From 89576b96fadb555f6728a22945898c9f2318d9ec Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Mon, 9 Nov 2009 14:50:35 +0000
Subject: [PATCH] Patch taxon example/counterexample selection

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPrimers/trunk@237 60f365c0-8329-0410-b2a4-ec073aeeaa1d
---
 src/ecoprimer.c              |  2 +-
 src/libecoprimer/goodtaxon.c | 15 ++++++++++++---
 src/libecoprimer/taxstats.c  |  2 +-
 3 files changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/ecoprimer.c b/src/ecoprimer.c
index deb6127..5715ad8 100644
--- a/src/ecoprimer.c
+++ b/src/ecoprimer.c
@@ -458,7 +458,7 @@ void updateseqparams (pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *taxo
 
     for (i=0;i<seqdbsize;i++)
     {
-    	seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options);
+    	seqdb[i]->isexample=isExampleTaxon(taxonomy,seqdb[i]->taxid,options);
     	if (seqdb[i]->isexample)
     		(*insamples)++;
     	else
diff --git a/src/libecoprimer/goodtaxon.c b/src/libecoprimer/goodtaxon.c
index 898b533..68f940c 100644
--- a/src/libecoprimer/goodtaxon.c
+++ b/src/libecoprimer/goodtaxon.c
@@ -12,7 +12,7 @@ int isGoodTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
 {
 	int result;
 
-	result=( (options->r == 0) || (eco_is_taxid_included(taxonomy,
+	result=((options->r == 0) || (eco_is_taxid_included(taxonomy,
 			                            options->restricted_taxid,
 			                            options->r,
 			                            taxonomy->taxons->taxon[taxon].taxid)
@@ -34,6 +34,11 @@ int isExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t options)
 			                            options->restricted_taxid,
 			                            options->r,
 			                            taxonomy->taxons->taxon[taxon].taxid)
+		   )) &&
+		   ((options->e == 0) || !(eco_is_taxid_included(taxonomy,
+				                        options->exception_taxid,
+		   		                        options->e,
+		   		                        taxonomy->taxons->taxon[taxon].taxid)
 		   ));
 
 	return result;
@@ -47,8 +52,12 @@ int isCounterExampleTaxon(ecotaxonomy_t *taxonomy,int32_t taxon,poptions_t optio
 	result=((options->g != 0) && (eco_is_taxid_included(taxonomy,
 								   options->ignored_taxid,
 								   options->g,
-								   taxonomy->taxons->taxon[taxon].taxid)
-           ));
+								   taxonomy->taxons->taxon[taxon].taxid))
+           ) || ((options->e != 0) && (eco_is_taxid_included(taxonomy,
+				                        options->exception_taxid,
+		   		                        options->e,
+		   		                        taxonomy->taxons->taxon[taxon].taxid))
+           );
 
 
 	return result;
diff --git a/src/libecoprimer/taxstats.c b/src/libecoprimer/taxstats.c
index a751d7d..da7de6f 100644
--- a/src/libecoprimer/taxstats.c
+++ b/src/libecoprimer/taxstats.c
@@ -64,7 +64,7 @@ int32_t getrankdbstats(pecodnadb_t seqdb, uint32_t seqdbsize, ecotaxonomy_t *tax
     for (i=0;i<seqdbsize;i++)
 	{
     	taxon = &(taxonomy->taxons->taxon[seqdb[i]->taxid]);
-	    seqdb[i]->isexample=isGoodTaxon(taxonomy,seqdb[i]->taxid,options);
+	    seqdb[i]->isexample=isExampleTaxon(taxonomy,seqdb[i]->taxid,options);
 
 		tmptaxon = eco_findtaxonatrank(taxon,
 									   options->taxonrankidx);