Docs For Class RestrictionDigester

Description

RestrictionDigester Contains definition of Restriction (restriction endonucleases) class.

author: Mark Brooks <markabrooks@users.sourceforge.net>
author: BioPHP
version: 0.8.2
copyright: 2004-2008 Mark Brooks <markabrooks@users.sourceforge.net>
uses: Class - for restriction enzymes

Located in /Restriction/RestrictionDigester.php (line 55)

PEAR
   |
   --Bio
      |
      --RestrictionDigester

Method Summary

RestrictionDigester __construct ( $oSeq, [ $oRestrictionEnzymeDictionary = NULL])

void digest ( $sEnzymeName)

void getDictionary ()

void getFragments ( $sEnzymeName)

void getNumSites ( $sEnzymeName)

void getSeq ()

void setDictionary ([RestrictionEnzymeDictionary $oRestrictionEnzymeDictionary = NULL])

void setSeq (Dna $oSeq)

TODO: __call (none $sMethod, $aArguments)

Variables

Inherited Variables

Inherited from Bio

Bio::$bWarnings

Methods

Constructor __construct (line 114)

function __construct Is the constructor method for the Restriction class. It creates a new RestrictionEnzyme object and initializes its properties accordingly.

If passed with make = 'custom', object will be added to Restriction_DB. If not, the function will attempt to retrieve data from Restriction_DB. If unsuccessful in retrieving data, it will return an error flag.

RestrictionDigester __construct ( $oSeq, [ $oRestrictionEnzymeDictionary = NULL])

$oSeq
$oRestrictionEnzymeDictionary

Redefinition of:

Bio::__construct(): function Bio ()

digest (line 229)

function digest

access: public
uses: Perform - the digestion

void digest ( $sEnzymeName)

$sEnzymeName

getDictionary (line 213)

function getDictionary

access: public
uses: accessor

void getDictionary ()

getFragments (line 276)

function getFragments

access: public
uses: Perform - the digestion

void getFragments ( $sEnzymeName)

$sEnzymeName

getNumSites (line 252)

function getNumSites

access: public
uses: Get - the number of sites in the sequence

void getNumSites ( $sEnzymeName)

$sEnzymeName

getSeq (line 180)

function getSeq

access: public
uses: accessor

void getSeq ()

setDictionary (line 196)

function setDictionary

access: public
uses: accessor

void setDictionary ([RestrictionEnzymeDictionary $oRestrictionEnzymeDictionary = NULL])

RestrictionEnzymeDictionary $oRestrictionEnzymeDictionary

setSeq (line 163)

function setSeq

access: public
uses: accessor

void setSeq (Dna $oSeq)

Dna $oSeq

__call (line 137)

function __call

TODO: __call (none $sMethod, $aArguments)

none $sMethod
$aArguments

Inherited Methods

Inherited From Bio

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

Class Constants

Inherited Constants

Inherited from Bio

Bio::NEWLINE