/********************************************************************
 * OBIDMS taxonomy header 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"


#define SWAPINT32(x)     ((((x) << 24) & 0xFF000000) | (((x) <<  8) & 0xFF0000) | \
                         (((x) >>  8) & 0xFF00)     | (((x) >> 24) & 0xFF))


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;
	int32_t			  idx;
	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;	// taxid idx
	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);


int write_rankidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name);
int write_taxonomyidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name);
int write_nameidx(OBIDMS_p dms, OBIDMS_taxonomy_p tax, const char* taxonomy_name);