From 957a59eb5df2c861d1b4f4eea9f54b8a5562b040 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Tue, 19 Jul 2011 06:44:47 +0000
Subject: [PATCH] Add management of local taxa from the new extension of the
 OBI Taxonomy library

git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@315 60f365c0-8329-0410-b2a4-ec073aeeaa1d
---
 src/ecopcr.c           |  1 +
 src/libecoPCR/ecoPCR.h |  2 +-
 src/libecoPCR/ecoseq.c |  2 +-
 src/libecoPCR/ecotax.c | 34 ++++++++++++++++++++++++++++------
 4 files changed, 31 insertions(+), 8 deletions(-)

diff --git a/src/ecopcr.c b/src/ecopcr.c
index 4d5a700..04a5148 100644
--- a/src/ecopcr.c
+++ b/src/ecopcr.c
@@ -527,6 +527,7 @@ int main(int argc, char **argv)
 	o1c = complementPattern(o1);
 	o2c = complementPattern(o2);
 	
+	printf("#@ecopcr-v2\n");
 	printf("#\n");
 	printf("# ecoPCR version %s\n",VERSION);
 	printf("# direct  strand oligo1 : %-32s ; oligo2c : %32s\n", o1->cpat,o2c->cpat);
diff --git a/src/libecoPCR/ecoPCR.h b/src/libecoPCR/ecoPCR.h
index 3e13b18..c5e2c69 100644
--- a/src/libecoPCR/ecoPCR.h
+++ b/src/libecoPCR/ecoPCR.h
@@ -220,7 +220,7 @@ econameidx_t     *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
 	 * @return pointer to a taxonomy index structure
 	 */
  
-ecotxidx_t       *read_taxonomyidx(const char *filename);
+ecotxidx_t       *read_taxonomyidx(const char *filename,const char *filename2);
 
 ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName);
 
diff --git a/src/libecoPCR/ecoseq.c b/src/libecoPCR/ecoseq.c
index 7f5ba27..fbea3e5 100644
--- a/src/libecoPCR/ecoseq.c
+++ b/src/libecoPCR/ecoseq.c
@@ -169,7 +169,7 @@ FILE *open_seqfile(const char *prefix,int32_t index)
 	                           prefix,
 	                           index);
 
-			fprintf(stderr,"# Coucou %s\n",filename_buffer);
+		//	fprintf(stderr,"# Coucou %s\n",filename_buffer);
 
 
 	if (filename_length >= 1024)
diff --git a/src/libecoPCR/ecotax.c b/src/libecoPCR/ecotax.c
index 89ac82b..2aba11a 100644
--- a/src/libecoPCR/ecotax.c
+++ b/src/libecoPCR/ecotax.c
@@ -10,23 +10,41 @@ static ecotx_t *readnext_ecotaxon(FILE *f,ecotx_t *taxon);
  * @param	pointer to the database (.tdx file) 
  * @return	a ecotxidx_t structure 
  */
-ecotxidx_t     *read_taxonomyidx(const char *filename)
+ecotxidx_t     *read_taxonomyidx(const char *filename,const char *filename2)
 {
 	int32_t      count;
+	int32_t      count2;
 	FILE         *f;
+	FILE         *f2;
 	ecotxidx_t *index;
 	int32_t      i;
 	
-	f = open_ecorecorddb(filename,&count,1);
+	f  = open_ecorecorddb(filename,&count,1);
+	f2 = open_ecorecorddb(filename2,&count2,0);
+
+
 	
-	index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count-1),
+	index = (ecotxidx_t*) ECOMALLOC(sizeof(ecotxidx_t) + sizeof(ecotx_t) * (count+count2-1),
 	                                  "Allocate taxonomy");
 	 
-	index->count=count;                                         
+	index->count=count+count2;
+
+	fprintf(stderr,"Readind %d taxa...\n",count);
 	for (i=0; i < count; i++){
 		readnext_ecotaxon(f,&(index->taxon[i]));
 		index->taxon[i].parent=index->taxon + (int32_t)index->taxon[i].parent;
 	}					
+
+	if (count2>0)
+		fprintf(stderr,"Readind %d local taxa...\n",count2);
+	else
+		fprintf(stderr,"No local taxon\n");
+
+	for (i=0; i < count2; i++){
+		readnext_ecotaxon(f2,&(index->taxon[count+i]));
+		index->taxon[count+i].parent=index->taxon + (int32_t)index->taxon[count+i].parent;
+	}
+
 	return index;
 }
 
@@ -111,6 +129,7 @@ ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName)
 {
 	ecotaxonomy_t *tax;
 	char          *filename;
+	char          *filename2;
 	int           buffsize;
 	
 	tax = ECOMALLOC(sizeof(ecotaxonomy_t),
@@ -120,14 +139,17 @@ ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName)
 	
 	filename = ECOMALLOC(buffsize,
 	                     "Allocate filename");
+	filename2= ECOMALLOC(buffsize,
+	                     "Allocate filename");
 	
 	snprintf(filename,buffsize,"%s.rdx",prefix);
 	
 	tax->ranks = read_rankidx(filename);
 	
 	snprintf(filename,buffsize,"%s.tdx",prefix);
+	snprintf(filename2,buffsize,"%s.ldx",prefix);
 	
-	tax->taxons = read_taxonomyidx(filename);
+	tax->taxons = read_taxonomyidx(filename,filename2);
 	
 	if (readAlternativeName)
 	{
@@ -326,4 +348,4 @@ ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,
 		ECOERROR(ECO_ASSERT_ERROR,"No taxonomy defined");
 		
 	return eco_findtaxonatrank(taxon,rankindex);
-}
\ No newline at end of file
+}