Documentation

RestrictionEnzymeCatalog
in package
implements RestrictionEnzymeCatalogInterface

Class RestrictionEnzymeCatalog - composes the three existing endonuclease adapters into a single, typed lookup of RestrictionEnzymeDefinition, without duplicating bioapi's data and without touching RestrictionEnzymeManager's private storage. Built once at construction, since the underlying sources are themselves immutable API snapshots.

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author

Amélie DUVERNET aka Amelaye amelieonline@gmail.com

Table of Contents

Interfaces

RestrictionEnzymeCatalogInterface
Interface RestrictionEnzymeCatalogInterface - gives typed, read-only access to restriction enzyme definitions merged from the Type II, Type IIb and Type IIs endonuclease sources, without exposing the private storage of any single one of them.

Properties

$aCanonicalNameByAlias  : array<string|int, string>
$aDefinitionsByName  : array<string|int, RestrictionEnzymeDefinition>

Methods

__construct()  : mixed
RestrictionEnzymeCatalog constructor.
findByFamily()  : array<string|int, RestrictionEnzymeDefinition>
Returns every enzyme belonging to the given family, sorted by canonical name.
findByName()  : RestrictionEnzymeDefinition|null
Looks a restriction enzyme up by its canonical name or one of its aliases, case-insensitively.
findByRecognitionSequence()  : array<string|int, RestrictionEnzymeDefinition>
Returns every enzyme whose recognition sequence, cleavage marks stripped, matches $sSequence case-insensitively : either alternative of a "SITE1 or SITE2" sequence, read on either strand (GAGCGG finds AccBSI, CCGCTC). Several enzymes (isoschizomers) may share the same recognition sequence.
getByName()  : RestrictionEnzymeDefinition
Same as findByName(), but throws instead of returning null.
mapDtoToDefinition()  : RestrictionEnzymeDefinition
Builds a RestrictionEnzymeDefinition from a Type II, IIb or IIs DTO. The three DTO classes share the same eight getters by construction; only their class name and family differ.
registerDtoCollection()  : void
Maps every DTO of a collection to a RestrictionEnzymeDefinition and registers it, keeping the first-registered definition whenever the same canonical name is found in more than one source.
sitesOf()  : array<string|int, string>
Lists the sites an enzyme binds, upper-cased : each alternative of a "SITE1 or SITE2" recognition sequence (AciI CCGC or GCGG), and the reverse complement of each, the same site read on the other strand (AccBSI CCGCTC, GAGCGG).
sortedByName()  : array<string|int, RestrictionEnzymeDefinition>

Properties

$aCanonicalNameByAlias

private array<string|int, string> $aCanonicalNameByAlias = []

Uppercase name or alias => uppercase canonical name

Methods

findByFamily()

Returns every enzyme belonging to the given family, sorted by canonical name.

public findByFamily(string $sFamily) : array<string|int, RestrictionEnzymeDefinition>
Parameters
$sFamily : string

One of RestrictionEnzymeDefinition::VALID_FAMILIES

Tags
inheritDoc
Return values
array<string|int, RestrictionEnzymeDefinition> —

Empty when the family is unknown or has no member

findByRecognitionSequence()

Returns every enzyme whose recognition sequence, cleavage marks stripped, matches $sSequence case-insensitively : either alternative of a "SITE1 or SITE2" sequence, read on either strand (GAGCGG finds AccBSI, CCGCTC). Several enzymes (isoschizomers) may share the same recognition sequence.

public findByRecognitionSequence(string $sSequence) : array<string|int, RestrictionEnzymeDefinition>
Parameters
$sSequence : string

The recognition sequence to search for, without cleavage marks

Tags
inheritDoc
Return values
array<string|int, RestrictionEnzymeDefinition> —

Sorted by canonical name, empty when nothing matches

mapDtoToDefinition()

Builds a RestrictionEnzymeDefinition from a Type II, IIb or IIs DTO. The three DTO classes share the same eight getters by construction; only their class name and family differ.

private mapDtoToDefinition(object $oDto, string $sFamily) : RestrictionEnzymeDefinition
Parameters
$oDto : object

TypeIIEndonucleaseDTO|TypeIIbEndonucleaseDTO|TypeIIsEndonucleaseDTO

$sFamily : string

One of RestrictionEnzymeDefinition::VALID_FAMILIES

Return values
RestrictionEnzymeDefinition

registerDtoCollection()

Maps every DTO of a collection to a RestrictionEnzymeDefinition and registers it, keeping the first-registered definition whenever the same canonical name is found in more than one source.

private registerDtoCollection(array<string|int, mixed> $aDtos, string $sFamily) : void

An entry whose name ends with "@" (FokI@) is not an enzyme : it is the reverse orientation of the Type IIS site of the enzyme it follows, kept for pattern searches. A digest already finds that orientation by searching both strands, so it is not registered.

Parameters
$aDtos : array<string|int, mixed>

TypeIIEndonucleaseDTO[]|TypeIIbEndonucleaseDTO[]|TypeIIsEndonucleaseDTO[]

$sFamily : string

One of RestrictionEnzymeDefinition::VALID_FAMILIES

sitesOf()

Lists the sites an enzyme binds, upper-cased : each alternative of a "SITE1 or SITE2" recognition sequence (AciI CCGC or GCGG), and the reverse complement of each, the same site read on the other strand (AccBSI CCGCTC, GAGCGG).

private sitesOf(RestrictionEnzymeDefinition $oDefinition) : array<string|int, string>
Parameters
$oDefinition : RestrictionEnzymeDefinition
Return values
array<string|int, string>
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