Play with sequencies

/**
  * Here is some samples of how to use the functions
  * @param SequenceAlignmentInterface $sequenceAlignmentManager
  * @param SequenceInterface $sequenceManager
  * @return Response
  * @throws \Exception
  */
public function playwithsequencies(
    SequenceAlignmentInterface $sequenceAlignmentManager,
    SequenceInterface $sequenceManager
) {
    $sequenceAlignmentManager->setFilename("data/fasta-2.txt");
    $sequenceAlignmentManager->setFormat("FASTA");
    $sequenceAlignmentManager->parseFile();
 
    // We take this sequence as example
    $oSequence = $sequenceAlignmentManager->getSeqSet()->offsetGet(0);
    $oSequence->setMolType("DNA");
    $sequenceManager->setSequence($oSequence);
 
    // Complement of the demo sequence
    $aComplement = $sequenceManager->complement("DNA");
 
    // Shows halfstring for pattern "GATTAG"
    $sHalfStr = $sequenceManager->halfSequence(0, "GATTAG");
 
     // Returns the sequence located between two palindromic halves of a palindromic string
     //$sBridge = $sequenceManager->getBridge("ATGcacgtcCAT");
     //dump($sBridge);
 
     // Returns the expansion of a nucleic acid sequence
     $sExpandNa = $sequenceManager->expandNa("GATTAGSW");
 
     // Computes the molecular weight of a particular sequence.
     $sMolWt = $sequenceManager->molwt();
 
     // Creates a new sequence object with a sequence that is a substring of another.
     $sCoupe = $sequenceManager->subSeq(2,100);
 
     // Array where each key is a substring matching a given pattern
     $aPatpos = $sequenceManager->patPos("TTT");
 
     // Similar to patPos() except that this allows for overlapping patterns.
     $aPatPoso = $sequenceManager->patPoso("TTT");
 
     // Returns the frequency of a given symbol in the sequence property string
     $iSymfreq = $sequenceManager->symFreq("A");
 
     // Returns the n-th codon in a sequence, with numbering starting at 0
     $sCodon = $sequenceManager->getCodon(3);
 
     // Translates a particular DNA sequence into its protein product sequence
     $sTranslate = $sequenceManager->translate();
 
     // Translates an amino acid sequence into its equivalent "charge sequence".
     $sCharge = $sequenceManager->charge("GAVLIFYWKRH");
 
     // Returns a string of symbols from an 8-letter alphabet: A, L, M, R, C, H, I, S.
     $sChemicalGroup = $sequenceManager->chemicalGroup("GAVLIFYWKRH");
 
     // Returns a two-dimensional array containing palindromic substrings found in a sequence
     $aTestPalindrome = $sequenceManager->findPalindrome(null, 2, 2);
 
     // New in biophp 1.1: the sequence as a validated, immutable value object
     $oDnaSeq = $sequenceManager->getMolecularSequence();
     $sVoComplement = (string) $oDnaSeq->complement();
     $sVoReverseComplement = (string) $oDnaSeq->reverseComplement();
     $fVoGcContent = $oDnaSeq->getGcContent();
     $sVoToRna = (string) $oDnaSeq->toRna();
     $sVoSubSequence = (string) $oDnaSeq->subSequence(2, 100);
     $bVoEquals = $oDnaSeq->equals($sequenceManager->getMolecularSequence());
 
     return $this->render('default/playwithsequencies.html.twig',
        [
            'complement'        => $aComplement,
            'halfStr'           => $sHalfStr,
            'expandNa'          => $sExpandNa,
            'molWt'             => $sMolWt,
            'coupe'             => $sCoupe,
            'patpos'            => $aPatpos,
            'patposo'           => $aPatPoso,
            'symfreq'           => $iSymfreq,
            'codon'             => $sCodon,
            'translate'         => $sTranslate,
            'charge'            => $sCharge,
            'chemicalGroup'     => $sChemicalGroup,
            'testPalindrome1'   => $aTestPalindrome,
            'voComplement'          => $sVoComplement,
            'voReverseComplement'   => $sVoReverseComplement,
            'voGcContent'           => $fVoGcContent,
            'voToRna'               => $sVoToRna,
            'voSubSequence'         => $sVoSubSequence,
            'voEquals'              => $bVoEquals
        ]
     );
}