MOD: Added a [P]ath option displaying for each taxon its full path

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@423 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/ecofind.c

@@ -9,7 +9,20 @@
 /**
  * display the result
  **/
-static void printresult(ecotx_t *taxon,econame_t* name,ecotaxonomy_t *taxonomy)
+
+void displayPath(ecotx_t *taxon, ecotaxonomy_t *taxonomy){
+
+	if (taxon != taxon->parent){
+		displayPath(taxon->parent,taxonomy);
+		printf(";");
+	}
+	if (rank_index("no rank",taxonomy->ranks) != taxon->rank)
+		printf("%s:", taxonomy->ranks->label[taxon->rank]);
+	printf("%s", taxon->name);
+}
+
+
+static void printresult(ecotx_t *taxon,econame_t* name,ecotaxonomy_t *taxonomy, int32_t pathDisplay)
 {
 	char* rankname;
 	char* classname;
@@ -24,32 +37,38 @@ static void printresult(ecotx_t *taxon,econame_t* name,ecotaxonomy_t *taxonomy)
 	
 	rankname= taxonomy->ranks->label[taxon->rank];	
 	
-	printf("%10d \t| %15s \t|\t %-50s \t|\t %15s \t|\t %s\n",
+	printf("%10d \t| %15s \t|\t %-50s \t|\t %15s \t|\t %s",
 			taxon->taxid,
 			rankname,
 			matchedname,
 			classname,
-			taxon->name);	
+			taxon->name);
+	if (pathDisplay) {
+	    printf("\t|\t");
+	    displayPath(taxon, taxonomy);
+	}
+    printf("\n");
 }
 
 /**
  * display header before printing any result
  **/
-static void printheader(void)
+static void printheader(int32_t pathDisplay)
 {
-	printf("# %12s \t| %15s \t|\t %-50s \t|\t %-15s \t|\t %s\n#\n",
+	printf("# %12s \t| %15s \t|\t %-50s \t|\t %-15s \t|\t %s%s\n#\n",
 			"taxonomy id",
 			"taxonomy rank",
 			"name",
 			"class name",
-			"scientific name");
+			"scientific name",
+			pathDisplay ? "\t|\t path":"");
 }
 
 
 /**
  * display son's list for given taxon
  **/
-static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count, char *rankname)
+static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count, char *rankname, int32_t pathDisplay)
 {
 	int32_t		i;
 	ecotx_t 	*current_taxon;
@@ -63,10 +82,10 @@ static void get_son(ecotaxonomy_t *taxonomy, ecotx_t *taxon, int32_t *count, cha
 		{
 			if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[current_taxon->rank]))
 			{
-				printresult(current_taxon, NULL, taxonomy);
+				printresult(current_taxon, NULL, taxonomy, pathDisplay);
 				(*count)++;	
 			}
-			get_son(taxonomy,current_taxon,count,rankname);
+			get_son(taxonomy,current_taxon,count,rankname, pathDisplay);
 		}
 	}
 }
@@ -97,23 +116,23 @@ static void listfilteroptions(ecorankidx_t *ranks)
 /* get back on given taxid taxonomic parent	*/
 /* and display it							*/
 /* ---------------------------------------- */
-void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy, char *rankname)
+void gettaxidparents(int32_t taxid, ecotaxonomy_t *taxonomy, char *rankname, int32_t pathDisplay)
 {
 	ecotx_t *next_parent;
 	int32_t	c = 0;
 	
 	next_parent = eco_findtaxonbytaxid(taxonomy, taxid);		
 	
-	printheader();
+	printheader(pathDisplay);
 	
-	printresult(next_parent, NULL,taxonomy);
+	printresult(next_parent, NULL,taxonomy, pathDisplay);
 		
 	while ( strcmp(next_parent->name, "root") )
 	{
 		next_parent = next_parent->parent;
 		if (rankname == NULL || !strcmp(rankname,taxonomy->ranks->label[next_parent->rank]))
 		{
-			printresult(next_parent, NULL,taxonomy);
+			printresult(next_parent, NULL,taxonomy, pathDisplay);
 			c++;
 		}
 	}
@@ -164,6 +183,7 @@ static void PrintHelp()
         PP      "-p : [P]arents : specifiying this option displays all parental tree's information for the given taxid.\n\n");
         PP      "-r : [R]estrict to given taxonomic rank\n\n");      
         PP      "-s : [S]ons: specifiying this option displays all subtree's information for the given taxid.\n\n");
+        PP      "-P : Display taxonomic [P]ath as suplementary column in output\n\n");
         PP      "arguments:\n");        
         PP      "<taxon> name pattern bearing regular expressions\n\n");
         PP      "------------------------------------------\n");
@@ -199,12 +219,13 @@ int main(int argc, char **argv)
 	char			*rankname	= NULL;
 	int32_t			rankfilter 	= 1;
 	int32_t			list 		= 0;
+	int32_t			path 		= 0;
 	
 	ecotx_t 		*subtree_parent;
 	int32_t			count_son = 0;
 
 
-	while ((carg = getopt(argc, argv, "had:p:s:r:l")) != -1) {
+	while ((carg = getopt(argc, argv, "had:p:s:r:lP")) != -1) {
 	    switch (carg) {                        
 	       case 's':               	/* path to the database     */
 	          sscanf(optarg,"%d",&subtree);
@@ -224,6 +245,10 @@ int main(int argc, char **argv)
 	       case 'l':               	/* list rank filter options */
 	          list = 1;
 	          break;
+
+	       case 'P':               	/* Path output option */
+	          path=1;
+	          break;
 	
 	       case 'a':               	/* allow alternative names  */
 	          alternative = 1;
@@ -281,7 +306,7 @@ int main(int argc, char **argv)
 	/* ----------------------------------------	*/	
 	if (uptree)
 	{
-		gettaxidparents(uptree,taxonomy,rankname);
+		gettaxidparents(uptree,taxonomy,rankname, path);
 		return 0;	
 	}
 	
@@ -291,10 +316,10 @@ int main(int argc, char **argv)
 	/* ----------------------------------------	*/		
 	if (subtree)
 	{
-		printheader();
+		printheader(path);
 		subtree_parent = eco_findtaxonbytaxid(taxonomy,subtree);
-		printresult(subtree_parent, NULL,taxonomy);
+		printresult(subtree_parent, NULL,taxonomy, path);
-		get_son(taxonomy, subtree_parent,&count_son,rankname);
+		get_son(taxonomy, subtree_parent,&count_son,rankname, path);
 		printf("#  %d son(s) found\n#\n",count_son);
 		return 0;
 	}
@@ -317,7 +342,7 @@ int main(int argc, char **argv)
 		
 		nummatch=0;
 		
-	    printheader();
+	    printheader(path);
 		
 		for (j=0,name=taxonomy->names->names;
 		     j < name_count;
@@ -331,7 +356,7 @@ int main(int argc, char **argv)
    			
    			if (!re_match && (alternative || name->is_scientificname) && rankfilter)
    			{
-   				printresult(name->taxon,name,taxonomy);
+   				printresult(name->taxon,name,taxonomy, path);
    				nummatch++;
    			}