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\Amelaye\BioPHP\Domain\Sequence\ServiceRestrictionEnzymeManager

Class RestrictionEnzymeManager - substances that can "cut" a DNA strand into two or more fragments along special sites called restriction sites. They are an important tool in recombinant DNA technology.

Summary

Methods
Properties
Constants
__construct()
setEnzyme()
getEnzyme()
setSequenceManager()
parseEnzyme()
cutSeq()
getPattern()
getCutPos()
getLength()
findRestEn()
No public properties found
No constants found
No protected methods found
No protected properties found
N/A
oTreatment()
nTreatment()
posTraitment()
fetchPatternOnly()
fetchPatternAndCutpos()
fetchCutpos()
fetchLength()
fetchCutposAndPlen()
$aRestEnzimDB
$enzyme
$sequenceManager
N/A

Properties

$aRestEnzimDB

$aRestEnzimDB : array

Type

normal

$enzyme

$enzyme : \Amelaye\BioPHP\Domain\Sequence\Entity\Enzyme

Type

normal

$sequenceManager

$sequenceManager : \Amelaye\BioPHP\Domain\Sequence\Service\SequenceManager

Type

normal

Methods

__construct()

__construct(\Amelaye\BioPHP\Api\Interfaces\TypeIIEndonucleaseApiAdapter  $typeIIEndonucleaseApi, \Amelaye\BioPHP\Domain\Sequence\Entity\Enzyme  $oEnzyme) : mixed

RestrictionEnzymeManager constructor.

Parameters

\Amelaye\BioPHP\Api\Interfaces\TypeIIEndonucleaseApiAdapter $typeIIEndonucleaseApi
\Amelaye\BioPHP\Domain\Sequence\Entity\Enzyme $oEnzyme

Returns

mixed

setEnzyme()

setEnzyme() : mixed

Sets a new enzyme element

Returns

mixed

getEnzyme()

getEnzyme() : \Amelaye\BioPHP\Domain\Sequence\Entity\Enzyme

Returns

\Amelaye\BioPHP\Domain\Sequence\Entity\Enzyme

setSequenceManager()

setSequenceManager(\Amelaye\BioPHP\Domain\Sequence\Interfaces\SequenceInterface  $sequenceManager) : mixed

Sets a sequence object

Parameters

\Amelaye\BioPHP\Domain\Sequence\Interfaces\SequenceInterface $sequenceManager

Returns

mixed

parseEnzyme()

parseEnzyme(string  $sName, string  $sPattern = null, string  $sCutpos = null, string  $sMake = "custom") : mixed

It creates a new Enzyme object and initializes its properties accordingly.

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

Parameters

string $sName
string $sPattern
string $sCutpos
string $sMake

Throws

\Exception

Returns

mixed

cutSeq()

cutSeq(string  $options = "N") : array

Cuts a DNA sequence into fragments using the restriction enzyme object.

Parameters

string $options

May be "N" or "O". If "N", the sequence is cut using the patpos() group of methods (no overlapping patterns). If "O", the sequence is cut using the patposo() group of methods (with overlapping patterns). If omitted, this defaults to "N".

Throws

\Exception

Returns

array —

An array of fragments (substrings of the parameter sequence)

getPattern()

getPattern(string  $RestEn_Name) : string

Returns the pattern associated with a given restriction endonuclease.

Parameters

string $RestEn_Name

Returns

string —

The sequence pattern (string) recognized by the given restriction enzyme.

getCutPos()

getCutPos(string  $RestEn_Name) : int

Returns the cutting position of the restriction enzyme object.

Parameters

string $RestEn_Name

Returns

int —

Returns the cutting position (an integer) of the restriction enzyme object.

getLength()

getLength(string  $RestEn_Name = "") : int

Returns the length of the cutting pattern of the restriction enzyme object.

Parameters

string $RestEn_Name

Returns

int —

The length (integer) of the restriction pattern recognized by the enzyme.

findRestEn()

findRestEn(string  $sPattern = null, int  $iCutpos = null, int  $iPlen = null) : array

A powerful method for searching our database of endonucleases for a particular restriction enzyme exhibiting certain properties like pattern, cutting position, and length, or combinations thereof.

5 Cases: pattern only, cutpos only, patternlength only, pattern and cutpos, cutpos and patternlength

Parameters

string $sPattern

The pattern of the restriction enzyme we wish to look for.
int $iCutpos

The cutting position of the restriction enzyme we wish to look for.
int $iPlen

The length of the restriction enzyme we wish to look for.

Throws

\Exception

Returns

array —

A list of restriction enyzmes that meet the criteria specified by the $pattern, $cutpos, and $plen parameters.

oTreatment()

oTreatment() : array

Cuts the sequence with option "O"

Throws

\Exception

Returns

array

nTreatment()

nTreatment() : array

Cuts the sequence with option "N"

Throws

\Exception

Returns

array

posTraitment()

posTraitment(array  $aFragment, array  $aPos, \Amelaye\BioPHP\Domain\Sequence\Entity\Sequence  $oSequence) : mixed

Fetchs insite a Patpos array

Parameters

array $aFragment
array $aPos
\Amelaye\BioPHP\Domain\Sequence\Entity\Sequence $oSequence

Returns

mixed

fetchPatternOnly()

fetchPatternOnly(string  $sPattern) : array

Parameters

string $sPattern

Returns

array

fetchPatternAndCutpos()

fetchPatternAndCutpos(string  $sPattern, int  $iCutpos) : array

Parameters

string $sPattern
int $iCutpos

Returns

array

fetchCutpos()

fetchCutpos(mixed  $sCutpos) : array

Parameters

mixed $sCutpos

Throws

\Exception

Returns

array

fetchLength()

fetchLength(int  $iPlen) : array

Parameters

int $iPlen

Returns

array

fetchCutposAndPlen()

fetchCutposAndPlen(int  $iCutpos, int  $iPlen) : array

Parameters

int $iCutpos
int $iPlen

Returns

array