git-svn-id: https://www.grenoble.prabi.fr/svn/LECASofts/ecoPCR/trunk@114 60f365c0-8329-0410-b2a4-ec073aeeaa1d

src/libecoPCR/ecoPCR.h

@@ -56,11 +56,11 @@ typedef struct {
 	
 } ecotxformat_t;
 
-typedef struct {
-	int32_t  taxid;
-	int32_t  rank;
-	int32_t  parent;
-	char     *name;
+typedef struct ecotxnode {
+	int32_t           taxid;
+	int32_t           rank;
+	struct ecotxnode  *parent;
+	char              *name;
 } ecotx_t;
 
 typedef struct {
@@ -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.
@@ -189,8 +222,11 @@ 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);
+
+int eco_isundertaxon(ecotx_t *taxon, int other_taxid);
 
 ecoseq_t *ecoseq_iterator(const char *prefix);
 
@@ -227,4 +263,7 @@ ecotx_t *eco_getfamily(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 ecotx_t *eco_getkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
 
+int eco_is_taxid_ignored(int32_t *ignored_taxid, int32_t tab_len, int32_t taxid);
+int eco_is_taxid_included(ecotaxonomy_t *taxonomy, int32_t *included_taxid, int32_t tab_len, int32_t taxid);
+
 #endif /*ECOPCR_H_*/