ajtranslate.c

Prototype

void ajTrnDel (
      AjPTrn* pthis
);

Type Name Read/Write Description

AjPTrn* pthis Delete Address of translation table object

void RETURN

Type	Name	Read/Write	Description
`AjPTrn*`	`pthis`	Delete	Address of translation table object
`void`		RETURN

From EMBOSS 1.0.0

Function ajTrnNewC

Initialises translation. Reads a translation data file.

Prototype

AjPTrn ajTrnNewC (
      const char* filename
);

Type Name Read/Write Description

const char* filename Input translation table file name

AjPTrn RETURN Translation object

Type	Name	Read/Write	Description
`const char*`	`filename`	Input	translation table file name
`AjPTrn`		RETURN	Translation object

From EMBOSS 1.0.0

Initialises translation. Reads a translation data file called 'EGC.x' where 'x' is supplied as an ajint parameter. The filename must exist somewhere in the data path. ajTrnDel should be called when translation has ceased.

Prototype

AjPTrn ajTrnNewI (
      ajint trnFileNameInt
);

Type Name Read/Write Description

ajint trnFileNameInt Input translation table file name number

AjPTrn RETURN Translation object

Type	Name	Read/Write	Description
`ajint`	`trnFileNameInt`	Input	translation table file name number
`AjPTrn`		RETURN	Translation object

From EMBOSS 1.0.0

Function ajTrnNew

Initialises translation. Reads a translation data file ajTrnDel should be called when translation has ceased.

Prototype

AjPTrn ajTrnNew (
      const AjPStr trnFileName
);

Type Name Read/Write Description

const AjPStr trnFileName Input translation table file name

AjPTrn RETURN Translation object

Type	Name	Read/Write	Description
`const AjPStr`	`trnFileName`	Input	translation table file name
`AjPTrn`		RETURN	Translation object

From EMBOSS 1.0.0

Function ajTrnReadFile

Reads a translation data file

Prototype

void ajTrnReadFile (
      AjPTrn trnObj,
      AjPFile trnFile
);

Type Name Read/Write Description

AjPTrn trnObj Output translation table object

AjPFile trnFile Modify translation table file handle

void RETURN

Type	Name	Read/Write	Description
`AjPTrn`	`trnObj`	Output	translation table object
`AjPFile`	`trnFile`	Modify	translation table file handle
`void`		RETURN

From EMBOSS 1.0.0

Function ajTrnNewPep

Creates a new AjPSeq set up with an appropriate name and description

Prototype

AjPSeq ajTrnNewPep (
      const AjPSeq nucleicSeq,
      ajint frame
);

Type Name Read/Write Description

const AjPSeq nucleicSeq Input nucleic sequence being translated

ajint frame Input frame of translation (-3,-2,-1,0,1,2,3,4,5,6)

AjPSeq RETURN New peptide object

Type	Name	Read/Write	Description
`const AjPSeq`	`nucleicSeq`	Input	nucleic sequence being translated
`ajint`	`frame`	Input	frame of translation (-3,-2,-1,0,1,2,3,4,5,6)
`AjPSeq`		RETURN	New peptide object

From EMBOSS 1.0.0

Function ajTrnCodonS

Translates a codon

Prototype

char ajTrnCodonS (
      const AjPTrn trnObj,
      const AjPStr codon
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const AjPStr codon Input codon to translate

char RETURN Amino acid translation

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPStr`	`codon`	Input	codon to translate
`char`		RETURN	Amino acid translation

From EMBOSS 6.2.0

Function ajTrnCodonRevS

Translates the reverse complement of a codon

Prototype

char ajTrnCodonRevS (
      const AjPTrn trnObj,
      const AjPStr codon
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const AjPStr codon Input codon to translate

char RETURN Amino acid translation

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPStr`	`codon`	Input	codon to translate
`char`		RETURN	Amino acid translation

From EMBOSS 6.2.0

Function ajTrnCodonC

Translates a const char * codon

Prototype

char ajTrnCodonC (
      const AjPTrn trnObj,
      const char* codon
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`codon`	Input	codon to translate (these 3 characters need not be NULL-terminated)
`char`		RETURN	Amino acid translation

From EMBOSS 1.0.0

Function ajTrnCodonRevC

Translates the reverse complement of a const char * codon

Prototype

char ajTrnCodonRevC (
      const AjPTrn trnObj,
      const char* codon
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`codon`	Input	codon to translate (these 3 characters need not be NULL-terminated)
`char`		RETURN	Amino acid translation

From EMBOSS 6.2.0

Function ajTrnCodonK

Translates a const char * codon to a char

Prototype

char ajTrnCodonK (
      const AjPTrn trnObj,
      const char* codon
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`codon`	Input	codon to translate (these 3 characters need not be NULL-terminated)
`char`		RETURN	Amino acid translation

From EMBOSS 1.0.0

Function ajTrnRevCodonK

Translates a the reverse complement of a const char * codon to a char

Prototype

char ajTrnRevCodonK (
      const AjPTrn trnObj,
      const char* codon
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`codon`	Input	codon to translate (these 3 characters need not be NULL-terminated)
`char`		RETURN	Amino acid translation

From EMBOSS 1.0.0

Function ajTrnSeqC

Translates a sequence in a char

Prototype

void ajTrnSeqC (
      const AjPTrn trnObj,
      const char* str,
      ajint len,
      AjPStr* pep
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const char* str Input sequence string to translate

ajint len Input length of sequence string to translate

AjPStr* pep Modify returned peptide translation (APPENDED TO INPUT)

void RETURN

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`str`	Input	sequence string to translate
`ajint`	`len`	Input	length of sequence string to translate
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqRevC

Translates the reverse complement of a sequence in a char *.

Prototype

void ajTrnSeqRevC (
      const AjPTrn trnObj,
      const char* str,
      ajint len,
      AjPStr* pep
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`str`	Input	sequence string to translate
`ajint`	`len`	Input	length of sequence string to translate
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqAltRevC

Translates the reverse complement of a sequence in a char *.

Prototype

void ajTrnSeqAltRevC (
      const AjPTrn trnObj,
      const char* str,
      ajint len,
      AjPStr* pep
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`str`	Input	sequence string to translate
`ajint`	`len`	Input	length of sequence string to translate
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqS

Translates a sequence in a AjPStr.

Prototype

void ajTrnSeqS (
      const AjPTrn trnObj,
      const AjPStr str,
      AjPStr* pep
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const AjPStr str Input sequence string to translate

AjPStr* pep Modify returned peptide translation (APPENDED TO INPUT)

void RETURN

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPStr`	`str`	Input	sequence string to translate
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnRevStr

Translates the reverse complement of a sequence in a AjPStr.

Prototype

void ajTrnRevStr (
      const AjPTrn trnObj,
      const AjPStr str,
      AjPStr* pep
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPStr`	`str`	Input	sequence string to translate
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 1.0.0

Function ajTrnSeqAltRevS

Translates the reverse complement of a sequence in a AjPStr.

Prototype

void ajTrnSeqAltRevS (
      const AjPTrn trnObj,
      const AjPStr str,
      AjPStr* pep
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPStr`	`str`	Input	sequence string to translate
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqSeq

Translates a sequence in a AjPSeq

Prototype

void ajTrnSeqSeq (
      const AjPTrn trnObj,
      const AjPSeq seq,
      AjPStr* pep
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const AjPSeq seq Input sequence to translate

AjPStr* pep Modify returned peptide translation (APPENDED TO INPUT)

void RETURN

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPSeq`	`seq`	Input	sequence to translate
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqRevSeq

Translates the reverse complement of a sequence in a AjPSeq The translation is APPENDED to the input peptide.

Prototype

void ajTrnSeqRevSeq (
      const AjPTrn trnObj,
      const AjPSeq seq,
      AjPStr* pep
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPSeq`	`seq`	Input	sequence to translate
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqAltRevSeq

Translates the reverse complement of a sequence in a AjPSeq The translation is APPENDED to the input peptide.

Prototype

void ajTrnSeqAltRevSeq (
      const AjPTrn trnObj,
      const AjPSeq seq,
      AjPStr* pep
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPSeq`	`seq`	Input	sequence to translate
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqFrameC

Translates a sequence in a char * in the specified frame. The translation is APPENDED to the input peptide.

Prototype

void ajTrnSeqFrameC (
      const AjPTrn trnObj,
      const char* seq,
      ajint len,
      ajint frame,
      AjPStr* pep
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const char* seq Input sequence string to translate

ajint len Input length of sequence string to translate

ajint frame Input frame to translate in

AjPStr* pep Modify returned peptide translation (APPENDED TO INPUT)

void RETURN

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`seq`	Input	sequence string to translate
`ajint`	`len`	Input	length of sequence string to translate
`ajint`	`frame`	Input	frame to translate in
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqFrameS

Translates a sequence in a AjStr in the specified frame. The translation is APPENDED to the input peptide.

Prototype

void ajTrnSeqFrameS (
      const AjPTrn trnObj,
      const AjPStr seq,
      ajint frame,
      AjPStr* pep
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const AjPStr seq Input sequence string to translate

ajint frame Input frame to translate in

AjPStr* pep Modify returned peptide translation (APPENDED TO INPUT)

void RETURN

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPStr`	`seq`	Input	sequence string to translate
`ajint`	`frame`	Input	frame to translate in
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqFrameSeq

Translates a sequence in a AjSeq in the specified frame. The translation is APPENDED to the input peptide.

Prototype

void ajTrnSeqFrameSeq (
      const AjPTrn trnObj,
      const AjPSeq seq,
      ajint frame,
      AjPStr* pep
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const AjPSeq seq Input sequence string to translate

ajint frame Input frame to translate in

AjPStr* pep Modify returned peptide translation (APPENDED TO INPUT)

void RETURN

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPSeq`	`seq`	Input	sequence string to translate
`ajint`	`frame`	Input	frame to translate in
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`void`		RETURN

From EMBOSS 6.2.0

Function ajTrnSeqFramePep

Translates a sequence in a AjSeq in the specified frame and returns a new peptide.

Prototype

AjPSeq ajTrnSeqFramePep (
      const AjPTrn trnObj,
      const AjPSeq seq,
      ajint frame
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPSeq`	`seq`	Input	sequence string to translate
`ajint`	`frame`	Input	frame to translate in
`AjPSeq`		RETURN	returned peptide translation

From EMBOSS 2.0.0

Function ajTrnSeqDangleC

Translates the last 1 or two bases of a sequence in a char that would not be translated if just translating complete codons in the specified frame. The translation is APPENDED to the input peptide.

Prototype

ajint ajTrnSeqDangleC (
      const AjPTrn trnObj,
      const char* seq,
      ajint frame,
      AjPStr* pep
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const char* seq Input sequence string to translate

ajint frame Input frame to translate in

AjPStr* pep Modify returned peptide translation (APPENDED TO INPUT)

ajint RETURN Number of dangling bases (0,1 or 2)

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`seq`	Input	sequence string to translate
`ajint`	`frame`	Input	frame to translate in
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`ajint`		RETURN	Number of dangling bases (0,1 or 2)

From EMBOSS 6.2.0

Function ajTrnSeqDangleS

Translates the last 1 or two bases of a sequence in a AjStr that would not be translated if just translating complete codons in the specified frame. The translation is APPENDED to the input peptide.

Prototype

ajint ajTrnSeqDangleS (
      const AjPTrn trnObj,
      const AjPStr seq,
      ajint frame,
      AjPStr* pep
);

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPStr`	`seq`	Input	sequence string to translate
`ajint`	`frame`	Input	frame to translate in
`AjPStr*`	`pep`	Modify	returned peptide translation (APPENDED TO INPUT)
`ajint`		RETURN	Number of dangling bases (0,1 or 2) dangle = len - end;

From EMBOSS 6.2.0

Function ajTrnSeqOrig

Translates a sequence.

Prototype

AjPSeq ajTrnSeqOrig (
      const AjPTrn trnObj,
      const AjPSeq seq,
      ajint frame
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const AjPSeq seq Input sequence to translate

ajint frame Input frame to translate in (-6 to 6)

AjPSeq RETURN Peptide translation

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPSeq`	`seq`	Input	sequence to translate
`ajint`	`frame`	Input	frame to translate in (-6 to 6)
`AjPSeq`		RETURN	Peptide translation

From EMBOSS 1.0.0

Function ajTrnCodonstrTypeC

Checks whether a const char * codon is a Start codon, a Stop codon or something else

Prototype

ajint ajTrnCodonstrTypeC (
      const AjPTrn trnObj,
      const char* codon,
      char* aa
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const char* codon Input codon to translate (these 3 characters need not be NULL-terminated)

char* aa Output returned translated amino acid (not a NULL-terminated array of char)

ajint RETURN 1 if it is a start codon, -1 if it is a stop codon, else 0

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const char*`	`codon`	Input	codon to translate (these 3 characters need not be NULL-terminated)
`char*`	`aa`	Output	returned translated amino acid (not a NULL-terminated array of char)
`ajint`		RETURN	1 if it is a start codon, -1 if it is a stop codon, else 0

From EMBOSS 6.2.0

Function ajTrnCodonstrTypeS

Checks whether the input codon is a Start codon, a Stop codon or something else

Prototype

ajint ajTrnCodonstrTypeS (
      const AjPTrn trnObj,
      const AjPStr codon,
      char* aa
);

Type Name Read/Write Description

const AjPTrn trnObj Input Translation tables

const AjPStr codon Input codon to check

char* aa Output returned translated amino acid (not a NULL-terminated array of char)

ajint RETURN 1 if it is a start codon, -1 if it is a stop codon, else 0

Type	Name	Read/Write	Description
`const AjPTrn`	`trnObj`	Input	Translation tables
`const AjPStr`	`codon`	Input	codon to check
`char*`	`aa`	Output	returned translated amino acid (not a NULL-terminated array of char)
`ajint`		RETURN	1 if it is a start codon, -1 if it is a stop codon, else 0

From EMBOSS 6.2.0

Function ajTrnGetTitle

Returns the translation table description. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

AjPStr ajTrnGetTitle (
      const AjPTrn thys
);

Type Name Read/Write Description

const AjPTrn thys Input Translation object.

AjPStr RETURN Description as a string.

Type	Name	Read/Write	Description
`const AjPTrn`	`thys`	Input	Translation object.
`AjPStr`		RETURN	Description as a string.

From EMBOSS 1.0.0

Function ajTrnGetFilename

Returns the file that the translation table was read from. Because this is a pointer to the real internal string the caller must take care not to change the character string in any way. If the string is to be changed (case for example) then it must first be copied.

Prototype

AjPStr ajTrnGetFilename (
      const AjPTrn thys
);

Type Name Read/Write Description

const AjPTrn thys Input Translation object.

AjPStr RETURN File name as a string.

Type	Name	Read/Write	Description
`const AjPTrn`	`thys`	Input	Translation object.
`AjPStr`		RETURN	File name as a string.

From EMBOSS 6.2.0

Function ajTrnName

Checks whether a const char * codon is a Start codon, a Stop codon or something else

Prototype

const AjPStr ajTrnName (
      ajint trnFileNameInt
);

Type Name Read/Write Description

ajint trnFileNameInt Input translation table file name number

const AjPStr RETURN Genetic code description

Type	Name	Read/Write	Description
`ajint`	`trnFileNameInt`	Input	translation table file name number
`const AjPStr`		RETURN	Genetic code description

From EMBOSS 3.0.0

Function ajTrnExit

Cleans up translation processing internal memory

Prototype

void ajTrnExit (
      void
);

Type Name Read/Write Description

void RETURN

Type	Name	Read/Write	Description
`void`		RETURN

From EMBOSS 4.0.0