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/* Unaligned ascii sequence file i/o.
*/
#ifndef eslSQIO_ASCII_INCLUDED
#define eslSQIO_ASCII_INCLUDED
#include "esl_config.h"
#include <stdio.h>
#ifdef HAVE_SYS_TYPES_H
#include <sys/types.h>
#endif
#include "esl_msa.h"
#include "esl_msafile.h"
#include "esl_sq.h"
#include "esl_sqio.h"
/* set the max residue count to 1 meg when reading a block */
#define MAX_RESIDUE_COUNT (1024 * 1024)
/* forward declaration */
struct esl_sqio_s;
/* ESL_SQASCII:
* An open sequence file for reading.
*/
typedef struct esl_sqascii_s {
FILE *fp; /* Open file ptr */
char errbuf[eslERRBUFSIZE];/* parse error mesg. Size must match msa.h */
int do_gzip; /* TRUE if we're reading from gzip -dc pipe */
int do_stdin; /* TRUE if we're reading from stdin */
int do_buffer; /* TRUE if we're reading from a buffer */
/* all input first gets buffered in memory; this gives us enough
* recall to use Guess*() functions even in nonrewindable streams
*/
char *mem; /* buffered input */
int allocm; /* <mem> size, multiples of eslREADBUFSIZE */
int mn; /* number of chars in <mem> (up to allocm) */
int mpos; /* pos of next <buf> to load from <mem> */
off_t moff; /* disk offset to start of <mem> */
int is_recording; /* TRUE if we need to keep buffering more */
/* input is either character-based [fread()] or line-based (esl_fgets())*/
char *buf; /* buffer for fread() or fgets() input */
off_t boff; /* disk offset to start of buffer */
int balloc; /* allocated size of buf */
int nc; /* #chars in buf (usually full, less at EOF)*/
int bpos; /* current position in the buffer (0..nc-1) */
int64_t L; /* #residues seen so far in current seq */
int64_t linenumber; /* What line of the file (1..N; -1=unknown)*/
off_t bookmark_offset; /* bookmark fwd position before reversing...*/
int64_t bookmark_linenum; /* in both linenumber and disk offset */
/* Format-specific configuration */
int is_linebased; /* TRUE for fgets() parsers; FALSE for fread() */
int eof_is_ok; /* TRUE if record can end on EOF */
int (*parse_header)(struct esl_sqio_s *, ESL_SQ *sq);
int (*skip_header) (struct esl_sqio_s *, ESL_SQ *sq);
int (*parse_end) (struct esl_sqio_s *, ESL_SQ *sq);
/* MSA files can be read as sequential seq files. */
ESL_MSAFILE *afp; /* open ESL_MSAFILE for reading */
ESL_MSA *msa; /* preloaded alignment to draw seqs from */
int idx; /* index of next seq to return, 0..nseq-1 */
/* SSI indexes allow fast random access of records in a seq file */
char *ssifile; /* path to expected SSI index file */
int rpl; /* residues per line in file; -1=unset 0=inval*/
int bpl; /* bytes per line in file; -1=unset, 0=inval */
int currpl; /* residues on current line (-1=unknown) */
int curbpl; /* bytes on current line (-1=unknown) */
int prvrpl; /* residues on previous line */
int prvbpl; /* bytes on previous line */
ESL_SSI *ssi; /* open ESL_SSI index, or NULL if none */
} ESL_SQASCII_DATA;
extern int esl_sqascii_Open(char *seqfile, int format, struct esl_sqio_s *sqfp);
extern int esl_sqascii_WriteFasta(FILE *fp, ESL_SQ *s, int update);
extern int esl_sqascii_Parse(char *buf, int size, ESL_SQ *s, int format);
#endif /*eslSQIO_ASCII_INCLUDED*/
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