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#ifndef ECOPCR_H_
#define ECOPCR_H_
#include <stdio.h>
#include <inttypes.h>
#ifndef H_apat
#include "../libapat/apat.h"
#endif
/*****************************************************
*
* Data type declarations
*
*****************************************************/
/*
*
* Sequence types
*
*/
typedef struct {
int32_t taxid;
char AC[20];
int32_t DE_length;
int32_t SQ_length;
int32_t CSQ_length;
char data[1];
} ecoseqformat_t;
typedef struct {
int32_t taxid;
int32_t SQ_length;
char *AC;
char *DE;
char *SQ;
} ecoseq_t;
/*
*
* Taxonomy taxon types
*
*/
typedef struct {
int32_t taxid;
int32_t rank;
int32_t parent;
int32_t namelength;
char name[1];
} ecotxformat_t;
typedef struct ecotxnode {
int32_t taxid;
int32_t rank;
struct ecotxnode *parent;
char *name;
} ecotx_t;
typedef struct {
int32_t count;
ecotx_t taxon[1];
} ecotxidx_t;
/*
*
* Taxonomy rank types
*
*/
typedef struct {
int32_t count;
char* label[1];
} ecorankidx_t;
/*
*
* Taxonomy name types
*
*/
typedef struct {
int32_t is_scientificname;
int32_t namelength;
int32_t classlength;
int32_t taxid;
char names[1];
} econameformat_t;
typedef struct {
char *name;
char *classname;
int32_t is_scientificname;
struct ecotxnode *taxon;
} econame_t;
typedef struct {
int32_t count;
econame_t names[1];
} econameidx_t;
typedef struct {
ecorankidx_t *ranks;
econameidx_t *names;
ecotxidx_t *taxons;
} ecotaxonomy_t;
/*****************************************************
*
* Function declarations
*
*****************************************************/
/*
*
* Low level system functions
*
*/
int32_t is_big_endian();
int32_t swap_int32_t(int32_t);
void *eco_malloc(int32_t chunksize,
const char *error_message,
const char *filename,
int32_t line);
void *eco_realloc(void *chunk,
int32_t chunksize,
const char *error_message,
const char *filename,
int32_t line);
void eco_free(void *chunk,
const char *error_message,
const char *filename,
int32_t line);
void eco_trace_memory_allocation();
void eco_untrace_memory_allocation();
#define ECOMALLOC(size,error_message) \
eco_malloc((size),(error_message),__FILE__,__LINE__)
#define ECOREALLOC(chunk,size,error_message) \
eco_realloc((chunk),(size),(error_message),__FILE__,__LINE__)
#define ECOFREE(chunk,error_message) \
eco_free((chunk),(error_message),__FILE__,__LINE__)
/*
*
* Error managment
*
*/
void ecoError(int32_t,const char*,const char *,int);
#define ECOERROR(code,message) ecoError((code),(message),__FILE__,__LINE__)
#define ECO_IO_ERROR (1)
#define ECO_MEM_ERROR (2)
#define ECO_ASSERT_ERROR (3)
#define ECO_NOTFOUND_ERROR (4)
/*
*
* Low level Disk access functions
*
*/
FILE *open_ecorecorddb(const char *filename,
int32_t *sequencecount,
int32_t abort_on_open_error);
void *read_ecorecord(FILE *,int32_t *recordSize);
/*
* Read function in internal binary format
*/
FILE *open_ecoseqdb(const char *filename,
int32_t *sequencecount);
ecoseq_t *readnext_ecoseq(FILE *);
ecorankidx_t *read_rankidx(const char *filename);
econameidx_t *read_nameidx(const char *filename,ecotaxonomy_t *taxonomy);
/**
* Read taxonomy data as formatted by the ecoPCRFormat.py script.
*
* This function is normaly uses internaly by the read_taxonomy
* function and should not be called directly.
*
* @arg filename path to the *.tdx file of the reformated db
*
* @return pointer to a taxonomy index structure
*/
ecotxidx_t *read_taxonomyidx(const char *filename,const char *filename2);
ecotaxonomy_t *read_taxonomy(const char *prefix,int32_t readAlternativeName);
ecotx_t *eco_findtaxonbytaxid(ecotaxonomy_t *taxonomy, int32_t taxid);
int eco_isundertaxon(ecotx_t *taxon, int other_taxid);
ecoseq_t *ecoseq_iterator(const char *prefix);
ecoseq_t *new_ecoseq();
int32_t delete_ecoseq(ecoseq_t *);
ecoseq_t *new_ecoseq_with_data( char *AC,
char *DE,
char *SQ,
int32_t taxid
);
int32_t delete_taxon(ecotx_t *taxon);
int32_t delete_taxonomy(ecotxidx_t *index);
int32_t rank_index(const char* label,ecorankidx_t* ranks);
int32_t delete_apatseq(SeqPtr pseq);
PatternPtr buildPattern(const char *pat, int32_t error_max);
PatternPtr complementPattern(PatternPtr pat);
SeqPtr ecoseq2apatseq(ecoseq_t *in,SeqPtr out,int32_t circular);
char *ecoComplementPattern(char *nucAcSeq);
char *ecoComplementSequence(char *nucAcSeq);
char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end);
ecotx_t *eco_getspecies(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getgenus(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getfamily(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
ecotx_t *eco_getsuperkingdom(ecotx_t *taxon,ecotaxonomy_t *taxonomy);
int eco_is_taxid_ignored(int32_t *ignored_taxid, int32_t tab_len, int32_t taxid);
int eco_is_taxid_included(ecotaxonomy_t *taxonomy, int32_t *included_taxid, int32_t tab_len, int32_t taxid);
#endif /*ECOPCR_H_*/
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