From 433a19fd87f42230ce84fee22f8816dc27cdcb80 Mon Sep 17 00:00:00 2001
From: Eric Coissac <eric.coissac@metabarcoding.org>
Date: Wed, 20 Jun 2007 07:38:54 +0000
Subject: [PATCH] git-svn-id:
 https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/branches/refactoring@73
 60f365c0-8329-0410-b2a4-ec073aeeaa1d

---
 src/libecoPCR/ecoPCR.h | 37 +++++++++++++++++++++++++++++++++++--
 1 file changed, 35 insertions(+), 2 deletions(-)

diff --git a/src/libecoPCR/ecoPCR.h b/src/libecoPCR/ecoPCR.h
index 2229151..4c26fc0 100644
--- a/src/libecoPCR/ecoPCR.h
+++ b/src/libecoPCR/ecoPCR.h
@@ -80,12 +80,42 @@ typedef struct {
 	char*   label[1];
 } ecorankidx_t;
 
+/*
+ * 
+ * Taxonomy name types
+ * 
+ */
+
 typedef struct {
+ 	int32_t is_scientificname;
+	int32_t  namelength;
+	int32_t  classlength;
+	int32_t  taxid;
+	char     names[1];	
+} econameformat_t;
+ 
+ 
+ typedef struct {
+ 	char 	*name;
+ 	char 	*classname;
+ 	int32_t is_scientificname;
+ 	struct ecotxnode  *taxon;
+} econame_t;
+
+ 
+typedef struct {
+	int32_t count;
+	econame_t   names[1];
+} econameidx_t;
+
+
+ typedef struct {
 	ecorankidx_t *ranks;
+	econameidx_t *names;
 	ecotxidx_t   *taxons;
 } ecotaxonomy_t;
 
-
+ 
 /*****************************************************
  * 
  *  Function declarations
@@ -175,6 +205,9 @@ ecoseq_t         *readnext_ecoseq(FILE *);
 
 ecorankidx_t     *read_rankidx(const char *filename);
 
+econameidx_t     *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
+
+
 
 	/**
 	 * Read taxonomy data as formated by the ecoPCRFormat.py script.
@@ -189,7 +222,7 @@ ecorankidx_t     *read_rankidx(const char *filename);
  
 ecotxidx_t       *read_taxonomyidx(const char *filename);
 
-ecotaxonomy_t    *read_taxonomy(const char *prefix);
+ecotaxonomy_t    *read_taxonomy(const char *prefix,int32_t readAlternativeName);
 
 ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy, int32_t taxid);