Class Translator

Description
Description | Vars | Methods (details) Constants

Translator

  • author: Bio::Python port
  • author: Mark Brooks <markabrooks@users.sourceforge.net>
  • version: 0.8.2
  • copyright: 2004-2008 Mark Brooks <markabrooks@users.sourceforge.net>

Located in /Translator.php (line 62) 

PEAR
   |
   --Bio
      |
      --Translator
Method Summary
Description | Constants Vars | Methods (details)
static string TranslateCodon_ ( $sCodon, [ $iCut = 11], [ $cStopChar = "*"], string $seqCodon)
static string TranslateStartCodon_ ( $sCodon, [ $iCut = 1], [ $cStartChar = "M"], string $seqCodon)
static string TranslateToStop_ ( $sSeq,  $sName, [ $iFrame = 1], [ $sCodonStyle = "SingleLetter"], [ $cStopSymbol = "*"], [ $iCut = 1], [ $bFromStartCodon = TRUE], int $frame, int $cut)
static string Translate_ ( $sSeq,  $sName, [ $iFrame = 1], [ $sCodonStyle = "SingleLetter"], [ $iCut = 11], int $frame, int $cut)
object __construct ([ $iTable = 1], codonTable $table)
object backTranslate (object $seq, [string $stopSymbol = "*"])
object backTranslateNoStop (object $seq)
Seq getEncoded (none 0)
codonTable getTable (none 0)
null setEncoded ( $oEncoded, Seq $encoded)
null setTable (codontable $iTable)
object translate (Dna $oSeq, [ $iFrame = "1"], [ $sCodonStyle = "SingleLetter"], [ $iCut = 1], [ $sStopSymbol = "*"], char $stopSymbol)
object translateToStop ( $oSeq, [ $iFrame = 1], [ $sCodonStyle = "SingleLetter"], [ $cStopSymbol = "*"], [ $iCut = 1], [ $bFromStartCodon = TRUE], object $seq, string $stopSymbol)
string translateToStopToString (Dna $oSeq, [ $iFrame = "1"], [ $sCodonStyle = "SingleLetter"], [ $cStopSymbol = "*"], char $stopSymbol)
string translateToString (Dna $oSeq, [ $iFrame = "1"], [ $sCodonStyle = "SingleLetter"], [ $iCut = 1], [ $sStopSymbol = "*"], char $stopSymbol)
Variables
Description | Vars (details) Constants | Methods (details)

Inherited Variables

Inherited from Bio

Bio::$bWarnings
Methods
Description | Vars Constants Methods (details)
static method TranslateCodon_ (line 338)

TranslateCodon_()

Translate a given 3 character "codon", using a given codon usage table (cut) *

  • access: public
static string TranslateCodon_ ( $sCodon, [ $iCut = 11], [ $cStopChar = "*"], string $seqCodon)
  • string $seqCodon
  • $sCodon
  • $iCut
  • $cStopChar
static method TranslateStartCodon_ (line 367)

TranslateStartCodon_()

Translate a given 3 character "codon", using a given codon usage table (cut) *

  • access: public
static string TranslateStartCodon_ ( $sCodon, [ $iCut = 1], [ $cStartChar = "M"], string $seqCodon)
  • string $seqCodon
  • $sCodon
  • $iCut
  • $cStartChar
static method TranslateToStop_ (line 281)

TranslateToStop_

Translate the sequence Object into Protein

  • access: public
static string TranslateToStop_ ( $sSeq,  $sName, [ $iFrame = 1], [ $sCodonStyle = "SingleLetter"], [ $cStopSymbol = "*"], [ $iCut = 1], [ $bFromStartCodon = TRUE], int $frame, int $cut)
  • int $frame: Frame to translate in (1-6)
  • int $cut: Codon usage table
  • $sSeq
  • $sName
  • $iFrame
  • $sCodonStyle
  • $cStopSymbol
  • $iCut
  • $bFromStartCodon
static method Translate_ (line 236)

Translate_

Translate the sequence Object into Protein

  • access: public
static string Translate_ ( $sSeq,  $sName, [ $iFrame = 1], [ $sCodonStyle = "SingleLetter"], [ $iCut = 11], int $frame, int $cut)
  • int $frame: Frame to translate in (1-6)
  • int $cut: Codon usage table
  • $sSeq
  • $sName
  • $iFrame
  • $sCodonStyle
  • $iCut
Constructor __construct (line 82)

function __construct

constructor for the Translator class

  • return: Translator object
  • access: public
object __construct ([ $iTable = 1], codonTable $table)
  • codonTable $table
  • $iTable
Redefinition of:
Bio::__construct()
function Bio ()
backTranslate (line 466)

function backTranslate

Translate to the stop codon & bail out

  • return: protein Seq object
  • access: public
object backTranslate (object $seq, [string $stopSymbol = "*"])
  • object $seq: Seq
  • string $stopSymbol: stop character used
backTranslateNoStop (line 484)

function backTranslateNoStop

Translate to the stop codon & bail out

  • return: protein Seq object
  • access: public
object backTranslateNoStop (object $seq)
  • object $seq: Seq
getEncoded (line 158)

function getEncoded

  • access: public
Seq getEncoded (none 0)
  • none 0
getTable (line 123)

function getTable

  • access: public
codonTable getTable (none 0)
  • none 0
setEncoded (line 140)

function setEncoded

  • access: public
null setEncoded ( $oEncoded, Seq $encoded)
  • Seq $encoded
  • $oEncoded
setTable (line 105)

function setTable

null setTable (codontable $iTable)
  • codontable $iTable
translate (line 177)

function translate

  • return: Seq object
object translate (Dna $oSeq, [ $iFrame = "1"], [ $sCodonStyle = "SingleLetter"], [ $iCut = 1], [ $sStopSymbol = "*"], char $stopSymbol)
  • object $oSeq: object $seq to translate
  • char $stopSymbol: opt.
  • $iFrame
  • $sCodonStyle
  • $iCut
  • $sStopSymbol
translateToStop (line 439)

function translateToStop

Translate to the stop codon & bail out

  • return: protein Seq object
  • access: public
object translateToStop ( $oSeq, [ $iFrame = 1], [ $sCodonStyle = "SingleLetter"], [ $cStopSymbol = "*"], [ $iCut = 1], [ $bFromStartCodon = TRUE], object $seq, string $stopSymbol)
  • object $seq: Seq
  • string $stopSymbol: stop character used
  • $oSeq
  • $iFrame
  • $sCodonStyle
  • $cStopSymbol
  • $iCut
  • $bFromStartCodon
translateToStopToString (line 217)

translateToStopToString

  • return: translated sequence
string translateToStopToString (Dna $oSeq, [ $iFrame = "1"], [ $sCodonStyle = "SingleLetter"], [ $cStopSymbol = "*"], char $stopSymbol)
  • object $oSeq: object $seq to translate
  • char $stopSymbol: opt.
  • $iFrame
  • $sCodonStyle
  • $cStopSymbol
translateToString (line 195)

translateToString

  • return: translated sequence
string translateToString (Dna $oSeq, [ $iFrame = "1"], [ $sCodonStyle = "SingleLetter"], [ $iCut = 1], [ $sStopSymbol = "*"], char $stopSymbol)
  • object $oSeq: object $seq to translate
  • char $stopSymbol: opt.
  • $iFrame
  • $sCodonStyle
  • $iCut
  • $sStopSymbol

Inherited Methods

Inherited From Bio

Bio::__construct()
Bio::printWithNl()
Class Constants
Description | Constants (details) Vars | Methods (details)

Inherited Constants

Inherited from Bio

Bio::NEWLINE

Documentation generated on Sun, 28 Sep 2008 11:09:42 +0200 by phpDocumentor 1.4.2