RestrictionEnzymeDefinition
in package
Wraps the normalized properties of a restriction enzyme (name, aliases, family, recognition and computing patterns, cleavage positions). It never computes an overhang: that requires a target sequence and belongs to the digestion services that compose this value object.
Class RestrictionEnzymeDefinition
Tags
Table of Contents
Constants
- TYPE_II : mixed = "TYPE_II"
- Recognizes and cuts within its own recognition sequence, at a fixed position.
- TYPE_IIB : mixed = "TYPE_IIB"
- Cuts on both sides of its recognition sequence, outside of it.
- TYPE_IIS : mixed = "TYPE_IIS"
- Recognizes an asymmetric sequence and cuts at a defined distance outside of it.
- VALID_FAMILIES : array<string|int, string> = [self::TYPE_II, self::TYPE_IIB, self::TYPE_IIS]
Properties
- $aliases : array<string|int, string>
- $cleavagePositionLower : int
- $cleavagePositionUpper : int
- $computingPattern : string
- $family : string
- $name : string
- $nonAmbiguousBaseCount : int
- $recognitionLength : int
- $recognitionPattern : string
Methods
- __construct() : mixed
- RestrictionEnzymeDefinition constructor.
- getAliases() : array<string|int, string>
- getCleanRecognitionSequence() : string
- Returns the recognition sequence stripped of its cleavage marks (' and _).
- getCleavagePositionLower() : int
- getCleavagePositionUpper() : int
- getComputingPattern() : string
- getFamily() : string
- getName() : string
- getNonAmbiguousBaseCount() : int
- getRecognitionLength() : int
- getRecognitionPattern() : string
- hasAmbiguousBases() : bool
- Tells whether the recognition sequence contains an IUPAC ambiguous base (anything but A, C, G, T or U). Only uppercase letters are inspected, since the recognition pattern notation uses uppercase for bases and lowercase only for the literal "or" separating alternative sites.
Constants
TYPE_II
Recognizes and cuts within its own recognition sequence, at a fixed position.
public
mixed
TYPE_II
= "TYPE_II"
TYPE_IIB
Cuts on both sides of its recognition sequence, outside of it.
public
mixed
TYPE_IIB
= "TYPE_IIB"
TYPE_IIS
Recognizes an asymmetric sequence and cuts at a defined distance outside of it.
public
mixed
TYPE_IIS
= "TYPE_IIS"
VALID_FAMILIES
public
array<string|int, string>
VALID_FAMILIES
= [self::TYPE_II, self::TYPE_IIB, self::TYPE_IIS]
The families a RestrictionEnzymeDefinition may belong to
Properties
$aliases
private
array<string|int, string>
$aliases
Isoschizomers or other names sharing the same recognition pattern
$cleavagePositionLower
private
int
$cleavagePositionLower
Cleavage position on the lower strand, relative to the upper one
$cleavagePositionUpper
private
int
$cleavagePositionUpper
Cleavage position on the upper strand
$computingPattern
private
string
$computingPattern
Recognition pattern meant for pattern searches
$family
private
string
$family
One of the VALID_FAMILIES constants
$name
private
string
$name
Canonical name
$nonAmbiguousBaseCount
private
int
$nonAmbiguousBaseCount
Number of non-N bases within the recognition pattern
$recognitionLength
private
int
$recognitionLength
Length of the recognition pattern
$recognitionPattern
private
string
$recognitionPattern
Human notation of the recognition sequence, with cleavage marks (' and _)
Methods
__construct()
RestrictionEnzymeDefinition constructor.
public
__construct(string $sName, array<string|int, string> $aAliases, string $sFamily, string $sRecognitionPattern, string $sComputingPattern, int $iRecognitionLength, int $iCleavagePositionUpper, int $iCleavagePositionLower, int $iNonAmbiguousBaseCount) : mixed
Parameters
- $sName : string
-
Canonical name, must not be empty
- $aAliases : array<string|int, string>
-
Isoschizomers or other names, may be empty
- $sFamily : string
-
One of self::VALID_FAMILIES
- $sRecognitionPattern : string
-
Human notation, with cleavage marks
- $sComputingPattern : string
-
Pattern meant for pattern searches
- $iRecognitionLength : int
-
Must be strictly positive
- $iCleavagePositionUpper : int
-
Cleavage position on the upper strand
- $iCleavagePositionLower : int
-
Cleavage position on the lower strand
- $iNonAmbiguousBaseCount : int
-
Must not be negative
getAliases()
public
getAliases() : array<string|int, string>
Return values
array<string|int, string>getCleanRecognitionSequence()
Returns the recognition sequence stripped of its cleavage marks (' and _).
public
getCleanRecognitionSequence() : string
Return values
stringgetCleavagePositionLower()
public
getCleavagePositionLower() : int
Return values
intgetCleavagePositionUpper()
public
getCleavagePositionUpper() : int
Return values
intgetComputingPattern()
public
getComputingPattern() : string
Return values
stringgetFamily()
public
getFamily() : string
Return values
stringgetName()
public
getName() : string
Return values
stringgetNonAmbiguousBaseCount()
public
getNonAmbiguousBaseCount() : int
Return values
intgetRecognitionLength()
public
getRecognitionLength() : int
Return values
intgetRecognitionPattern()
public
getRecognitionPattern() : string
Return values
stringhasAmbiguousBases()
Tells whether the recognition sequence contains an IUPAC ambiguous base (anything but A, C, G, T or U). Only uppercase letters are inspected, since the recognition pattern notation uses uppercase for bases and lowercase only for the literal "or" separating alternative sites.
public
hasAmbiguousBases() : bool