Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
157 lines (131 sloc) 6.52 KB
/* Simple sequence indices:
* Fast sequence record lookup in large files by keywords, such
* as names or accessions.
*/
#ifndef eslSSI_INCLUDED
#define eslSSI_INCLUDED
#include "esl_config.h"
#ifdef HAVE_SYS_TYPES_H
#include <sys/types.h>
#endif
#ifdef HAVE_STDINT_H
#include <stdint.h>
#endif
#ifdef HAVE_INTTYPES_H
#include <inttypes.h>
#endif
#define eslSSI_MAXFILES 32767 /* 2^15-1 */
#define eslSSI_MAXKEYS 2147483647L /* 2^31-1 */
#define eslSSI_MAXRAM 256 /* >256MB indices trigger external sort */
#ifndef HAVE_FSEEKO
#define fseeko fseek
#define ftello ftell
#endif
/* ESL_SSI
* Using an existing SSI index file.
*/
typedef struct {
FILE *fp; /* open SSI index file */
uint32_t flags; /* optional behavior flags */
uint32_t offsz; /* sizeof(off_t)'s in the SSI file */
uint16_t nfiles; /* number of files = 16 bit int */
uint64_t nprimary; /* number of primary keys */
uint64_t nsecondary; /* number of secondary keys */
uint32_t flen; /* length of filenames (inc '\0') */
uint32_t plen; /* length of primary keys (inc '\0') */
uint32_t slen; /* length of secondary keys (inc '\0') */
uint32_t frecsize; /* # bytes in a file record */
uint32_t precsize; /* # bytes in a primary key record */
uint32_t srecsize; /* # bytes in a secondary key record */
off_t foffset; /* disk offset, start of file records */
off_t poffset; /* disk offset, start of pri key recs */
off_t soffset; /* disk offset, start of sec key recs */
/* File information: */
char **filename; /* list of file names [0..nfiles-1] */
uint32_t *fileformat; /* file formats */
uint32_t *fileflags; /* optional per-file behavior flags */
uint32_t *bpl; /* bytes per line in file */
uint32_t *rpl; /* residues per line in file */
} ESL_SSI;
/* Flags for the <ssi->fileflags> bit vectors. */
#define eslSSI_FASTSUBSEQ (1<<0) /* we can do fast subseq lookup calculations on this file */
/* ESL_NEWSSI
* Used to create a new SSI index.
*/
typedef struct { /* Primary key data: */
char *key; /* key name */
uint16_t fnum; /* file number */
off_t r_off; /* record offset */
off_t d_off; /* data offset */
int64_t len; /* sequence length */
} ESL_PKEY;
typedef struct { /* Secondary key data: */
char *key; /* secondary key name */
char *pkey; /* primary key name */
} ESL_SKEY;
typedef struct {
char *ssifile; /* name of the SSI file we're creating */
FILE *ssifp; /* open SSI file being created */
int external; /* TRUE if pkeys and skeys are on disk */
int max_ram; /* threshold in MB to trigger extern sort */
char **filenames;
uint32_t *fileformat;
uint32_t *bpl;
uint32_t *rpl;
uint32_t flen; /* length of longest filename, inc '\0' */
uint16_t nfiles; /* can store up to 2^15-1 (32767) files */
ESL_PKEY *pkeys;
uint32_t plen; /* length of longest pkey, including '\0' */
uint64_t nprimary; /* can store up to 2^63-1 = 9.2e18 keys */
char *ptmpfile; /* primary key tmpfile name, for extern sort */
FILE *ptmp; /* handle on open ptmpfile */
ESL_SKEY *skeys;
uint32_t slen; /* length of longest skey, including '\0' */
uint64_t nsecondary;
char *stmpfile; /* secondary key tmpfile name, for extern sort */
FILE *stmp; /* handle on open ptmpfile */
char errbuf[eslERRBUFSIZE];
} ESL_NEWSSI;
#define eslSSI_FCHUNK 16 /* chunk size for file name reallocation */
#define eslSSI_KCHUNK 128 /* and for key reallocation */
/* 1. Using (reading) SSI indices */
extern int esl_ssi_Open(const char *filename, ESL_SSI **ret_ssi);
extern void esl_ssi_Close(ESL_SSI *ssi);
extern int esl_ssi_FindName(ESL_SSI *ssi, const char *key,
uint16_t *ret_fh, off_t *ret_roff, off_t *opt_doff, int64_t *opt_L);
extern int esl_ssi_FindNumber(ESL_SSI *ssi, int64_t nkey,
uint16_t *opt_fh, off_t *opt_roff, off_t *opt_doff, int64_t *opt_L, char **opt_pkey);
extern int esl_ssi_FindSubseq(ESL_SSI *ssi, const char *key, int64_t requested_start,
uint16_t *ret_fh, off_t *ret_roff, off_t *ret_doff, int64_t *ret_L, int64_t *ret_actual_start);
extern int esl_ssi_FileInfo(ESL_SSI *ssi, uint16_t fh, char **ret_filename, int *ret_format);
/* 2. Creating (writing) SSI indices. */
extern int esl_newssi_Open(const char *ssifile, int allow_overwrite, ESL_NEWSSI **ret_newssi);
extern int esl_newssi_AddFile (ESL_NEWSSI *ns, const char *filename, int fmt, uint16_t *ret_fh);
extern int esl_newssi_SetSubseq(ESL_NEWSSI *ns, uint16_t fh, uint32_t bpl, uint32_t rpl);
extern int esl_newssi_AddKey (ESL_NEWSSI *ns, const char *key, uint16_t fh, off_t r_off, off_t d_off, int64_t L);
extern int esl_newssi_AddAlias (ESL_NEWSSI *ns, const char *alias, const char *key);
extern int esl_newssi_Write (ESL_NEWSSI *ns);
extern void esl_newssi_Close (ESL_NEWSSI *ns);
/* 3. Portable binary i/o. */
extern void esl_byteswap(char *swap, int nbytes);
extern uint16_t esl_ntoh16(uint16_t netshort);
extern uint32_t esl_ntoh32(uint32_t netlong);
extern uint64_t esl_ntoh64(uint64_t net_int64);
extern uint16_t esl_hton16(uint16_t hostshort);
extern uint32_t esl_hton32(uint32_t hostlong);
extern uint64_t esl_hton64(uint64_t host_int64);
extern int esl_fread_u16(FILE *fp, uint16_t *ret_result);
extern int esl_fread_u32(FILE *fp, uint32_t *ret_result);
extern int esl_fread_u64(FILE *fp, uint64_t *ret_result);
extern int esl_fread_i16(FILE *fp, int16_t *ret_result);
extern int esl_fread_i32(FILE *fp, int32_t *ret_result);
extern int esl_fread_i64(FILE *fp, int64_t *ret_result);
extern int esl_fwrite_u16(FILE *fp, uint16_t n);
extern int esl_fwrite_u32(FILE *fp, uint32_t n);
extern int esl_fwrite_u64(FILE *fp, uint64_t n);
extern int esl_fwrite_i16(FILE *fp, int16_t n);
extern int esl_fwrite_i32(FILE *fp, int32_t n);
extern int esl_fwrite_i64(FILE *fp, int64_t n);
extern int esl_fread_offset(FILE *fp, int mode, off_t *ret_offset);
extern int esl_fwrite_offset(FILE *fp, off_t offset);
#endif /* eslSSI_INCLUDED */
You can’t perform that action at this time.