This file is indexed.

/usr/lib/emboss/include/embmat.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
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
/* @include embmat ************************************************************
**
** General match routines
**
** @author Copyright (c) 1999 Alan Bleasby
** @version $Revision: 1.17 $
** @modified $Date: 2013/03/05 23:08:59 $ 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 EMBMAT_H
#define EMBMAT_H

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

#include "ajdefine.h"
#include "ajmem.h"
#include "ajmess.h"
#include "ajstr.h"
#include "ajsys.h"
#include "ajbase.h"
#include "ajfileio.h"

AJ_BEGIN_DECLS




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




#define PRINTS_MAT "PRINTS/prints.mat"

typedef ajuint *PMAT_INT[26];




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




/* @data EmbPMatPrints ********************************************************
**
** NUCLEUS data structure for PRINTS protein fingerprints
**
** @attr cod [AjPStr] gc line
** @attr acc [AjPStr] gx line
** @attr tit [AjPStr] gt line
** @attr len [ajuint*] Lengths of motifs
** @attr thresh [ajuint*] % of maximum score for matrix
** @attr max [ajuint*] Maximum score for matrix
** @attr matrix [PMAT_INT*] Matrices
** @attr n [ajuint] Number of motifs in fingerprint
** @attr Padding [char[4]] Padding to alignment boundary
** @@
******************************************************************************/

typedef struct EmbSMatPrints
{
    AjPStr cod;
    AjPStr acc;
    AjPStr tit;
    ajuint    *len;
    ajuint    *thresh;
    ajuint    *max;
    PMAT_INT  *matrix;
    ajuint    n;
    char      Padding[4];
} EmbOMatPrint;
#define EmbPMatPrints EmbOMatPrint*




/* @data EmbPMatMatch *********************************************************
**
** NUCLEUS data structure for sequence matrix matches
**
** @attr seqname [AjPStr] Sequence name
** @attr cod [AjPStr] Matrix name
** @attr acc [AjPStr] Matrix accession number
** @attr tit [AjPStr] Matrix title
** @attr pat [AjPStr] Pattern
** @attr n [ajuint] Number of motifs in fingerprint
** @attr len [ajuint] Lengths of motifs
** @attr thresh [ajuint] % of maximum score for matrix
** @attr max [ajuint] Maximum score for matrix
** @attr element [ajuint] Number of matching element
** @attr start [ajuint] Start of match
** @attr end [ajuint] End of match
** @attr score [ajuint] Score of match
** @attr hpe [ajuint] Hits per element (so far)
** @attr hpm [ajuint] Hits per motif (so far)
** @attr all [AjBool] Can be set if all elements match
** @attr ordered [AjBool] Can be set if "all" and in order
** @attr forward [AjBool] on forward strand
** @attr mm [ajuint] Number of mismatches
** @attr cut1 [ajint] First 5' cut
** @attr cut2 [ajint] First 3' cut
** @attr cut3 [ajint] Reverse 5' cut
** @attr cut4 [ajint] Reverse 3' cut
** @attr len1 [ajuint] Fragment length 5'
** @attr len2 [ajuint] Fragment length 3'
** @attr len3 [ajuint] Fragment length reverse 5'
** @attr len4 [ajuint] Fragment length reverse 3'
** @attr circ12 [AjBool] Circular for cut1 and/or cut2
** @attr circ34 [AjBool] Circular for cut3 and/or cut4
** @attr iso [AjPStr] Holds names of isoschizomers
** @@
******************************************************************************/

typedef struct EmbSMatMatch
{
    AjPStr seqname;
    AjPStr cod;
    AjPStr acc;
    AjPStr tit;
    AjPStr pat;
    ajuint  n;
    ajuint  len;
    ajuint  thresh;
    ajuint  max;
    ajuint  element;
    ajuint  start;
    ajuint  end;
    ajuint  score;
    ajuint  hpe;
    ajuint  hpm;
    AjBool all;
    AjBool ordered;
    AjBool forward;
    ajuint  mm;
    ajint  cut1;
    ajint  cut2;
    ajint  cut3;
    ajint  cut4;
    ajuint len1;
    ajuint len2;
    ajuint len3;
    ajuint len4;
    AjBool circ12;
    AjBool circ34;
    AjPStr iso;
} EmbOMatMatch;
#define EmbPMatMatch EmbOMatMatch*




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



/*
** Prototype definitions
*/

void   embMatMatchDel (EmbPMatMatch *s);
void   embMatPrintsInit (AjPFile *fp);
void   embMatProtDelInt (EmbPMatPrints *s);
EmbPMatPrints embMatProtReadInt (AjPFile fp);
ajuint    embMatProtScanInt (const AjPStr s, const AjPStr n,
			    const EmbPMatPrints m, AjPList *l,
			    AjBool *all, AjBool *ordered, AjBool overlap);

/*
** End of prototype definitions
*/


AJ_END_DECLS

#endif  /* !EMBMAT_H */