Taxonomy: added functions to check if a taxonomy already exists in a

DMS, and added taxdump import from a compressed file

src/obidms_taxonomy.h

@@ -183,6 +183,25 @@ typedef struct OBIDMS_taxonomy_t {
 } OBIDMS_taxonomy_t, *OBIDMS_taxonomy_p;
 
 
+
+/**
+ * @brief Function checking whether a taxonomy is already registered in a DMS using its name.
+ *
+ * @param dms The path to the taxdump directory.
+ *
+ * @param dms A pointer on the DMS.
+ * @param taxonomy_name The name (prefix) of the taxonomy.
+ *
+ * @retval 1 if the taxonomy exists.
+ * @retval 0 if the taxonomy does not exist
+ * @retval -1 if an error occurred.
+ *
+ * @since June 2018
+ * @author Celine Mercier (celine.mercier@metabarcoding.org)
+ */
+int obi_taxonomy_exists(OBIDMS_p dms, const char* taxonomy_name);
+
+
 /**
  * @brief Function reading an NCBI taxdump and loading its information into a taxonomy structure.
  *
@@ -414,3 +433,10 @@ ecotx_t* obi_taxo_get_superkingdom(ecotx_t* taxon, OBIDMS_taxonomy_p taxonomy);
  * @see rank_label_to_index()
  */
 const char* obi_taxo_rank_index_to_label(int32_t rank_idx, ecorankidx_t* ranks);
+
+
+// TODO
+int obi_taxo_is_taxid_included(OBIDMS_taxonomy_p taxonomy,
+			     			   int32_t* restrict_to_taxids,
+				    		   int32_t count,
+					    	   int32_t taxid);