/usr/include/io_lib/seqIOABI.h is in libstaden-read-dev 1.12.4-1build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 | /*
* Copyright (c) Medical Research Council 1994. All rights reserved.
*
* Permission to use, copy, modify and distribute this software and its
* documentation for any purpose is hereby granted without fee, provided that
* this copyright and notice appears in all copies.
*
* This file was written by James Bonfield, Simon Dear, Rodger Staden,
* as part of the Staden Package at the MRC Laboratory of Molecular
* Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
*
* MRC disclaims all warranties with regard to this software.
*/
#ifndef _seqIOABI_h_
#define _seqIOABI_h_
#include <sys/types.h> /* off_t */
#include "io_lib/os.h"
#ifdef __cplusplus
extern "C" {
#endif
/*
* The ABI magic number - "ABIF"
*/
#define ABI_MAGIC ((int_4) ((((('A'<<8)+'B')<<8)+'I')<<8)+'F')
/*
* The index is located towards the end of the ABI trace file.
* It's location is given by a longword at a fixed place.
*/
#define IndexPO ((off_t)26)
#define IndexEntryLength 28
/*
* Here are some labels we will be looking for, four chars packed
* into an int_4
*/
#define LABEL(a) ((int_4) ((((((a)[0]<<8)+(a)[1])<<8)+(a)[2])<<8)+(a)[3])
#define DataEntryLabel LABEL("DATA")
#define BaseEntryLabel LABEL("PBAS")
#define BasePosEntryLabel LABEL("PLOC")
#define SpacingEntryLabel LABEL("SPAC")
#define SignalEntryLabel LABEL("S/N%")
#define FWO_Label LABEL("FWO_")
#define MCHNLabel LABEL("MCHN")
#define PDMFLabel LABEL("PDMF")
#define SMPLLabel LABEL("SMPL")
#define PPOSLabel LABEL("PPOS")
#define CMNTLabel LABEL("CMNT")
#define GelNameLabel LABEL("GELN")
#define LANELabel LABEL("LANE")
#define RUNDLabel LABEL("RUND")
#define RUNTLabel LABEL("RUNT")
#define MTXFLabel LABEL("MTXF")
#define SPACLabel LABEL("SPAC")
#define SVERLabel LABEL("SVER")
#define MODLLabel LABEL("MODL")
#define BaseConfLabel LABEL("PCON")
/*
* From the ABI results file connected to `fp' whose index starts
* at byte offset `indexO', return in `val' the `lw'th long word
* from the `count'th entry labelled `label'.
* The result is 0 for failure, or index offset for success.
*/
int getABIIndexEntryLW(FILE *fp, off_t indexO,
uint_4 label, uint_4 count, int lw,
uint_4 *val);
/*
* From the ABI results file connected to `fp' whose index starts
* at byte offset `indexO', return in `val' the `sw'th short word
* from the `count'th entry labelled `label'.
* The result is 0 for failure, or index offset for success.
*/
int getABIIndexEntrySW(FILE *fp, off_t indexO,
uint_4 label, uint_4 count, int sw,
uint_2 *val);
/*
* Gets the offset of the ABI index.
* Returns -1 for failure, 0 for success.
*/
int getABIIndexOffset(FILE *fp, uint_4 *indexO);
/*
* Get an "ABI String". These strings are either pointed to by the index
* offset, or held in the offset itself when the string is <= 4 characters.
* The first byte of the string determines its length.
* 'string' is a buffer 256 characters long.
*
* Returns -1 for failure, string length for success.
*/
int getABIString(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
char *string);
/*
* Get an "ABI Int_1". This is raw 1-byte integer data pointed to by the
* offset, or held in the offset itself when the data is <= 4 characters.
*
* If indexO is 0 then we do not search for (or indeed use) label and count,
* but simply assume that we are already at the correct offset and read from
* here. (NB: This negates the length <= 4 check.)
*
* Returns -1 for failure, length desired for success (it'll only fill out
* up to max_data_len elements, but it gives an indication of whether there
* was more to come).
*/
int getABIint1(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
uint_1 *data, int max_data_len);
/*
* Get an "ABI Int_2". This is raw 2-byte integer data pointed to by the
* offset, or held in the offset itself when the data is <= 4 characters.
*
* Returns -1 for failure, length desired for success (it'll only fill out
* up to max_data_len elements, but it gives an indication of whether there
* was more to come).
*/
int getABIint2(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
uint_2 *data, int max_data_len);
/*
* Get an "ABI Int_4". This is raw 4-byte integer data pointed to by the
* offset, or held in the offset itself when the data is <= 4 characters.
*
* Returns -1 for failure, length desired for success (it'll only fill out
* up to max_data_len elements, but it gives an indication of whether there
* was more to come).
*/
int getABIint4(FILE *fp, off_t indexO, uint_4 label, uint_4 count,
uint_4 *data, int max_data_len);
int dump_labels(FILE *fp, off_t indexO);
/*
* Change the DATA counts for fetching traces
*/
void abi_set_data_counts(int f, int w, int o, int _);
/*
* Put the DATA counts back to their defaults.
*/
void abi_reset_data_counts(void);
#ifdef __cplusplus
}
#endif
#endif /* _seqIOABI_h_ */
|