/usr/lib/emboss/include/ajbase.h is in emboss-lib 6.6.0-1.
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 | /* @include ajbase ************************************************************
**
** AJAX IUB base nucleic acid functions
**
** @author Copyright (C) 1999 Alan Bleasby
** @version $Revision: 1.15 $
** @modified Feb 28 ajb First version
** @modified $Date: 2011/10/18 14:23:40 $ 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 AJBASE_H
#define AJBASE_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ajdefine.h"
#include "ajstr.h"
#include <ctype.h>
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** Prototype definitions
*/
const AjPStr ajBaseGetCodes(ajint ibase);
const AjPStr ajBaseGetMnemonic(ajint base);
char ajBaseAlphacharComp(char base);
void ajBaseExit(void);
float ajBaseAlphaCompare(ajint base1, ajint base2);
ajint ajBaseAlphaToBin(ajint c);
char ajBaseBinToAlpha(ajint c);
char ajBaseAlphacharToBin(char c);
float ajBaseAlphacharCompare(char c, char c2);
AjBool ajBaseFromDoublet(const AjPStr nuc2, char* Pc);
ajint ajBasecodeToInt(ajint c);
ajint ajBasecodeFromInt(ajint n);
ajint ajResidueAlphaToBin(ajint c);
char ajResidueBinToAlpha(ajint c);
const AjPStr ajResidueGetCodes(ajint ires);
const AjPStr ajResidueGetMnemonic(ajint base);
AjBool ajResidueFromTriplet(const AjPStr aa3, char *Pc);
AjBool ajResidueToTriplet(char c, AjPStr *Paa3);
AjBool ajBaseExistsBin(ajint base);
AjBool ajBaseExistsChar(char c);
AjBool ajResidueExistsBin(ajint base);
AjBool ajResidueExistsChar(char c);
/*
** End of prototype definitions
*/
#ifdef AJ_COMPILE_DEPRECATED_BOOK
#endif /* AJ_COMPILE_DEPRECATED_BOOK */
#ifdef AJ_COMPILE_DEPRECATED
__deprecated AjBool ajBaseAa1ToAa3(char aa1, AjPStr *aa3);
__deprecated AjBool ajBaseAa3ToAa1(char *aa1, const AjPStr aa3);
__deprecated const AjPStr ajBaseCodes(ajint ibase);
__deprecated char ajSeqBaseComp(char base);
__deprecated ajint ajAZToInt(ajint c);
__deprecated ajint ajAZToBin(ajint c);
__deprecated char ajAZToBinC(char c);
__deprecated char ajBinToAZ(ajint c);
__deprecated ajint ajIntToAZ(ajint n);
__deprecated char ajBaseComp(char base);
__deprecated float ajBaseProb(ajint base1, ajint base2);
#endif /* AJ_COMPILE_DEPRECATED */
AJ_END_DECLS
#endif /* !AJBASE_H */
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