185 lines
3.2 KiB
C
185 lines
3.2 KiB
C
#ifndef _dapIO_h
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#define _dapIO_h
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#include "newtypes.h"
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/*
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** Definition of dap database files
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*/
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/*
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** Archive file (*.AR?)
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*/
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#define DAP_FILE_NAME_LENGTH 12
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typedef union {
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struct _ar_header {
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int_4 idbsiz;
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int_4 maxgel;
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int_4 idm;
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} header;
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struct _ar_lines {
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char name[DAP_FILE_NAME_LENGTH];
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} lines;
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} dap_ar_file_rec;
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#define dap_ar_header_rec(I) ( 1000 )
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#define dap_ar_byte_index(I,R) ( ((R)-1) * sizeof(dap_ar_file_rec) )
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/*
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** Relationships file (*.RL?)
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*/
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typedef union {
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struct _rl_header {
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int_4 num_gels;
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int_4 num_contigs;
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int_4 spare1;
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int_4 spare2;
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} header;
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struct _rl_lines {
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int_4 rel_pos;
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int_4 length;
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int_4 left_nbr;
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int_4 right_nbr;
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} lines;
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struct _rl_clines {
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int_4 length;
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int_4 spare3;
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int_4 left_end;
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int_4 right_end;
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} clines;
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} dap_rl_file_rec;
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#define dap_rl_header_rec(I) ( (I)->max_gels )
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#define dap_rl_byte_index(I,R) ( ((R)-1) * sizeof(dap_rl_file_rec) )
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/*
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** Sequence file (*.SQ?)
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*/
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typedef char *dap_sq_file_rec;
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#define dap_sq_byte_index(I,R) ( ((R)-1) * ((I)->max_gel_length) )
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/*
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** Tag files (*.TG?)
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*/
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typedef union {
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int i;
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char c[4];
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} dap_tag_type;
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typedef union {
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struct _tg_header {
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int_4 count;
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int_4 spare1;
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int_4 spare2;
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dap_tag_type spare3;
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int_4 free_list;
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} header;
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struct _tg_lines {
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int_4 position;
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int_4 length;
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int_4 comment;
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dap_tag_type type;
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int_4 next;
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} lines;
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} dap_tg_file_rec;
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#define dap_tg_byte_index(I,R) ( ((R)-1) *sizeof(dap_tg_file_rec) )
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#define dap_tg_header_rec(I) ( (I)->max_gels )
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/*
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** Comment files (*.CC?)
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*/
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#define DAP_COMMENT_SIZE 40
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typedef union {
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struct _cc_header {
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int_4 free_list;
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int_4 count;
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char spare[DAP_COMMENT_SIZE - sizeof(int_4)];
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} header;
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struct _cc_lines {
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int_4 next;
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char comment[DAP_COMMENT_SIZE];
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} lines;
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} dap_cc_file_rec;
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#define dap_cc_byte_index(I,R) ( ((R)-1) * sizeof(dap_cc_file_rec) )
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#define dap_cc_header_rec(I) (1)
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/*
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** Useful variables
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*/
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typedef char IOString[200];
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typedef struct {
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int max_gels;
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int num_gels;
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int num_contigs;
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int max_gel_length;
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int data_class;
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FILE *ar_fp;
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FILE *rl_fp;
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FILE *sq_fp;
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FILE *tg_fp;
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FILE *cc_fp;
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IOString ar_file;
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IOString rl_file;
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IOString sq_file;
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IOString tg_file;
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IOString cc_file;
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} DapIO;
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extern void dap_read_tg(DapIO *io, int rec, dap_tg_file_rec *t);
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extern void dap_write_tg(DapIO *io, int rec, dap_tg_file_rec *t);
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extern void dap_read_ar(DapIO *io, int rec, dap_ar_file_rec *t);
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extern void dap_write_ar(DapIO *io, int rec, dap_ar_file_rec *t);
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extern void dap_read_rl(DapIO *io, int rec, dap_rl_file_rec *t);
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extern void dap_write_rl(DapIO *io, int rec, dap_rl_file_rec *t);
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extern void dap_read_cc(DapIO *io, int rec, dap_cc_file_rec *t);
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extern void dap_write_cc(DapIO *io, int rec, dap_cc_file_rec *t);
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extern void dap_read_sq(DapIO *io, int rec, dap_sq_file_rec t);
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extern void dap_write_sq(DapIO *io, int rec, dap_sq_file_rec t);
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extern char *dap_read_comment(DapIO *io, int_4 cp);
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extern void dap_open_for_read(DapIO *io, char *name, char *version);
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extern void dap_open_for_write(DapIO *io, char *name, char *version);
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extern void dap_close_files(DapIO *io);
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#endif /* _dapIO_h */
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