git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@44 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/ecofind_makefile

@@ -1,22 +0,0 @@
-
-CC=gcc
-CFLAGS= -W -Wall -O2 -g
-LDFLAGS= -lm
-EXEC=ecofind
-SRC= ecofind.c
-OBJ= $(SRC:.c=.o)
-LIBPATH= -LlibecoPCR/
-LIB= -lecoPCR
-
-MACHINE=MAC_OS_X
-
-all: $(EXEC)
-
-ecofind: $(OBJ)
-	$(CC) $(LDFLAGS) -o $@ $< $(LIBPATH) $(LIB)
-	
-ecofind.o: $(SRC)
-	$(CC) -D$(MACHINE) -o $@ -c $< $(CFLAGS)
-	
-clean:
-	rm -f *.o

src/ecopcr.c

@@ -52,7 +52,7 @@ static void PrintHelp()
         PP      "datafile radical without any extension. For example /database/gbmam\n");
         PP      "------------------------------------------\n");
         PP		"Table result description : \n");
-        PP		"column 1 :	\n");
+        PP		"column 1 :	accession number\n");
         PP		"column 2 :	sequence length\n");
         PP		"column 3 :	taxonomic id\n");
         PP		"column 4 :	rank\n");
@@ -70,7 +70,7 @@ static void PrintHelp()
         PP		"column 16 : second oligonucleotide\n");
         PP		"column 17 : number of errors for the second strand\n");
         PP		"column 18 : amplification length\n");
-        PP		"column 19 : \n");
+        PP		"column 19 : sequence description\n");
         PP      "------------------------------------------\n");
         PP      "\n");
 
@@ -87,7 +87,7 @@ static void PrintHelp()
 static void ExitUsage(stat)
         int stat;
 {
-        PP      "usage: ecoPCR [-1 oligo1] [-2 oligo2] [-l value] [-L value] [-e value] [-k] datafile\n");
+        PP      "usage: ecoPCR [-1 oligo1] [-2 oligo2] [-l value] [-L value] [-e value] [-r taxid] [-i taxid] [-k] datafile\n");
         PP      "type \"ecoPCR -h\" for help\n");
 
         if (stat)
@@ -295,12 +295,12 @@ int main(int argc, char **argv)
 	int32_t		  errj;
 	
 	int32_t		  *restricted_taxid = NULL;
-	int32_t       *excluded_taxid	= NULL;
+	int32_t       *ignored_taxid	= NULL;
 	int32_t		  r=0;
 	int32_t		  g=0;	
 	
 
-    while ((carg = getopt(argc, argv, "h1:2:l:L:e:E:r:k")) != -1) {
+    while ((carg = getopt(argc, argv, "h1:2:l:L:e:i:r:k")) != -1) {
   
      switch (carg) {
                                 /* -------------------- */
@@ -359,11 +359,11 @@ int main(int argc, char **argv)
           break;
           
          						/* --------------------------------- */
-        case 'E':               /* stores the taxonomic id to ignore */
+        case 'i':               /* stores the taxonomic id to ignore */
         						/* --------------------------------- */
-		  excluded_taxid = ECOREALLOC(excluded_taxid,sizeof(int32_t)*(g+1),
+		  ignored_taxid = ECOREALLOC(ignored_taxid,sizeof(int32_t)*(g+1),
           									"Error on excluded_taxid reallocation");
-          sscanf(optarg,"%d",&excluded_taxid[g]);
+          sscanf(optarg,"%d",&ignored_taxid[g]);
           g++;
           break;
           
@@ -428,14 +428,21 @@ int main(int argc, char **argv)
 		/**
 		* check if current sequence should be ignored
 		**/
-		if ( (g > 0) && (eco_is_taxid_ignored(excluded_taxid, g, taxonomy->taxons->taxon[seq->taxid].taxid)) )
+		if ( (r == 0) || 
-			goto next;
+		     (eco_is_taxid_included(taxonomy, 
-			
+		                            restricted_taxid, 
-		/**
+		                            r, 
-		* check current sequence is included
+		                            taxonomy->taxons->taxon[seq->taxid].taxid)
-		**/
+		     ) 
-		if ( (r > 0) && (!eco_is_taxid_included(taxonomy, restricted_taxid, r, taxonomy->taxons->taxon[seq->taxid].taxid)) )
+		   )
-			goto next;	
+		     if ((g == 0) || 
+		         !(eco_is_taxid_included(taxonomy, 
+		                                 ignored_taxid, 
+		                                 g, 
+		                                 taxonomy->taxons->taxon[seq->taxid].taxid)
+		          )
+		        )
+		     {
 		
 				scname = taxonomy->taxons->taxon[seq->taxid].name;
 				strncpy(head,seq->SQ,10);
@@ -512,7 +519,7 @@ int main(int argc, char **argv)
 						}
 				}	
 				
-		next:
+		} /* End of taxonomic selection */
 		
 		delete_ecoseq(seq);
 		
@@ -520,7 +527,7 @@ int main(int argc, char **argv)
 	}
 	
 	ECOFREE(restricted_taxid, "Error: could not free restricted_taxid\n");
-	ECOFREE(excluded_taxid, "Error: could not free excluded_taxid\n");
+	ECOFREE(ignored_taxid, "Error: could not free excluded_taxid\n");
 		
 	return 0;
 }

src/libecoPCR/ecoError.c

@@ -2,7 +2,15 @@
 #include <stdio.h>
 #include <stdlib.h>
 
-
+/*
+ * print the message given as argument and exit the program
+ * @param error		error number	
+ * @param message 	the text explaining what's going on
+ * @param filename	the file source where the program failed
+ * @param linenumber	the line where it has failed
+ * filename and linenumber are written at pre-processing 
+ * time by a macro
+ */
 void ecoError(int32_t error,
               const char* message,
               const char * filename,

src/libecoPCR/ecoIOUtils.c

@@ -16,20 +16,19 @@ int32_t is_big_endian()
 
 
 
-
-
-
 int32_t swap_int32_t(int32_t i)
 {
 	return SWAPINT32(i);
 }
 
 
-
+/**
-
+ * Read part of the file
-
+ * @param	*f	the database
-
+ * @param	recordSize the size to be read
-
+ * 
+ * @return	buffer
+ */
 void *read_ecorecord(FILE *f,int32_t *recordSize)
 {
 	static void *buffer    =NULL;
@@ -79,10 +78,14 @@ void *read_ecorecord(FILE *f,int32_t *recordSize)
 
 
 
-
+/**
-
+ * Open the database and check it's readable
-
+ * @param 	filename 		name of the database (.sdx, .rdx, .tbx)
-
+ * @param 	sequencecount	buffer - pointer to variable storing the number of occurence    
+ * @param 	abort_on_open_error		 	boolean to define the behaviour in case of error 
+ * 										while opening the database
+ * @return 	FILE type
+ **/
 FILE *open_ecorecorddb(const char *filename,
                        int32_t    *sequencecount,
                        int32_t    abort_on_open_error)

src/libecoPCR/ecoPCR.h

@@ -230,7 +230,7 @@ ecotx_t *eco_getfamily(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 ecotx_t *eco_getkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 
-int eco_is_taxid_ignored(int *ignored_taxid, int tab_len, int taxid);
+int eco_is_taxid_ignored(int32_t *ignored_taxid, int32_t tab_len, int32_t taxid);
-int eco_is_taxid_included(ecotaxonomy_t *taxonomy, int *included_taxid, int tab_len, int taxid);
+int eco_is_taxid_included(ecotaxonomy_t *taxonomy, int32_t *included_taxid, int32_t tab_len, int32_t taxid);
 
 #endif /*ECOPCR_H_*/

src/libecoPCR/ecofilter.c

@@ -1,8 +1,8 @@
 #include "ecoPCR.h"
 
-int eco_is_taxid_ignored(	int *ignored_taxid, 
+int eco_is_taxid_ignored(	int32_t *ignored_taxid, 
-							int tab_len, 
+							int32_t tab_len, 
-							int taxid)
+							int32_t taxid)
 {
 	int i;
 	for (i=0; i < tab_len; i++){
@@ -14,7 +14,7 @@ int eco_is_taxid_ignored(	int *ignored_taxid,
 
 
 int eco_is_taxid_included(	ecotaxonomy_t *taxonomy, 
-							int *restricted_taxid, 
+							int32_t *restricted_taxid, 
 							int32_t tab_len, 
 							int32_t taxid)
 {

src/libecoPCR/ecoseq.c

@@ -79,7 +79,9 @@ ecoseq_t *new_ecoseq_with_data( char *AC,
 
 }
 
-
+/**
+ * ?? used ??
+ **/
 FILE *open_ecoseqdb(const char *filename,
                     int32_t    *sequencecount)
 {
@@ -140,6 +142,13 @@ ecoseq_t *readnext_ecoseq(FILE *f)
 	return seq;
 }
 
+/**
+ * Open the sequences database (.sdx file)
+ * @param	prefix	name of the database (radical without extension) 
+ * @param	index 	integer
+ * 
+ * @return	file object 
+ */
 FILE *open_seqfile(const char *prefix,int32_t index)
 {
 	char           filename_buffer[1024];