Class CodonTable

Description
Description | Descendents | Methods (details)

class CodonTable

Located in /Data/CodonTable.php (line 54) 

PEAR
   |
   --CodonTable
Direct descendents
Description | Descendents | Methods (details)
Class Description
NCBICodonTable NCBICodonTable
Method Summary
Description | Descendents | Methods (details)
object __construct ([integer $iNcbiTable = 1], [Alphabet $sNucleotideAlphabet = "NucleotideAlphabet"], [Alphabet $sProteinAlphabet = "ProteinAlphabet"])
void checkIsStartCodon ( $sStartCodon, string $aStopCodons)
void checkIsStopCodon ( $sStopCodon, string $aStopCodons)
void getBackwardTable (string $aBackwardTable)
void getForwardTable (string 0)
object getNucleotideAlphabet ()
void getProteinAlphabet (string $sProteinAlphabet)
void getStartCodons (string $startCodon)
void getStopCodons (string $aStopCodons)
void setBackwardTable (string $aBackwardTable)
void setForwardTable (string $aForwardTable)
void setNucleotideAlphabet (string $sNucleotideAlphabet)
void setProteinAlphabet (string $sProteinAlphabet)
void setStartCodons ( $aStartCodons, string $startCodon)
void setStopCodons (string $aStopCodons)
Methods
Description | Descendents | Methods (details)
Constructor __construct (line 107)

function __construct

  • return: CodonTable object
  • access: public
object __construct ([integer $iNcbiTable = 1], [Alphabet $sNucleotideAlphabet = "NucleotideAlphabet"], [Alphabet $sProteinAlphabet = "ProteinAlphabet"])
  • integer $iNcbiTable: Number of the NCBI codon table
  • Alphabet $sNucleotideAlphabet
  • Alphabet $sProteinAlphabet
Redefined in descendants as:
checkIsStartCodon (line 361)

function checkIsStartCodon

Validate that is a start codons

  • access: public
void checkIsStartCodon ( $sStartCodon, string $aStopCodons)
  • string $aStopCodons: name of the aStopCodons return object $this aStopCodons object
  • $sStartCodon
checkIsStopCodon (line 337)

function checkIsStopCodon

Accessor for aStopCodons

  • access: public
void checkIsStopCodon ( $sStopCodon, string $aStopCodons)
  • string $aStopCodons: name of the aStopCodons return object $this aStopCodons object
  • $sStopCodon
getBackwardTable (line 263)

function getBackwardTable

Accessor for aBackwardTable

  • access: public
void getBackwardTable (string $aBackwardTable)
  • string $aBackwardTable: name of the aBackwardTable return object $this aBackwardTable object
getForwardTable (line 226)

function getForwardTable

Accessor for forwardTable

  • access: public
void getForwardTable (string 0)
  • string 0: aForwardTable name of the forwardTable return object $this forwardTable object
getNucleotideAlphabet (line 152)

function getNucleotideAlphabet

Accessor for sNucleotideAlphabet

  • return: sNucleotideAlphabet object
  • access: public
object getNucleotideAlphabet ()
getProteinAlphabet (line 189)

function getProteinAlphabet

Accessor for proteinAlphabet

  • access: public
void getProteinAlphabet (string $sProteinAlphabet)
  • string $sProteinAlphabet: name of the proteinAlphabet return object $this proteinAlphabet object
getStartCodons (line 300)

function getStartCodons

Accessor for aStartCodons

  • access: public
void getStartCodons (string $startCodon)
  • string $startCodon: name of the aStartCodons return object $this startCodon object
getStopCodons (line 386)

function getStopCodons

Accessor for aStopCodons

  • access: public
void getStopCodons (string $aStopCodons)
  • string $aStopCodons: name of the aStopCodons return object $this aStopCodons object
setBackwardTable (line 244)

function setBackwardTable

Accessor for aBackwardTable

  • access: public
void setBackwardTable (string $aBackwardTable)
  • string $aBackwardTable: name of the aBackwardTable return object $this aBackwardTable object
setForwardTable (line 207)

function setForwardTable

Accessor for forwardTable

  • access: public
void setForwardTable (string $aForwardTable)
  • string $aForwardTable: aForwardTable name of the forwardTable return object $this forwardTable object
setNucleotideAlphabet (line 134)

function setNucleotideAlphabet

Accessor for sNucleotideAlphabet

  • access: public
void setNucleotideAlphabet (string $sNucleotideAlphabet)
  • string $sNucleotideAlphabet: name of the sNucleotideAlphabet return object $this sNucleotideAlphabet object
setProteinAlphabet (line 170)

function setProteinAlphabet

Accessor for proteinAlphabet

  • access: public
void setProteinAlphabet (string $sProteinAlphabet)
  • string $sProteinAlphabet: name of the ProteinAlphabet return void
setStartCodons (line 281)

function setStartCodons

Accessor for aStartCodons

  • access: public
void setStartCodons ( $aStartCodons, string $startCodon)
  • string $startCodon: name of the startCodon return object $this startCodon object
  • $aStartCodons
setStopCodons (line 318)

function setStopCodons

Accessor for aStopCodons

  • access: public
void setStopCodons (string $aStopCodons)
  • string $aStopCodons: name of the aStopCodons return object $this aStopCodons object

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