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Taxonomy: adding, writing and reading preferred names, changed some

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function names, and fixed a bug with taxa indices not being properly
initialized
This commit is contained in:
Celine Mercier
2017-01-16 17:28:20 +01:00
parent 0385a92e02
commit c065c1914a
5 changed files with 444 additions and 57 deletions
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13
src/obidms_taxonomy.h
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@ -36,7 +36,8 @@ typedef struct ecotxnode {
int32_t farest;
int32_t idx;
struct ecotxnode* parent;
char* name;
char* name; // scientific name
char* preferred_name; // preferred name
bool local;
} ecotx_t;
@ -98,6 +99,7 @@ typedef struct OBIDMS_taxonomy_t {
ecomergedidx_t* merged_idx;
ecorankidx_t* ranks;
econameidx_t* names;
econameidx_t* preferred_names;
ecotxidx_t* taxa;
} OBIDMS_taxonomy_t, *OBIDMS_taxonomy_p;
@ -127,4 +129,11 @@ int obi_write_taxonomy(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* tax_name
OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump);
int obi_taxonomy_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid);
int obi_taxo_add_local_taxon(OBIDMS_taxonomy_p tax, const char* name, const char* rank_name, int32_t parent_taxid, int32_t min_taxid);
int obi_taxo_add_preferred_name_with_taxid(OBIDMS_taxonomy_p tax, int32_t taxid, const char* preferred_name);
int obi_taxo_add_preferred_name_with_taxon(OBIDMS_taxonomy_p tax, ecotx_t* taxon, const char* preferred_name);