/usr/lib/emboss/include/ajtranslate.h is in emboss-lib 6.6.0+dfsg-1.
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**
** AJAX translate functions
**
** These functions control all aspects of sequence translation
**
** These functions do not translate to the 'ambiguity' residues
** 'B' (Asn or Asp) and 'Z' (Glu or Gln). So the codons:
** RAC, RAT, RAY, RAU which could code for 'B' return 'X'
** and SAA, SAG, SAR which could code for 'Z' return 'X'.
**
** This translation table doesn't have the doubly ambiguous
** codons set up:
** YTR - L
** MGR - R
** YUR - L
**
** This should be attended to at some time.
**
** @author Copyright (C) 1999 Gary Williams
** @version $Revision: 1.24 $
** @modified Feb 15 1999 GWW First version
** @modified April 19 1999 GWW Second version using NCBI's GC tables
** @modified April 18 2000 GWW Reorganised many of the routines
** @modified 2001-2011 Peter Rice
** @modified $Date: 2013/02/07 10:32:50 $ 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 AJTRANSLATE_H
#define AJTRANSLATE_H
/* ========================================================================= */
/* ============================= include files ============================= */
/* ========================================================================= */
#include "ajdefine.h"
#include "ajstr.h"
#include "ajfile.h"
#include "ajseq.h"
AJ_BEGIN_DECLS
/* ========================================================================= */
/* =============================== constants =============================== */
/* ========================================================================= */
/* ========================================================================= */
/* ============================== public data ============================== */
/* ========================================================================= */
/* @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*
/* ========================================================================= */
/* =========================== public functions ============================ */
/* ========================================================================= */
/*
** 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 ajTrnRevStr(const AjPTrn trnObj, const AjPStr str,
AjPStr *pep);
void ajTrnSeqC(const AjPTrn trnObj, const char *str, ajint len,
AjPStr *pep);
void ajTrnSeqInitC(const AjPTrn trnObj, const char *str, ajint len,
AjPStr *pep);
void ajTrnSeqRevC(const AjPTrn trnObj, const char *str, ajint len,
AjPStr *pep);
void ajTrnSeqRevinitC(const AjPTrn trnObj, const char *str, ajint len,
AjPStr *pep);
void ajTrnSeqAltRevC(const AjPTrn trnObj, const char *str, ajint len,
AjPStr *pep);
void ajTrnSeqAltRevinitC(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);
void ajTrnSeqFrameInitC(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 ajTrnSeqFrameInitS(const AjPTrn trnObj, const AjPStr seq,
ajint frame, AjPStr *pep);
void ajTrnSeqFrameSeq(const AjPTrn trnObj, const AjPSeq seq,
ajint frame, AjPStr *pep);
void ajTrnSeqFrameSeqInit(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);
AjPSeq ajTrnSeqFramePep(const AjPTrn trnObj, const AjPSeq seq,
ajint frame);
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 ajTrnSeqInit(const AjPTrn trnObj, const AjPSeq seq,
ajint frame);
AjPSeq ajTrnSeqOrig(const AjPTrn trnObj, const AjPSeq seq,
ajint frame);
/*
** End of prototype definitions
*/
#ifdef AJ_COMPILE_DEPRECATED_BOOK
#endif /* AJ_COMPILE_DEPRECATED_BOOK */
#ifdef AJ_COMPILE_DEPRECATED
__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 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 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 /* AJ_COMPILE_DEPRECATED */
AJ_END_DECLS
#endif /* !AJTRANSLATE_H */
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