142 lines
3 KiB
C
142 lines
3 KiB
C
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#include <stdio.h>
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#include <limits.h>
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#include <string.h>
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#include <malloc.h>
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#include <time.h>
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#define const /* const is not defined in non-ansi C,
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* so it does not affect anything.
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* Take this define off when using
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* ANSI C compiler.
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*/
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#define NUM_OF_FIELDS 24 /* number of fields in "struct Sequence" other
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than *len and *maxlen fields.
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update this number when changing at[] list. */
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/* c style T/F definitions. */
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#ifndef TRUE
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#define TRUE 1
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#endif
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#ifndef FALSE
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#define FALSE 0
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#endif
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#ifndef MAX
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#define MAX(a,b) ( (a) > (b) ? (a) : (b))
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#endif
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#ifndef MIN
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#define MIN(a,b) ( (a) < (b) ? (a) : (b))
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#endif
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typedef struct
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{
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char type[32]; /* DNA, RNA, AA/PROTEIN, TEXT, SCORE(0-F) */
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char status[32]; /* unmade, pending, unsolved, solved. */
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char name[64];
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char sequence_ID[32];
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char *c_elem;
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int seqlen;
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int seqmaxlen;
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int creation_date[6]; /* yy/mm/dd/hh/mn/sc */
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char creator[32];
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char film[32];
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char membrane[32];
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int laneset;
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char source_ID[32];
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char contig[32];
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int strandedness; /* 0: unspecified, 1:pri(default), 2:sec */
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int direction; /* 0: unspecified, 1:5to3>(default), -1:3to5< */
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int offset;
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char *comments;
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int commentslen;
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int commentsmaxlen;
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char *baggage;
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int baglen;
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int bagmaxlen;
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int group_number;
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int group_ID;
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char barcode[16];
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int orig_direction; /* 0: unknown, 1:5'->3', 0:3'->5'*/
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int orig_strand; /* 0: unknown, 1:primary, 0:secondary */
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int probing_date[6];
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int autorad_date[6];
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} Sequence;
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/***
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*** Elements in at[] and e_tags should be IN THE SAME ORDER.
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***/
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static char *at[NUM_OF_FIELDS] = {
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"type",
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"status",
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"name",
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"sequence-ID",
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"sequence" ,
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"creation-date" ,
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"creator" ,
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"film" ,
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"membrane" ,
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"laneset" ,
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"source-ID" ,
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"contig" ,
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"strandedness" ,
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"direction" ,
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"offset" ,
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"comments" ,
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"baggage",
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"group-number",
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"barcode",
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"orig_direction",
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"orig_strand",
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"probing-date",
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"autorad-date",
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"group-ID"
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};
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enum e_tags { e_type, /*0*/
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e_status,
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e_name, /*2*/
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e_sequence_ID , /*3*/
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e_c_elem ,
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e_creation_date,
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e_creator, /*6*/
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e_film,
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e_membrane,
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e_laneset,
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e_source_ID,
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e_contig,
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e_strandedness,
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e_direction,
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e_offset, /*14*/
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e_comments,
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e_baggage,
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e_group_number, /*17*/
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e_barcode, /*18*/
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e_orig_direction,
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e_orig_strand, /*20*/
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e_probing_date,
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e_autorad_date,
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e_group_ID /*23*/
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};
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typedef struct {
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char symbol[2];
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int field;
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char *value;
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} str_cond ;
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typedef struct {
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char prompt[20];
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int optional; /* 'T' or 'F' */
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char tag;
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char strvalue[100]; /* default value or fill in by this program. */
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} Args;
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