First implementation of taxonomy reading

src/obidms_taxonomy.h

@@ -0,0 +1,101 @@
+/********************************************************************
+ * OBIDMS taxonomy headeer file                                     *
+ ********************************************************************/
+
+/**
+ * @file obidms_taxonomy.h
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ * @date March 2nd 2016
+ * @brief Header file for the functions handling the reading of binary taxonomy files.
+ */
+
+
+#include <stdlib.h>
+#include <stdio.h>
+#include <stdbool.h>
+
+#include "obidms.h"
+
+
+typedef struct {
+	int32_t  taxid;
+	int32_t  rank;
+	int32_t	 parent;
+	int32_t  name_length;
+	char     name[1];
+} ecotxformat_t;
+
+
+typedef struct ecotxnode {
+	int32_t           taxid;
+	int32_t           rank;
+	int32_t  		  farest;
+	struct ecotxnode* parent;
+	char*			  name;
+} ecotx_t;
+
+
+typedef struct {
+	int32_t count;
+	int32_t max_taxid;
+	int32_t buffer_size;
+	ecotx_t taxon[1];
+} ecotxidx_t;
+
+
+typedef struct {
+	int32_t count;
+	char*   label[1];
+} ecorankidx_t;
+
+
+typedef struct {
+ 	int32_t is_scientific_name;
+	int32_t  name_length;
+	int32_t  class_length;
+	int32_t  taxid;
+	char     names[1];
+} econameformat_t;
+
+
+typedef struct {
+	char*   		  name;
+	char*   		  class_name;
+	int32_t 		  is_scientific_name;
+	struct ecotxnode* taxon;
+} econame_t;
+
+
+typedef struct {
+	int32_t 	count;
+	econame_t   names[1];
+} econameidx_t;
+
+
+typedef struct OBIDMS_taxonomy_t {
+	ecorankidx_t* ranks;
+	econameidx_t* names;
+	ecotxidx_t*   taxa;
+} OBIDMS_taxonomy_t, *OBIDMS_taxonomy_p;
+
+
+OBIDMS_taxonomy_p obi_read_taxonomy(OBIDMS_p dms, const char* taxonomy_name, bool read_alternative_names);
+
+int obi_close_taxonomy(OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_parent_at_rank(ecotx_t* taxon, int32_t rankidx);
+
+ecotx_t* obi_taxo_get_taxon_with_taxid(OBIDMS_taxonomy_p taxonomy, int32_t taxid);
+
+bool obi_taxo_is_taxon_under_taxid(ecotx_t* taxon, int32_t other_taxid);
+
+ecotx_t* obi_taxo_get_species(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_genus(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_family(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_kingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+
+ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
+