/usr/lib/emboss/include/embest.h is in emboss-lib 6.6.0+dfsg-6build1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 | /* @include embest ************************************************************
**
** NUCLEUS EST alignment functions
**
** @author Copyright (C) 1996 Richard Mott
** @author Copyright (C) 1998 Peter Rice revised for EMBOSS
** @version $Revision: 1.13 $
** @@
**
** 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 EMBEST_H
#define EMBEST_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ajdefine.h"
#include "ajseqdata.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* Definition of the padding-character in CAF */
#define padding_char '-'
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* @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;
/* @enum directions ***********************************************************
**
** Path matrix cell type and direction
**
** @value INTRON Intron
** @value DIAGONAL Diagonal in path
** @value DELETE_EST Delete in EST sequence
** @value DELETE_GENOME Delete in genome sequence
** @value FORWARD_SPLICED_INTRON Forward spliced intron
** @value REVERSE_SPLICED_INTRON Reverse spliced intron
******************************************************************************/
typedef enum { INTRON=0, DIAGONAL=1, DELETE_EST=2, DELETE_GENOME=3,
FORWARD_SPLICED_INTRON=-1, REVERSE_SPLICED_INTRON=-2
} directions;
/* @enum donor_acceptor *******************************************************
**
** Donors and acceptors for slice site junctions
**
** @value NOT_A_SITE Not a splice site
** @value DONOR Donor site
** @value ACCEPTOR Acceptor site
******************************************************************************/
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
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** 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
*/
AJ_END_DECLS
#endif /* !EMBEST_H */
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