/usr/lib/emboss/include/embmat.h is in emboss-lib 6.3.1-6ubuntu3.
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 | #ifdef __cplusplus
extern "C"
{
#endif
#ifndef embmat_h
#define embmat_h
#define PRINTS_MAT "PRINTS/prints.mat"
typedef ajuint *PMAT_INT[26];
/* @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] Undocumented
** @attr cut2 [ajint] Undocumented
** @attr cut3 [ajint] Undocumented
** @attr cut4 [ajint] Undocumented
** @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;
AjBool circ12;
AjBool circ34;
AjPStr iso;
} EmbOMatMatch;
#define EmbPMatMatch EmbOMatMatch*
/*
** 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
*/
#endif
#ifdef __cplusplus
}
#endif
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