145 lines
3.1 KiB
C
145 lines
3.1 KiB
C
|
#include <stdio.h>
|
||
|
|
#include <limits.h>
|
||
|
|
#include <string.h>
|
||
|
|
#include <malloc.h>
|
||
|
|
#include <time.h>
|
||
|
|
|
||
|
|
#define const /* const is not defined in non-ansi C,
|
||
|
|
* so it does not affect anything.
|
||
|
|
* Take this define off when using
|
||
|
|
* ANSI C compiler.
|
||
|
|
*/
|
||
|
|
|
||
|
|
#define NUM_OF_FIELDS 25 /* number of fields in "struct Sequence" other
|
||
|
|
than *len and *maxlen fields.
|
||
|
|
update this number when changing at[] list. */
|
||
|
|
|
||
|
|
/* C style T/F definitions. */
|
||
|
|
#ifndef TRUE
|
||
|
|
#define TRUE 1
|
||
|
|
#endif
|
||
|
|
|
||
|
|
#ifndef FALSE
|
||
|
|
#define FALSE 0
|
||
|
|
#endif
|
||
|
|
|
||
|
|
#ifndef MAX
|
||
|
|
#define MAX(a,b) ( (a) > (b) ? (a) : (b))
|
||
|
|
#endif
|
||
|
|
|
||
|
|
#ifndef MIN
|
||
|
|
#define MIN(a,b) ( (a) < (b) ? (a) : (b))
|
||
|
|
#endif
|
||
|
|
|
||
|
|
typedef struct
|
||
|
|
{
|
||
|
|
char type[32]; /* DNA, RNA, AA/PROTEIN, TEXT, SCORE(0-F) */
|
||
|
|
char status[32]; /* unmade, pending, unsolved, solved. */
|
||
|
|
char name[64];
|
||
|
|
char sequence_ID[32];
|
||
|
|
|
||
|
|
char *c_elem;
|
||
|
|
int seqlen;
|
||
|
|
int seqmaxlen;
|
||
|
|
|
||
|
|
int creation_date[6]; /* yy/mm/dd/hh/mn/sc */
|
||
|
|
char creator[32];
|
||
|
|
char film[32];
|
||
|
|
char membrane[32];
|
||
|
|
int laneset;
|
||
|
|
char source_ID[32];
|
||
|
|
char contig[32];
|
||
|
|
int strandedness; /* 0: unspecified, 1:pri(default), 2:sec */
|
||
|
|
int direction; /* 0: unspecified, 1:5to3>(default), -1:3to5< */
|
||
|
|
int offset;
|
||
|
|
char *comments;
|
||
|
|
int commentslen;
|
||
|
|
int commentsmaxlen;
|
||
|
|
char *baggage;
|
||
|
|
int baglen;
|
||
|
|
int bagmaxlen;
|
||
|
|
int group_number;
|
||
|
|
int group_ID;
|
||
|
|
char barcode[16];
|
||
|
|
int orig_direction; /* 0: unknown, 1:5'->3', 0:3'->5'*/
|
||
|
|
int orig_strand; /* 0: unknown, 1:primary, 0:secondary */
|
||
|
|
int probing_date[6];
|
||
|
|
int autorad_date[6];
|
||
|
|
char walk[32]; /* "TRUE", "FALSE" or whatever */
|
||
|
|
} Sequence;
|
||
|
|
|
||
|
|
|
||
|
|
/***
|
||
|
|
*** Elements in at[] and e_tags should be IN THE SAME ORDER.
|
||
|
|
***/
|
||
|
|
|
||
|
|
static char *at[NUM_OF_FIELDS] = {
|
||
|
|
"type",
|
||
|
|
"status",
|
||
|
|
"name",
|
||
|
|
"sequence-ID",
|
||
|
|
"sequence" ,
|
||
|
|
"creation-date" ,
|
||
|
|
"creator" ,
|
||
|
|
"film" ,
|
||
|
|
"membrane" ,
|
||
|
|
"laneset" ,
|
||
|
|
"source-ID" ,
|
||
|
|
"contig" ,
|
||
|
|
"strandedness" ,
|
||
|
|
"direction" ,
|
||
|
|
"offset" ,
|
||
|
|
"comments" ,
|
||
|
|
"baggage",
|
||
|
|
"group-number",
|
||
|
|
"barcode",
|
||
|
|
"orig_direction",
|
||
|
|
"orig_strand",
|
||
|
|
"probing-date",
|
||
|
|
"autorad-date",
|
||
|
|
"group-ID",
|
||
|
|
"walk"
|
||
|
|
};
|
||
|
|
|
||
|
|
|
||
|
|
enum e_tags { e_type, /*0*/
|
||
|
|
e_status,
|
||
|
|
e_name, /*2*/
|
||
|
|
e_sequence_ID , /*3*/
|
||
|
|
e_c_elem ,
|
||
|
|
e_creation_date,
|
||
|
|
e_creator, /*6*/
|
||
|
|
e_film,
|
||
|
|
e_membrane,
|
||
|
|
e_laneset,
|
||
|
|
e_source_ID,
|
||
|
|
e_contig,
|
||
|
|
e_strandedness,
|
||
|
|
e_direction,
|
||
|
|
e_offset, /*14*/
|
||
|
|
e_comments,
|
||
|
|
e_baggage,
|
||
|
|
e_group_number, /*17*/
|
||
|
|
e_barcode, /*18*/
|
||
|
|
e_orig_direction,
|
||
|
|
e_orig_strand, /*20*/
|
||
|
|
e_probing_date,
|
||
|
|
e_autorad_date,
|
||
|
|
e_group_ID, /*23*/
|
||
|
|
e_walk
|
||
|
|
};
|
||
|
|
|
||
|
|
typedef struct {
|
||
|
|
char symbol[2];
|
||
|
|
int field;
|
||
|
|
char *value;
|
||
|
|
} str_cond ;
|
||
|
|
|
||
|
|
typedef struct {
|
||
|
|
char prompt[20];
|
||
|
|
int optional; /* 'T' or 'F' */
|
||
|
|
char tag;
|
||
|
|
char strvalue[100]; /* default value or fill in by this program. */
|
||
|
|
} Args;
|
||
|
|
|