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

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DMS, and added taxdump import from a compressed file
This commit is contained in:
Celine Mercier
2018-07-28 16:48:11 +02:00
parent 1de308a856
commit 7f6d1597fc
5 changed files with 120 additions and 12 deletions
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51
src/obidms_taxonomy.c
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@ -2740,6 +2740,35 @@ int read_names_dmp(const char* taxdump, OBIDMS_taxonomy_p tax)
**********************************************************************/
int obi_taxonomy_exists(OBIDMS_p dms, const char* taxonomy_name)
{
char* taxonomy_path;
DIR* dir;
taxonomy_path = get_taxonomy_path(dms, taxonomy_name);
if (taxonomy_path == NULL)
return -1;
dir = opendir(taxonomy_path);
if (dir)
{
/* Directory exists. */
closedir(dir);
return 1;
}
else if (ENOENT == errno)
{
/* Directory does not exist. */
return 0;
}
else
{
/* opendir() failed for some other reason. */
return -1;
}
}
OBIDMS_taxonomy_p obi_read_taxdump(const char* taxdump)
{
OBIDMS_taxonomy_p tax;
@ -3705,7 +3734,7 @@ 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)
{
static int32_t rankindex = -1;
static int32_t rankindex = -1;
if (taxonomy == NULL)
{
@ -3738,3 +3767,23 @@ const char* obi_taxo_rank_index_to_label(int32_t rank_idx, ecorankidx_t* ranks)
return (ranks->label)[rank_idx];
}
int obi_taxo_is_taxid_included(OBIDMS_taxonomy_p taxonomy,
int32_t* restrict_to_taxids,
int32_t count,
int32_t taxid)
{
int i;
ecotx_t* taxon;
taxon = obi_taxo_get_taxon_with_taxid(taxonomy, taxid);
if (taxon)
for (i=0; i < count; i++)
if ((taxon->taxid == restrict_to_taxids[i]) ||
(obi_taxo_is_taxon_under_taxid(taxon, restrict_to_taxids[i])))
return 1;
return 0;
}