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