Docs For Class ProteinAlphabet

Description

ProteinAlphabet

One letter protein seqs

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 /Alphabet/Alphabet.php (line 316)

PEAR
   |
   --Bio
      |
      --IUPACData
         |
         --Alphabet
            |
            --SingleLetterAlphabet
               |
               --ProteinAlphabet

Direct descendents

Class	Description
IUPACProtein	class IUPACProtein
ExtendedIUPACProtein	class ExtendedIUPACProtein
Murphy15	Murphy15

Method Summary

object __construct ([ $aLetters = ""], [ $weights = NULL], string $letters)

Variables

Inherited Variables

Inherited from IUPACData

IUPACData::$aAvgPeptideWeights
IUPACData::$aMonoPeptideWeights

Inherited from Bio

Bio::$bWarnings

Methods

Constructor __construct (line 328)

function __construct

constructor

return: ProteinAlphabet object
access: public

object __construct ([ $aLetters = ""], [ $weights = NULL], string $letters)

string $letters: opt.
$aLetters
$weights

Redefinition of:

SingleLetterAlphabet::__construct(): function __construct

Redefined in descendants as:

IUPACProtein::__construct() : function __construct
ExtendedIUPACProtein::__construct() : function __construct

Inherited Methods

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