Restriction Enzyme

/**
  * Here is some samples of how to use the functions
  * @param   RestrictionEnzymeInterface  $restrictionEnzymeManager
  * @param   SequenceInterface           $sequenceManager
  * @param   SequenceAlignmentInterface  $sequenceAlignmentManager
  * @return  Response
  * @throws  \Exception
  */
public function restrictionenzyme(
    RestrictionEnzymeInterface $restrictionEnzymeManager,
    SequenceInterface $sequenceManager,
    SequenceAlignmentInterface $sequenceAlignmentManager
) {
    $sequenceAlignmentManager->setFilename("data/fasta-2.txt");
    $sequenceAlignmentManager->setFormat("FASTA");
    $sequenceAlignmentManager->parseFile();
    $oSequence = $sequenceAlignmentManager->getSeqSet()->offsetGet(0);
    $oSequence->setMolType("DNA");
    $sequenceManager->setSequence($oSequence);
    $restrictionEnzymeManager->setSequenceManager($sequenceManager);
 
    // Gets the enzyme "AatI" properties
    $restrictionEnzymeManager->parseEnzyme('AatI', null, null, "inner");
    $oEnzymeParsed = $restrictionEnzymeManager->getEnzyme();
 
    // Cuts a DNA sequence into fragments using the restriction enzyme object - patpos group
    $sCutseq = $restrictionEnzymeManager->cutSeq();
    // Patposo group
    $sCutseq2 = $restrictionEnzymeManager->cutSeq('O');
 
    // Searching the database (api) of endonucleases for a particular restriction enzyme
    $aList = $restrictionEnzymeManager->findRestEn("AGGCCT"); // fetch pattern only
    $aList2 = $restrictionEnzymeManager->findRestEn("AGGCCT",3); // fetch pattern and cutpos
    $aList3 = $restrictionEnzymeManager->findRestEn(null,3); // fetch Cutpos
    $aList4 = $restrictionEnzymeManager->findRestEn(null,null, 6); // fetch Length
    $aList5 = $restrictionEnzymeManager->findRestEn(null,3, 6); // fetch Cutpos And Plen
 
    return $this->render('default/restrictionenzyme.html.twig',
        [
            "enzymeParsed"  => $oEnzymeParsed,
            "cutseq"        => $sCutseq,
            "cutseq2"       => $sCutseq2,
            "list"          => $aList,
            "list2"         => $aList2,
            "list3"         => $aList3,
            "list4"         => $aList4,
            "list5"         => $aList5
        ]
    );
}