Add a new option -E to considere some example sequences as counterexamples

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@235 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/ecoprimer.c

@@ -125,6 +125,7 @@ void initoptions(poptions_t options)
 	options->primer_length=18;          //**< minimal length of the primers
 	options->restricted_taxid=NULL;      //**< limit amplification below these taxid
 	options->ignored_taxid=NULL;         //**< no amplification below these taxid
+	options->exception_taxid=NULL;         //**< no amplification below these taxid
 	options->prefix=NULL;
 	options->reference=NULL;
 	options->refseq=NULL;
@@ -137,6 +138,7 @@ void initoptions(poptions_t options)
 	options->strict_three_prime=0;
 	options->r=0;
 	options->g=0;
+	options->e=0;
 	options->no_multi_match=FALSE;
 	options->pnparm = NULL;
 	strcpy(options->taxonrank, DEFAULTTAXONRANK);			/*taxon level for results, species by default*/
@@ -525,7 +527,7 @@ int main(int argc, char **argv)
 
 	initoptions(&options);
 
-    while ((carg = getopt(argc, argv, "hAfvcUDSd:l:L:e:i:r:R:q:3:s:x:t:O:m:a:")) != -1) {
+    while ((carg = getopt(argc, argv, "hAfvcUDSE:d:l:L:e:i:r:R:q:3:s:x:t:O:m:a:")) != -1) {
 
      switch (carg) {
 								 /* ---------------------------- */
@@ -638,6 +640,15 @@ int main(int argc, char **argv)
           options.r++;
           break;
 
+								/* ------------------------------------------ */
+        case 'E':               /* stores the restricting search taxonomic id */
+								/* ------------------------------------------ */
+        	options.exception_taxid = ECOREALLOC(options.exception_taxid,sizeof(int32_t)*(options.e+1),
+						            "Error on exception_taxid reallocation");
+			sscanf(optarg,"%d",&(options.exception_taxid[options.e]));
+			options.e++;
+			break;
+
 								/* -------------------- */
         case 'R':               /* reference sequence   */
                                 /* -------------------- */

src/libecoprimer/ecoprimer.h

@@ -256,6 +256,7 @@ typedef struct {
 	uint32_t        primer_length;          //**< minimal length of the primers
 	int32_t		  *restricted_taxid;      //**< limit amplification below these taxid
 	int32_t       *ignored_taxid;         //**< no amplification below these taxid
+	int32_t		  *exception_taxid;
 	char          *prefix;
 	char          *reference;
 	pecoseq_t      refseq;
@@ -269,6 +270,7 @@ typedef struct {
 	uint32_t      strict_three_prime;
 	int32_t		  r;                      //**< count of restrited taxa (restricted_taxid array size)
 	int32_t		  g;                      //**< count of ignored taxa (ignored_taxid array size)
+	int32_t		  e;                      //**< count of ignored taxa (ignored_taxid array size)
 	bool_t        no_multi_match;
 	char		  taxonrank[20];  //TR to count ranks against a pair
 	int32_t		  taxonrankidx;   //TR to count ranks against a pair

src/libecoprimer/goodtaxon.c

@@ -17,9 +17,9 @@ int isGoodTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
 			                            options->r,
 			                            taxonomy->taxons->taxon[taxon].taxid)
 		   )) &&
-		   ((options->g == 0) || !(eco_is_taxid_included(taxonomy,
+		   ((options->e == 0) || !(eco_is_taxid_included(taxonomy,
-				                        options->ignored_taxid,
+				                        options->exception_taxid,
-		   		                        options->g,
+		   		                        options->e,
 		   		                        taxonomy->taxons->taxon[taxon].taxid)
 		   ));