Docs For Class IUPACAmbiguousDna

Description

class IUPACAmbiguousDna

author: Port from Bio::Python
author: Mark Brooks <markabrooks@users.sourceforge.net>
version: 0.8.2
copyright: 2004-2008 Mark Brooks <markabrooks@users.sourceforge.net>
access: public

Located in /Alphabet/IUPAC.php (line 150)

PEAR
   |
   --Bio
      |
      --IUPACData
         |
         --Alphabet
            |
            --SingleLetterAlphabet
               |
               --NucleotideAlphabet
                  |
                  --DnaAlphabet
                     |
                     --IUPACAmbiguousDna

Direct descendents

Class	Description
IUPACUnambiguousDna	IUPACUnambiguousDna

Method Summary

Alphabet __construct ([string $letters = ""])

Variables

Inherited Variables

Inherited from IUPACData

IUPACData::$aAvgPeptideWeights
IUPACData::$aMonoPeptideWeights

Inherited from Bio

Bio::$bWarnings

Methods

Constructor __construct (line 161)

function __construct

uses:

Alphabet __construct ([string $letters = ""])

string $letters

Redefinition of:

DnaAlphabet::__construct(): function __construct

Redefined in descendants as:

IUPACUnambiguousDna::__construct() : function __construct

Inherited Methods

Inherited From DnaAlphabet

DnaAlphabet::__construct()

Inherited From NucleotideAlphabet

NucleotideAlphabet::__construct()

Inherited From SingleLetterAlphabet

SingleLetterAlphabet::__construct()

Inherited From Alphabet

Alphabet::__construct()
Alphabet::contains()
Alphabet::getAlphabetType()
Alphabet::getLetters()
Alphabet::getSize()
Alphabet::getWeights()
Alphabet::setLetters()
Alphabet::setSize()
Alphabet::setWeights()
Alphabet::__toString()

Inherited From IUPACData

IUPACData::__construct()
IUPACData::getAmbiguousDnaComplement()
IUPACData::getAmbiguousDnaLetters()
IUPACData::getAmbiguousDnaValues()
IUPACData::getAmbiguousRnaLetters()
IUPACData::getAmbiguousRnaValues()
IUPACData::getExtendedDnaLetters()
IUPACData::getExtendedProteinLetters()
IUPACData::getExtendedProteinValues()
IUPACData::getExtendedRnaLetters()
IUPACData::getProteinLetters()
IUPACData::getProteinWeights()
IUPACData::getProteinWithStopLetters()
IUPACData::getUnambiguousDnaLetters()
IUPACData::getUnambiguousDnaWeights()
IUPACData::getUnambiguousRnaLetters()
IUPACData::getUnambiguousRnaWeights()

Inherited From Bio

Bio::__construct()
Bio::printWithNl()

Class Constants

Inherited Constants

Inherited from Bio

Bio::NEWLINE