/usr/lib/emboss/include/embest.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 | #ifdef __cplusplus
extern "C"
{
#endif
#ifndef embest_h
#define embest_h
/* Definition of the padding-character in CAF */
#define padding_char '-'
/* @data hash_list ************************************************************
**
** NUCLEUS internal data structure for est2genome EMBOSS application
** to maintain internal hash lists.
**
** @attr name [char*] Name
** @attr offset [unsigned long] Offset
** @attr text_offset [unsigned long] Text offset
** @attr next [struct hash_list*] Next in list
** @@
******************************************************************************/
typedef struct hash_list
{
char *name;
unsigned long offset;
unsigned long text_offset;
struct hash_list *next;
}
HASH_LIST;
typedef enum { INTRON=0, DIAGONAL=1, DELETE_EST=2, DELETE_GENOME=3,
FORWARD_SPLICED_INTRON=-1, REVERSE_SPLICED_INTRON=-2
} directions;
typedef enum { NOT_A_SITE=1, DONOR=2, ACCEPTOR=4 } donor_acceptor;
/* @data EmbPEstAlign *********************************************************
**
** NUCLEUS data structure for EST alignments (originally for est2genome)
**
** @attr gstart [ajint] Genomic start
** @attr estart [ajint] EST start
** @attr gstop [ajint] Genomic stop
** @attr estop [ajint] EST stop
** @attr score [ajint] Score
** @attr len [ajint] Length
** @attr align_path [ajint*] Path
** @@
******************************************************************************/
typedef struct EmbSEstAlign
{
ajint gstart;
ajint estart;
ajint gstop;
ajint estop;
ajint score;
ajint len;
ajint *align_path;
} EmbOEstAlign;
#define EmbPEstAlign EmbOEstAlign*
enum base_types /* just defines a, c, g, t as 0-3, for indexing purposes. */
{
base_a, base_c, base_g, base_t, base_n, base_i, base_o, nucleotides, anybase
};
/* Definitions for nucleotides */
#define MINUS_INFINITY -10000000
/*
** Prototype definitions
*/
EmbPEstAlign embEstAlignNonRecursive ( const AjPSeq est, const AjPSeq genome,
ajint gap_penalty, ajint intron_penalty,
ajint splice_penalty,
const AjPSeq splice_sites,
ajint backtrack, ajint needleman,
ajint init_path );
EmbPEstAlign embEstAlignLinearSpace ( const AjPSeq est, const AjPSeq genome,
ajint match, ajint mismatch,
ajint gap_penalty, ajint intron_penalty,
ajint splice_penalty,
const AjPSeq splice_sites,
float max_area );
AjPSeq embEstFindSpliceSites( const AjPSeq genome, ajint direction );
void embEstFreeAlign( EmbPEstAlign *ge );
ajint embEstGetSeed (void);
void embEstMatInit (ajint match, ajint mismatch, ajint gap,
ajint neutral, char pad_char);
void embEstOutBlastStyle ( AjPFile ofile,
const AjPSeq genome, const AjPSeq est,
const EmbPEstAlign ge, ajint gap_penalty,
ajint intron_penalty,
ajint splice_penalty,
ajint gapped, ajint reverse );
void embEstPrintAlign( AjPFile ofile,
const AjPSeq genome, const AjPSeq est,
const EmbPEstAlign ge, ajint width );
void embEstSetDebug (void);
void embEstSetVerbose (void);
AjPSeq embEstShuffleSeq( AjPSeq seq, ajint in_place, ajint *seed );
/*
** End of prototype definitions
*/
#endif
#ifdef __cplusplus
}
#endif
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