/usr/lib/emboss/include/ajtranslate.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 | #ifdef __cplusplus
extern "C"
{
#endif
#ifndef ajtranslate_h
#define ajtranslate_h
#include "ajax.h"
/* @data AjPTrn ***************************************************************
**
** Ajax Sequence translation object.
**
** Holds the Genetic Code specification and information needed to translate
** the sequence and find initiation sites.
**
** @new ajTrnNew Default constructor
** @new ajTrnNewI Default constructor
** @new ajTrnNewC Default constructor
** @delete ajTrnDel Default destructor
** @input ajTrnReadFile Reads a Genetic Code file
** @use ajTrnCodon Translating a codon from an AjPStr
** @use ajTrnRevCodon Reverse complement translating a codon from an AjPStr
** @use ajTrnCodonC Translating a codon from a char* text
** @use ajTrnRevCodonC Translating a codon from a char* text
** @use ajTrnCodonK Translating a codon from a char* to a char
** @use ajTrnRevCodonK Reverse complement translating a codon
** from a char* to a char
** @use ajTrnC Translating a sequence from a char* text
** @use ajTrnRevC Reverse complement translating a sequence from a char* text
** @use ajTrnAltRevC (Alt) Reverse complement translating a sequence
** from a char* text
** @use ajTrnStr Translating a sequence from a AjPStr
** @use ajTrnRevStr Reverse complement translating a sequence from a AjPStr
** @use ajTrnAltRevStr (Alt) Reverse complement translating a sequence
** from a AjPStr
** @use ajTrnSeq Translating a sequence from a AjPSeq
** @use ajTrnRevSeq Reverse complement translating a sequence from a AjPSeq
** @use ajTrnAltRevSeq Reverse complement translating a sequence from a AjPSeq
** @use ajTrnCFrame Translating a sequence from a char* in a frame
** @use ajTrnStrFrame Translating a sequence from a AjPStr in a frame
** @use ajTrnSeqFrame Translating a sequence from a AjPSeq in a frame
** @use ajTrnSeqFramePep Translating a sequence from a AjPSeq in a frame
** and returns a new peptide
** @use ajTrnDangleC Translates the last 1 or two bases of a sequence
** in a char* text
** @use ajTrnDangleS Translates the last 1 or two bases of a sequence
** in a AjStr
** @use ajTrnSeqOrig Translating a sequence
** @cast ajTrnGetTitle Returns description of the translation table
** @cast ajTrnGetFilename Returns file name the translation table was read from
** @use ajTrnCodonstrTypeS Checks whether the input codon is a Start codon,
** a Stop codon or something else
** @use ajTrnCodonstrTypeC Checks whether a const char* codon is
** a Start codon, a Stop codon or something else
**
** @attr FileName [AjPStr] name of file that held the data
** @attr Title [AjPStr] title of data read from file
** @attr GC [char[16][16][16]] genetic codon table
** @attr Starts [char[16][16][16]] initiation site table
**
** @alias AjSTrn
** @alias AjOTrn
** @@
******************************************************************************/
typedef struct AjSTrn {
AjPStr FileName;
AjPStr Title;
char GC[16][16][16];
char Starts[16][16][16];
} AjOTrn;
#define AjPTrn AjOTrn*
/* table to convert character of base to translation array element value */
/*static ajint trnconv[] = {*/
/* characters less than 64 */
/* 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14,
14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, */
/* @ A B C D E F G H I J K L M N O */
/* 14, 0, 13, 1, 12, 14, 14, 2, 11, 14, 14, 9, 14, 4, 14, 14,*/
/* P Q R S T U V W X Y Z [ \ ] ^ _ */
/* 14, 14, 5, 7, 3, 3, 10, 6, 14, 8, 14, 14, 14, 14, 14, 14, */
/* ` a b c d e f g h i j k l m n o */
/* 14, 0, 13, 1, 12, 14, 14, 2, 11, 14, 14, 9, 14, 4, 14, 14,*/
/* p q r s t u v w x y z { | } ~ del */
/* 14, 14, 5, 7, 3, 3, 10, 6, 14, 8, 14, 14, 14, 14, 14, 14
};*/
/*
** Prototype definitions
*/
void ajTrnDel (AjPTrn* pthis);
void ajTrnExit(void);
AjPTrn ajTrnNew (const AjPStr trnFileName);
AjPTrn ajTrnNewI (ajint trnFileNameInt);
AjPTrn ajTrnNewC (const char *trnFileName);
void ajTrnReadFile (AjPTrn trnObj, AjPFile trnFile);
AjPSeq ajTrnNewPep(const AjPSeq nucleicSeq, ajint frame);
char ajTrnCodonS (const AjPTrn trnObj, const AjPStr codon);
char ajTrnCodonRevS (const AjPTrn trnObj, const AjPStr codon);
char ajTrnCodonC (const AjPTrn trnObj, const char *codon);
char ajTrnCodonRevC (const AjPTrn trnObj, const char *codon);
char ajTrnCodonK (const AjPTrn trnObj, const char *codon);
char ajTrnRevCodonK (const AjPTrn trnObj, const char *codon);
void ajTrnSeqC (const AjPTrn trnObj, const char *str, ajint len,
AjPStr *pep);
void ajTrnSeqRevC (const AjPTrn trnObj, const char *str, ajint len,
AjPStr *pep);
void ajTrnSeqAltRevC (const AjPTrn trnObj, const char *str, ajint len,
AjPStr *pep);
void ajTrnSeqS (const AjPTrn trnObj, const AjPStr str,
AjPStr *pep);
void ajTrnSeqAltRevS (const AjPTrn trnObj, const AjPStr str,
AjPStr *pep);
void ajTrnSeqSeq (const AjPTrn trnObj, const AjPSeq seq,
AjPStr *pep);
void ajTrnSeqRevSeq (const AjPTrn trnObj, const AjPSeq seq,
AjPStr *pep);
void ajTrnSeqAltRevSeq (const AjPTrn trnObj, const AjPSeq seq,
AjPStr *pep);
void ajTrnSeqFrameC (const AjPTrn trnObj, const char *seq, ajint len,
ajint frame, AjPStr *pep);
const AjPStr ajTrnName(ajint trnFileNameInt);
void ajTrnSeqFrameS (const AjPTrn trnObj, const AjPStr seq,
ajint frame, AjPStr *pep);
void ajTrnSeqFrameSeq (const AjPTrn trnObj, const AjPSeq seq,
ajint frame, AjPStr *pep);
ajint ajTrnSeqDangleC (const AjPTrn trnObj, const char *seq,
ajint frame, AjPStr *pep);
ajint ajTrnSeqDangleS (const AjPTrn trnObj, const AjPStr seq,
ajint frame, AjPStr *pep);
AjPStr ajTrnGetTitle (const AjPTrn thys);
AjPStr ajTrnGetFilename (const AjPTrn thys);
ajint ajTrnCodonstrTypeC (const AjPTrn trnObj,
const char *codon, char *aa);
ajint ajTrnCodonstrTypeS (const AjPTrn trnObj,
const AjPStr codon, char *aa);
AjPSeq ajTrnSeqOrig (const AjPTrn trnObj, const AjPSeq seq,
ajint frame);
/*
** End of prototype definitions
*/
__deprecated ajint ajTrnStartStop (const AjPTrn trnObj,
const AjPStr codon, char *aa);
__deprecated ajint ajTrnStartStopC (const AjPTrn trnObj,
const char *codon, char *aa);
__deprecated AjPStr ajTrnGetFileName (const AjPTrn thys);
__deprecated const AjPStr ajTrnCodon (const AjPTrn trnObj, const AjPStr codon);
__deprecated const AjPStr ajTrnRevCodon (const AjPTrn trnObj,
const AjPStr codon);
__deprecated void ajTrnC (const AjPTrn trnObj, const char *str, ajint len,
AjPStr *pep);
__deprecated void ajTrnRevC (const AjPTrn trnObj, const char *str,
ajint len, AjPStr *pep);
__deprecated void ajTrnAltRevC (const AjPTrn trnObj, const char *str,
ajint len, AjPStr *pep);
__deprecated void ajTrnStr (const AjPTrn trnObj, const AjPStr str,
AjPStr *pep);
__deprecated void ajTrnRevStr (const AjPTrn trnObj, const AjPStr str,
AjPStr *pep);
__deprecated void ajTrnAltRevStr (const AjPTrn trnObj, const AjPStr str,
AjPStr *pep);
__deprecated void ajTrnSeq (const AjPTrn trnObj, const AjPSeq seq,
AjPStr *pep);
__deprecated void ajTrnRevSeq (const AjPTrn trnObj, const AjPSeq seq,
AjPStr *pep);
__deprecated void ajTrnAltRevSeq (const AjPTrn trnObj, const AjPSeq seq,
AjPStr *pep);
__deprecated void ajTrnCFrame (const AjPTrn trnObj, const char *seq,
ajint len, ajint frame, AjPStr *pep);
__deprecated void ajTrnStrFrame (const AjPTrn trnObj, const AjPStr seq,
ajint frame, AjPStr *pep);
__deprecated void ajTrnSeqFrame (const AjPTrn trnObj, const AjPSeq seq,
ajint frame, AjPStr *pep);
__deprecated AjPSeq ajTrnSeqFramePep (const AjPTrn trnObj, const AjPSeq seq,
ajint frame);
__deprecated ajint ajTrnCDangle (const AjPTrn trnObj, const char *seq,
ajint len, ajint frame, AjPStr *pep);
__deprecated ajint ajTrnStrDangle (const AjPTrn trnObj, const AjPStr seq,
ajint frame, AjPStr *pep);
#endif
#ifdef __cplusplus
}
#endif
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