This file is indexed.

/usr/lib/emboss/include/ajfileio.h is in emboss-lib 6.6.0+dfsg-1.

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
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
/* @include ajfileio **********************************************************
**
** AJAX file routines
**
** @author Copyright (C) 1999 Peter Rice
** @version $Revision: 1.9 $
** @modified Peter Rice pmr@ebi.ac.uk I/O file functions from ajfile.c
** @modified $Date: 2011/12/19 16:35:36 $ by $Author: rice $
** @@
**
** This library is free software; you can redistribute it and/or
** modify it under the terms of the GNU Lesser General Public
** License as published by the Free Software Foundation; either
** version 2.1 of the License, or (at your option) any later version.
**
** This library is distributed in the hope that it will be useful,
** but WITHOUT ANY WARRANTY; without even the implied warranty of
** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
** Lesser General Public License for more details.
**
** You should have received a copy of the GNU Lesser General Public
** License along with this library; if not, write to the Free Software
** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
** MA  02110-1301,  USA.
**
******************************************************************************/

#ifndef AJFILEIO_H
#define AJFILEIO_H

/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */

#include "ajdefine.h"
#include "ajfile.h"
#include <sys/stat.h>

AJ_BEGIN_DECLS




/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */




/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */




/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */




/*
** Prototype definitions
*/

size_t         ajReadbinBinary(AjPFile thys, size_t count,
                               size_t element_size, void* ptr);
size_t         ajReadbinChar(AjPFile file, size_t len, char* buffer);
size_t         ajReadbinCharTrim(AjPFile file, size_t len, char* buffer);
size_t         ajReadbinInt(AjPFile thys, ajint *val);
size_t         ajReadbinIntEndian(AjPFile thys, ajint *val);
size_t         ajReadbinIntLocal(AjPFile thys, ajint *val);
size_t         ajReadbinInt2(AjPFile thys, ajshort *val);
size_t         ajReadbinInt2Endian(AjPFile thys, ajshort *val);
size_t         ajReadbinInt2Local(AjPFile thys, ajshort *val);
size_t         ajReadbinInt4(AjPFile thys, ajint *val);
size_t         ajReadbinInt4Endian(AjPFile thys, ajint *val);
size_t         ajReadbinInt4Local(AjPFile thys, ajint *val);
size_t         ajReadbinInt8(AjPFile thys, ajlong *val);
size_t         ajReadbinInt8Endian(AjPFile thys, ajlong *val);
size_t         ajReadbinInt8Local(AjPFile thys, ajlong *val);
size_t         ajReadbinStr(AjPFile file, size_t len, AjPStr* buffer);
size_t         ajReadbinStrTrim(AjPFile file, size_t len, AjPStr* buffer);
size_t         ajReadbinUint(AjPFile thys, ajuint *val);
size_t         ajReadbinUint2(AjPFile thys, ajushort *val);
size_t         ajReadbinUint4(AjPFile thys, ajuint *val);
size_t         ajReadbinUint8(AjPFile thys, ajulong *val);
size_t         ajReadbinUintEndian(AjPFile thys, ajuint *val);
size_t         ajReadbinUint2Endian(AjPFile thys, ajushort *val);
size_t         ajReadbinUint4Endian(AjPFile thys, ajuint *val);
size_t         ajReadbinUint8Endian(AjPFile thys, ajulong *val);
size_t         ajReadbinUintLocal(AjPFile thys, ajuint *val);
size_t         ajReadbinUint2Local(AjPFile thys, ajushort *val);
size_t         ajReadbinUint4Local(AjPFile thys, ajuint *val);
size_t         ajReadbinUint8Local(AjPFile thys, ajulong *val);

size_t         ajWritebinBinary(AjPFile file, size_t count,
                                size_t size, const void* buffer);
size_t         ajWritebinByte(AjPFile thys, char ch);
size_t         ajWritebinChar(AjPFile thys, const char* txt, size_t len);
size_t         ajWritebinInt2(AjPFile thys, ajshort i);
size_t         ajWritebinInt4(AjPFile thys, ajint i);
size_t         ajWritebinInt8(AjPFile thys, ajlong i);
size_t         ajWritebinNewline(AjPFile thys);
size_t         ajWritebinStr(AjPFile thys, const AjPStr str, size_t len);
size_t         ajWritebinUint2(AjPFile thys, ajushort u);
size_t         ajWritebinUint4(AjPFile thys, ajuint u);
size_t         ajWritebinUint8(AjPFile thys, ajulong iu);
AjBool         ajWriteline(AjPFile file, const AjPStr line);
AjBool         ajWritelineNewline(AjPFile file, const AjPStr line);
AjBool         ajWritelineSpace(AjPFile file, const AjPStr line);

AjBool         ajReadline(AjPFile file, AjPStr *Pdest);
AjBool         ajReadlinePos(AjPFile file, AjPStr *Pdest, ajlong* Ppos);
AjBool         ajReadlineTrim(AjPFile file, AjPStr *Pdest);
AjBool         ajReadlineTrimPos(AjPFile file, AjPStr *Pdest, ajlong* Ppos);
AjBool         ajReadlineAppend(AjPFile file, AjPStr* Pdest);

AjBool         ajBuffreadLine(AjPFilebuff buff, AjPStr *pdest);
AjBool         ajBuffreadLinePos(AjPFilebuff buff, AjPStr *pdest,
                                 ajlong* Ppos);
AjBool         ajBuffreadLineStore(AjPFilebuff buff, AjPStr* pdest,
                                   AjBool store, AjPStr *astr);
AjBool         ajBuffreadLinePosStore(AjPFilebuff buff, AjPStr* pdest,
                                      ajlong* Ppos, AjBool store, AjPStr *astr);
AjBool         ajBuffreadLineTrim(AjPFilebuff buff, AjPStr* pdest);

/*
** End of prototype definitions
*/




#ifdef AJ_COMPILE_DEPRECATED_BOOK
#endif /* AJ_COMPILE_DEPRECATED_BOOK */

#ifdef AJ_COMPILE_DEPRECATED

__deprecated void    ajFileBuffLoad(AjPFilebuff thys);
__deprecated AjBool  ajFileBuffGet(AjPFilebuff thys, AjPStr *pdest);
__deprecated AjBool  ajFileBuffGetL(AjPFilebuff thys, AjPStr *pdest,
                                    ajlong* fpos);
__deprecated AjBool  ajFileBuffGetStore(AjPFilebuff thys, AjPStr* pdest,
                                        AjBool store, AjPStr *astr);
__deprecated AjBool  ajFileBuffGetStoreL(AjPFilebuff thys,
                                         AjPStr* pdest, ajlong* fpos,
                                         AjBool store, AjPStr *astr);
__deprecated AjBool  ajFileBuffGetTrim(AjPFilebuff thys, AjPStr* pdest);

__deprecated AjBool  ajFileGets(AjPFile thys, AjPStr *pdest);
__deprecated AjBool  ajFileGetsL(AjPFile thys,
                                 AjPStr *pdest, ajlong* fpos);
__deprecated AjBool  ajFileGetsTrim(AjPFile thys, AjPStr *pdest);
__deprecated AjBool  ajFileGetsTrimL(AjPFile thys,
                                     AjPStr *pdest, ajlong* fpos);
__deprecated AjBool  ajFileReadAppend(AjPFile thys, AjPStr* pbuff);
__deprecated AjBool  ajFileReadLine(AjPFile thys, AjPStr *pdest);
__deprecated ajint   ajFileWriteByte(AjPFile thys, char ch);
__deprecated ajint   ajFileWriteInt2(AjPFile thys, ajshort i);
__deprecated ajint   ajFileWriteInt4(AjPFile thys, ajint i);
__deprecated size_t  ajFileRead(void* ptr, size_t element_size,
                                size_t count, AjPFile thys);
__deprecated size_t  ajFileWrite(AjPFile file, const void* ptr,
                                 size_t element_size, size_t count);
__deprecated ajint   ajFileWriteStr(AjPFile thys,
                                    const AjPStr str, ajuint len);

#endif /* AJ_COMPILE_DEPRECATED */




AJ_END_DECLS

#endif /* !AJFILEIO_H */