RestrictionEnd
in package
The overhang sequence, when there is one, is always given as the top-strand bases spanning the upper and lower cut positions, read 5' -> 3' on the strand the cut positions were computed from.
For a 5' overhang those bases are literally the single-stranded protrusion; for a 3' overhang they are the bases the opposite strand protrudes past, which is what RestrictionEndCompatibilityManager needs to test complementarity either way. UNKNOWN represents an end nothing could be determined for, which must never be treated as compatible or incompatible by mistake. Class RestrictionEnd
Tags
Table of Contents
Constants
- BLUNT : mixed = "BLUNT"
- FIVE_PRIME : mixed = "FIVE_PRIME"
- THREE_PRIME : mixed = "THREE_PRIME"
- UNKNOWN : mixed = "UNKNOWN"
- VALID_TYPES : array<string|int, string> = [self::BLUNT, self::FIVE_PRIME, self::THREE_PRI...
Properties
- $overhangSequence : string|null
- $type : string
Methods
- __construct() : mixed
- RestrictionEnd constructor.
- blunt() : self
- fivePrime() : self
- getOverhangSequence() : string|null
- getType() : string
- isBlunt() : bool
- isDeterminate() : bool
- threePrime() : self
- unknown() : self
Constants
BLUNT
public
mixed
BLUNT
= "BLUNT"
FIVE_PRIME
public
mixed
FIVE_PRIME
= "FIVE_PRIME"
THREE_PRIME
public
mixed
THREE_PRIME
= "THREE_PRIME"
UNKNOWN
public
mixed
UNKNOWN
= "UNKNOWN"
VALID_TYPES
public
array<string|int, string>
VALID_TYPES
= [self::BLUNT, self::FIVE_PRIME, self::THREE_PRIME, self::UNKNOWN]
Properties
$overhangSequence
private
string|null
$overhangSequence
= null
$type
private
string
$type
= null
Methods
__construct()
RestrictionEnd constructor.
public
__construct(string $sType[, string|null $sOverhangSequence = null ]) : mixed
Parameters
- $sType : string
-
One of self::VALID_TYPES
- $sOverhangSequence : string|null = null
-
Required for FIVE_PRIME/THREE_PRIME, must be null for BLUNT and UNKNOWN
blunt()
public
static blunt() : self
Return values
selffivePrime()
public
static fivePrime(string $sOverhangSequence) : self
Parameters
- $sOverhangSequence : string
-
Must not be empty
Return values
selfgetOverhangSequence()
public
getOverhangSequence() : string|null
Return values
string|nullgetType()
public
getType() : string
Return values
stringisBlunt()
public
isBlunt() : bool
Return values
boolisDeterminate()
public
isDeterminate() : bool
Return values
bool —False only for UNKNOWN
threePrime()
public
static threePrime(string $sOverhangSequence) : self
Parameters
- $sOverhangSequence : string
-
Must not be empty
Return values
selfunknown()
public
static unknown() : self