RestrictionCut
in package
All positions are zero-based, consistently with CircularDnaSequence, and already wrapped within [0, plasmid length[. recognitionPosition is where the enzyme's recognition pattern was matched; upperCutPosition and lowerCutPosition are the boundary positions where the upper and lower strands are actually severed, which may differ from recognitionPosition for enzymes cutting outside their own recognition sequence (Type IIb and IIs). reverseStrand tells whether the recognition sequence was found on the plasmid's own reference strand (false) or only detectable as its reverse complement, i.e. the enzyme actually binds the other strand (true) ; upperCutPosition and lowerCutPosition are always expressed in the reference strand's coordinates either way.
Class RestrictionCut
Tags
Table of Contents
Properties
- $end : RestrictionEnd
- $enzymeName : string
- $lowerCutPosition : int
- $recognitionPosition : int
- $reverseStrand : bool
- $upperCutPosition : int
Methods
- __construct() : mixed
- RestrictionCut constructor.
- getEnd() : RestrictionEnd
- getEnzymeName() : string
- getLowerCutPosition() : int
- getRecognitionPosition() : int
- getUpperCutPosition() : int
- isReverseStrand() : bool
Properties
$end
private
RestrictionEnd
$end
$enzymeName
private
string
$enzymeName
$lowerCutPosition
private
int
$lowerCutPosition
$recognitionPosition
private
int
$recognitionPosition
$reverseStrand
private
bool
$reverseStrand
$upperCutPosition
private
int
$upperCutPosition
Methods
__construct()
RestrictionCut constructor.
public
__construct(string $sEnzymeName, int $iRecognitionPosition, int $iUpperCutPosition, int $iLowerCutPosition, RestrictionEnd $oEnd[, bool $bReverseStrand = false ]) : mixed
Parameters
- $sEnzymeName : string
- $iRecognitionPosition : int
-
Zero-based
- $iUpperCutPosition : int
-
Zero-based
- $iLowerCutPosition : int
-
Zero-based
- $oEnd : RestrictionEnd
- $bReverseStrand : bool = false
-
True when the recognition sequence was only found as the reverse complement of the reference strand
getEnd()
public
getEnd() : RestrictionEnd
Return values
RestrictionEndgetEnzymeName()
public
getEnzymeName() : string
Return values
stringgetLowerCutPosition()
public
getLowerCutPosition() : int
Return values
intgetRecognitionPosition()
public
getRecognitionPosition() : int
Return values
intgetUpperCutPosition()
public
getUpperCutPosition() : int
Return values
intisReverseStrand()
public
isReverseStrand() : bool
Return values
bool —True when the recognition sequence was only found as the reverse complement of the reference strand, i.e. the enzyme actually binds the other strand