Class Alphabet

Description
Description | Descendents | Vars | Methods (details) Constants

Alphabet This is used by sequences which contain a finite number of similar words.

  • 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 45) 

PEAR
   |
   --Bio
      |
      --IUPACData
         |
         --Alphabet
Direct descendents
Description | Descendents | Vars | Methods (details) Constants
Class Description
SingleLetterAlphabet SingleLetterAlphabet
ThreeLetterProtein ThreeLetterProtein
Method Summary
Description | Descendents | Constants Vars | Methods (details)
object __construct ([string $letters = ""], [int $size = ""], [ $weights = NULL])
true contains (Seq $other)
string getAlphabetType (none 0)
$this->letters getLetters (none 0)
$this->size getSize (none 0)
$this->weights getWeights (none 0)
void setLetters ($letters $letters)
void setSize (int $size)
void setWeights (int $weights)
string __toString (none 0)
Variables
Description | Descendents | Vars (details) Constants | Methods (details)

Inherited Variables

Inherited from IUPACData

IUPACData::$aAvgPeptideWeights
 IUPACData::$aMonoPeptideWeights

Inherited from Bio

Bio::$bWarnings
Methods
Description | Descendents | Vars Constants Methods (details)
Constructor __construct (line 82)

function Alphabet

Alphabet base class with no default letters or size

  • return: Alphabet object
object __construct ([string $letters = ""], [int $size = ""], [ $weights = NULL])
  • string $letters
  • int $size: size
  • $weights
Redefinition of:
IUPACData::__construct()
function __construct
Redefined in descendants as:
contains (line 106)

function contains

Compares Alphabets. If $this is of the same class or is a parent, returns true

  • return: if is the same or is parent of seq2
true contains (Seq $other)
  • Seq $other: Second sequence to compare
getAlphabetType (line 232)

function getAlphabetType

returns the type of class required

string getAlphabetType (none 0)
  • none 0
getLetters (line 147)

function getLetters

accessor

$this->letters getLetters (none 0)
  • none 0
getSize (line 181)

function getSize

accessor for the length of letters

$this->size getSize (none 0)
  • none 0
getWeights (line 215)

function getWeights

accessor for the weights of letters

$this->weights getWeights (none 0)
  • none 0
setLetters (line 130)

function setLetters

accessor

void setLetters ($letters $letters)
  • $letters $letters
setSize (line 164)

function setSize

accessor for the length of letters

void setSize (int $size)
  • int $size: to set, usuall`y 1 to 3
setWeights (line 198)

function setWeights

accessor for the weights of letters

void setWeights (int $weights)
  • int $weights: to set
__toString (line 252)

function __toString

  • return: letters
string __toString (none 0)
  • none 0

Inherited Methods

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
Description | Descendants | Constants (details) Vars | Methods (details)

Inherited Constants

Inherited from Bio

Bio::NEWLINE

Documentation generated on Sun, 28 Sep 2008 11:09:00 +0200 by phpDocumentor 1.4.2