_file(csa, (string(argv[1]) + "." + string(SUF)).c_str());

benchmark/indexing_extract/Makefile

@@ -31,7 +31,7 @@ TIME_FILES  = $(foreach IDX_ID,$(IDX_IDS),\
 				  $(foreach SAMPLE_ID,$(SAMPLE_IDS),results/$(TC_ID).$(IDX_ID).$(SAMPLE_ID))))
 COMP_FILES  = $(addsuffix .z.info,$(TC_PATHS))
 
-all: $(BUILD_EXECS) $(QUERY_EXECS) intervals
+all: $(BUILD_EXECS) $(QUERY_EXECS) $(INFO_EXECS)
 
 info: $(INFO_EXECS) $(INFO_FILES) 
 
@@ -139,9 +139,13 @@ $(BIN_DIR)/info_%: $(SRC_DIR)/info.cpp index.config
 
 include ../Make.download
 
+clean-build:
+	@echo "Remove executables"
+	@rm -f $(QUERY_EXECS) $(BUILD_EXECS) $(INFO_EXECS)
+
 clean:
 	@echo "Remove executables"
-	@rm -f $(QUERY_EXECS) $(LOCATE_EXECS) $(BUILD_EXECS) $(INFO_EXECS) \
+	@rm -f $(QUERY_EXECS) $(BUILD_EXECS) $(INFO_EXECS) \
 		   $(BIN_DIR)/genintervals
 
 cleanresults: 

benchmark/indexing_extract/src/info.cpp

@@ -4,14 +4,11 @@
 #include <sdsl/suffix_arrays.hpp>
 #include <string>
 
-#include <cstdlib>
-
 using namespace sdsl;
 using namespace std;
 
 int main(int argc, char* argv[])
 {
-    char* filename;
     if (argc < 2)  {
         cout << "./" << argv[0] << " index_file " << endl;
         return 1;

benchmark/indexing_extract/src/run_queries_sdsl.cpp

@@ -20,9 +20,6 @@
 #define DISPLAY 	('D')
 #define VERBOSE 	('V')
 
-/* macro to detect and to notify errors */
-#define IFERROR(error) {{if (error) { fprintf(stderr, "%s\n", error_index(error)); exit(1); }}}
-
 using namespace sdsl;
 using namespace std;
 
@@ -36,7 +33,6 @@ void pfile_info(ulong* length, ulong* numpatt);
 double getTime(void);
 void usage(char* progname);
 
-static void* Index;	 /* opaque data type */
 static int Verbose = 0;
 static ulong Index_size, Text_length;
 static double Load_time;
@@ -46,7 +42,6 @@ static double Load_time;
  */
 int main(int argc, char* argv[])
 {
-    int error = 0;
     char* filename;
     char querytype;
 
@@ -59,20 +54,15 @@ int main(int argc, char* argv[])
     querytype = *argv[2];
 
     CSA_TYPE csa;
-    fprintf(stderr, "Load from file %s\n",(string(argv[1]) + "." + string(SDSL_XSTR(SUF))).c_str());
+    fprintf(stderr, "Load from file %s\n",(string(filename) + "." + string(SDSL_XSTR(SUF))).c_str());
     Load_time = getTime();
     load_from_file(csa, (string(argv[1]) + "." + string(SDSL_XSTR(SUF))).c_str());
-    IFERROR(error);
     Load_time = getTime() - Load_time;
     fprintf(stderr, "# Load_index_time_in_sec = %.2f\n", Load_time);
     std::cerr << "# text_size = " << csa.size()-1 << std::endl;
 
     Index_size = size_in_bytes(csa);
-    IFERROR(error);
     Text_length = csa.size()-1; // -1 since we added a sentinel character
-//	error = get_length(Index, &Text_length);
-    IFERROR(error);
-    /*	Index_size /=1024; */
     fprintf(stderr, "# Index_size_in_bytes = %lu\n", Index_size);
 #ifdef USE_HP
     bool mapped = mm::map_hp();
@@ -105,20 +95,7 @@ int main(int argc, char* argv[])
 
             do_extract(csa);
             break;
-            /*		case DISPLAY:
-            			if (argc < 4) {
-            				usage(argv[0]);
-            				exit (1);
-            			}
-            			if (argc > 4)
-            				if (*argv[4] == VERBOSE){
-            						Verbose = 1;
-            						fprintf(stdout,"%c", DISPLAY);
-
-            				}
-            			do_display((ulong) atol(argv[3]));
-            			break;
-        */		default:
+        default:
             fprintf(stderr, "Unknow option: main ru\n");
             exit(1);
     }
@@ -127,18 +104,13 @@ int main(int argc, char* argv[])
         mm::unmap_hp();
     }
 #endif
-
-//	error = free_index(Index);
-    IFERROR(error);
-
     return 0;
 }
 
 
 void
 do_count(const CSA_TYPE& csa)
 {
-    int error = 0;
     ulong numocc, length, tot_numocc = 0, numpatt, res_patt;
     double time, tot_time = 0;
     uchar* pattern;
@@ -163,8 +135,6 @@ do_count(const CSA_TYPE& csa)
         /* Count */
         time = getTime();
         numocc = count(csa, pattern, pattern+length);
-//		error = count (Index, pattern, length, &numocc);
-        IFERROR(error);
 
         if (Verbose) {
             fwrite(&length, sizeof(length), 1, stdout);
@@ -194,7 +164,6 @@ do_count(const CSA_TYPE& csa)
 void
 do_locate(const CSA_TYPE& csa)
 {
-    int error = 0;
     ulong numocc, length; //, *occ,
     int_vector<32> occ;
     ulong tot_numocc = 0, numpatt = 0, processed_pat = 0;
@@ -219,7 +188,6 @@ do_locate(const CSA_TYPE& csa)
         // Locate
         time = getTime();
         numocc = locate(csa, pattern, pattern+length, occ);
-        IFERROR(error);
         tot_time += (getTime() - time);
         ++processed_pat;
 
@@ -242,80 +210,6 @@ do_locate(const CSA_TYPE& csa)
     free(pattern);
 }
 
-
-/*
-void do_display(ulong numc) {
-
-	int error = 0;
-	ulong numocc, length, i, *snippet_len, tot_numcharext = 0, numpatt;
-	double time, tot_time = 0;
-	uchar *pattern, *snippet_text;
-
-	pfile_info (&length, &numpatt);
-
-	pattern = (uchar *) malloc (sizeof (uchar) * (length));
-	if (pattern == NULL)
-	{
-		fprintf (stderr, "Error: cannot allocate\n");
-		exit (1);
-	}
-
-	fprintf(stderr, "Snippet length %lu\n", numc);
-
-	while (numpatt)
-	{
-
-		if (fread (pattern, sizeof (*pattern), length, stdin) != length)
-		{
-			fprintf (stderr, "Error: cannot read patterns file\n");
-			perror ("run_queries");
-			exit (1);
-		}
-
-		// Display
-		time = getTime ();
-		error =	display (Index, pattern, length, numc, &numocc,
-				    	 &snippet_text, &snippet_len);
-		IFERROR (error);
-		tot_time += (getTime () - time);
-
-		if (Verbose) {
-			ulong j, len = length + 2*numc;
-		    char blank = '\0';
-			fwrite(&length, sizeof(length), 1, stdout);
-			fwrite(pattern, sizeof(*pattern), length, stdout);
-			fwrite(&numocc, sizeof(numocc), 1, stdout);
-			fwrite(&len, sizeof(len), 1, stdout);
-
-			for (i = 0; i < numocc; i++){
-				fwrite(snippet_text+len*i,sizeof(uchar),snippet_len[i],stdout);
-				for(j=snippet_len[i];j<len;j++)
-				   fwrite(&blank,sizeof(uchar),1,stdout);
-			}
-
-		}
-		numpatt--;
-
-		for(i=0; i<numocc; i++) {
-			tot_numcharext += snippet_len[i];
-		}
-
-		if (numocc) {
-			free (snippet_len);
-			free (snippet_text);
-		}
-	}
-
-	fprintf (stderr, "#Total_num_chars_extracted = %lu\n", tot_numcharext);
-	fprintf (stderr, "#Display_time_in_sec = %.2f secs\n", tot_time);
-	fprintf (stderr, "#Time_display/Tot_num_chars = %.4f\n\n", (tot_time*1000) / tot_numcharext);
-	fprintf (stderr, "#(Load_time+Time_display)/Tot_num_chars = %.4f\n\n", ((Load_time+tot_time)*1000) / tot_numcharext);
-
-	free (pattern);
-}
-*/
-
-
 /* Open patterns file and read header */
 void
 pfile_info(ulong* length, ulong* numpatt)

benchmark/indexing_locate/Makefile

@@ -31,7 +31,7 @@ TIME_FILES  = $(foreach IDX_ID,$(IDX_IDS),\
 				  $(foreach SAMPLE_ID,$(SAMPLE_IDS),results/$(TC_ID).$(IDX_ID).$(SAMPLE_ID))))
 COMP_FILES  = $(addsuffix .z.info,$(TC_PATHS))
 
-all: $(BUILD_EXECS) $(QUERY_EXECS) pattern
+all: $(BUILD_EXECS) $(QUERY_EXECS) $(INFO_EXECS)
 
 info: $(INFO_EXECS) $(INFO_FILES) 
 
@@ -139,9 +139,13 @@ $(BIN_DIR)/info_%: $(SRC_DIR)/info.cpp index.config
 
 include ../Make.download
 
+clean-build:
+	@echo "Remove executables"
+	@rm -f $(QUERY_EXECS) $(BUILD_EXECS) $(INFO_EXECS)
+
 clean:
 	@echo "Remove executables"
-	@rm -f $(QUERY_EXECS) $(LOCATE_EXECS) $(BUILD_EXECS) $(INFO_EXECS) \
+	@rm -f $(QUERY_EXECS) $(BUILD_EXECS) $(INFO_EXECS) \
 		   $(BIN_DIR)/pattern_random
 
 cleanresults: 

benchmark/indexing_locate/src/info.cpp

@@ -11,7 +11,6 @@ using namespace std;
 
 int main(int argc, char* argv[])
 {
-    char* filename;
     if (argc < 2)  {
         cout << "./" << argv[0] << " index_file " << endl;
         return 1;