$aRestEnzimDB
$aRestEnzimDB : array
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.
$enzyme : \App\Domain\Sequence\Entity\Enzyme
__construct(\App\Api\Interfaces\TypeIIEndonucleaseApiAdapter $typeIIEndonucleaseApi, \App\Domain\Sequence\Entity\Enzyme $oEnzyme)
RestrictionEnzymeManager constructor.
| \App\Api\Interfaces\TypeIIEndonucleaseApiAdapter | $typeIIEndonucleaseApi | |
| \App\Domain\Sequence\Entity\Enzyme | $oEnzyme |
getEnzyme() : \App\Domain\Sequence\Entity\Enzyme
parseEnzyme(string $sName, string $sPattern, string $sCutpos, string $sMake = "custom")
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.
| string | $sName | |
| string | $sPattern | |
| string | $sCutpos | |
| string | $sMake |
cutSeq(string $options = "N") : array
Cuts a DNA sequence into fragments using the restriction enzyme object.
| 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". |
An array of fragments (substrings of the parameter sequence)
findRestEn(string $sPattern = null, integer $iCutpos = null, integer $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
| string | $sPattern | The pattern of the restriction enzyme we wish to look for. |
| integer | $iCutpos | The cutting position of the restriction enzyme we wish to look for. |
| integer | $iPlen | The length of the restriction enzyme we wish to look for. |
A list of restriction enyzmes that meet the criteria specified by the $pattern, $cutpos, and $plen parameters.
posTraitment(array $aFragment, array $aPos, \App\Domain\Sequence\Entity\Sequence $oSequence)
Fetchs insite a Patpos array
| array | $aFragment | |
| array | $aPos | |
| \App\Domain\Sequence\Entity\Sequence | $oSequence |