191 lines
3.4 KiB
C
191 lines
3.4 KiB
C
#ifndef _bapIO_h
|
|
#define _bapIO_h
|
|
|
|
#include "newtypes.h"
|
|
|
|
/*
|
|
** Definition of dap database files
|
|
*/
|
|
|
|
|
|
|
|
/*
|
|
** Archive file (*.AR?)
|
|
*/
|
|
#define BAP_FILE_NAME_LENGTH 16
|
|
typedef union {
|
|
|
|
struct _ar_lines {
|
|
char name[BAP_FILE_NAME_LENGTH];
|
|
} lines;
|
|
|
|
} bap_ar_file_rec;
|
|
|
|
#define bap_ar_byte_index(I,R) ( ((R)-1) *sizeof(bap_ar_file_rec) )
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
/*
|
|
** Relationships file (*.RL?)
|
|
*/
|
|
typedef union {
|
|
|
|
struct _rl_dbheader {
|
|
int_4 maxdb;
|
|
int_4 idbsiz;
|
|
int_4 maxgel;
|
|
int_4 idm;
|
|
} dbheader;
|
|
|
|
struct _rl_header {
|
|
int_4 num_gels;
|
|
int_4 num_contigs;
|
|
int_4 spare1;
|
|
int_4 spare2;
|
|
} header;
|
|
|
|
struct _rl_lines {
|
|
int_4 rel_pos;
|
|
int_4 length;
|
|
int_4 left_nbr;
|
|
int_4 right_nbr;
|
|
} lines;
|
|
|
|
struct _rl_clines {
|
|
int_4 length;
|
|
int_4 spare3;
|
|
int_4 left_end;
|
|
int_4 right_end;
|
|
} clines;
|
|
|
|
} bap_rl_file_rec;
|
|
|
|
#define bap_rl_header_rec(I) ( (I)->max_gels )
|
|
#define bap_rl_byte_index(I,R) ( (R) * sizeof(bap_rl_file_rec) )
|
|
#define bap_rl_dbheader_rec(I) (0)
|
|
|
|
|
|
|
|
|
|
|
|
|
|
/*
|
|
** Sequence file (*.SQ?)
|
|
*/
|
|
typedef char *bap_sq_file_rec;
|
|
#define bap_sq_byte_index(I,R) ( ((R)-1) * ((I)->max_gel_length) )
|
|
|
|
|
|
|
|
/*
|
|
** Tag files (*.TG?)
|
|
*/
|
|
typedef union {
|
|
int i;
|
|
char c[4];
|
|
} bap_tag_type;
|
|
|
|
|
|
|
|
typedef union {
|
|
|
|
struct _tg_header {
|
|
int_4 count;
|
|
int_4 spare1;
|
|
int_4 spare2;
|
|
bap_tag_type spare3;
|
|
int_4 free_list;
|
|
} header;
|
|
|
|
struct _tg_lines {
|
|
int_4 position;
|
|
int_4 length;
|
|
int_4 comment;
|
|
bap_tag_type type;
|
|
int_4 next;
|
|
} lines;
|
|
|
|
} bap_tg_file_rec;
|
|
|
|
#define bap_tg_byte_index(I,R) ( ((R)-1) *sizeof(bap_tg_file_rec) )
|
|
#define bap_tg_header_rec(I) ( (I)->max_gels )
|
|
|
|
/*
|
|
** Comment files (*.CC?)
|
|
*/
|
|
#define BAP_COMMENT_SIZE 40
|
|
typedef union {
|
|
|
|
struct _cc_header {
|
|
int_4 free_list;
|
|
int_4 count;
|
|
char spare[BAP_COMMENT_SIZE - sizeof(int_4)];
|
|
} header;
|
|
|
|
struct _cc_lines {
|
|
int_4 next;
|
|
char comment[BAP_COMMENT_SIZE];
|
|
} lines;
|
|
|
|
} bap_cc_file_rec;
|
|
|
|
#define bap_cc_byte_index(I,R) ( ((R)-1) *sizeof(bap_cc_file_rec) )
|
|
#define bap_cc_header_rec(I) (1)
|
|
|
|
|
|
|
|
/*
|
|
** Useful variables
|
|
*/
|
|
typedef char IOString[200];
|
|
|
|
typedef struct {
|
|
int max_gels;
|
|
int num_gels;
|
|
int num_contigs;
|
|
int max_gel_length;
|
|
int data_class;
|
|
int max_db_size;
|
|
|
|
FILE *ar_fp;
|
|
FILE *rl_fp;
|
|
FILE *sq_fp;
|
|
FILE *tg_fp;
|
|
FILE *cc_fp;
|
|
|
|
IOString ar_file;
|
|
IOString rl_file;
|
|
IOString sq_file;
|
|
IOString tg_file;
|
|
IOString cc_file;
|
|
} BapIO;
|
|
|
|
|
|
|
|
|
|
|
|
extern void bap_read_tg(BapIO *io, int rec, bap_tg_file_rec *t);
|
|
extern void bap_write_tg(BapIO *io, int rec, bap_tg_file_rec *t);
|
|
extern void bap_read_ar(BapIO *io, int rec, bap_ar_file_rec *t);
|
|
extern void bap_write_ar(BapIO *io, int rec, bap_ar_file_rec *t);
|
|
extern void bap_read_rl(BapIO *io, int rec, bap_rl_file_rec *t);
|
|
extern void bap_write_rl(BapIO *io, int rec, bap_rl_file_rec *t);
|
|
extern void bap_read_cc(BapIO *io, int rec, bap_cc_file_rec *t);
|
|
extern void bap_write_cc(BapIO *io, int rec, bap_cc_file_rec *t);
|
|
extern void bap_read_sq(BapIO *io, int rec, bap_sq_file_rec t);
|
|
extern void bap_write_sq(BapIO *io, int rec, bap_sq_file_rec t);
|
|
extern char *bap_read_comment(BapIO *io, int_4 cp);
|
|
extern int_4 bap_write_comment(BapIO *io, char *c);
|
|
extern int_4 bap_get_free_tag(BapIO *io);
|
|
extern void bap_insert_tag(BapIO *io, int_4 gel, bap_tg_file_rec t);
|
|
extern void bap_open_for_read(BapIO *io, char *name, char *version);
|
|
extern void bap_open_for_write(BapIO *io, char *name, char *version);
|
|
extern void bap_close_files(BapIO *io);
|
|
|
|
|
|
#endif /* _bapIO_h */
|