Examples of GapPenaltyDefinitionAffine

Examples of org.lightforge.bioinformatics.alignment.GapPenaltyDefinitionAffine

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//        new SubstitutionMatrix("BLOSUM50", "BLOSUM50.txt"));

    Sdpa sdpa = new Sdpa("MAVEDEGLRVFQSVKIKIGEAKNLPSYPGPSKMRDCYCTVNLDQEEVFRTKIVEKSLCPFYGEDFYCEIPRSFRHLSFYIFDRDVFRRDSIIGKVAIQKEDLQKYHNRDTWFQLQHVDADSEVQGKVHLELRLSEVITDTGVVCHKLATRIVECQGLPIVNGQCDPYATVTLAGPFRSEAKKTKVKRKTNNPQFDEVFYFEVTRPCSYSKKSHFDFEEEDVDKLEIRVDLWNASNLKFGDEFLGELRIPLKVLRQSSSYEAWYFLQPRDNGSKSLKPDDLGSLRLNVVYTEDHVFSSDYYSPLRDLLLKSADVEPVSASAAHILGEVCREKQEAAVPLVRLFLHYGRVVPFISAIASAEVKRTQDPNTIFRGNSLASKCIDETMKLAGMHYLHVTLKPAIEEICQSHKPCEIDPVKLKDGENLENNMENLRQYVDRVFHAITESGVSCPTVMCDIFFSLREAAAKRFQDDPDVRYTAVSSFIFLRFFAPAILSPNLFQLTPHHTDPQTSRTLTLISKTVQTLGSLSKSKSASFKESYMATFYEFFNEQKYADAVKNFLDLISSSGRRDPKSVEQPIVLKEGFMIKRAQGRKRFGMKNFKKRWFRLTNHEFTYHKSKGDQPLYSIPIENILAVEKLEEESFKMKNMFQVIQPERALYIQANNCVEAKDWIDILTKVSQCNQKRLTVYHPSAYLSGHWLCCRAPSDSAPGCSPCTGGLPANIQLDIDGDRETERIYSLFNLYMSKLEKMQEACGSKSVYDGPEQEEYSTFVIDDPQETYKTLKQVIAGVGALEQEHAQYKRDKFKKTKYGSQEHPIGDKSFQNYIRQQSETSTHSI",
    "MGHHHHHHGSPDREGWLLKLGGGRVKTWKRRWFILTDNCLYYFEYTTDKEPRGIIPLENLSIREVDDPRKPNCFELYIPNNKGQLIKACKTEADGRVVEGNHMVYRISAPTQEEKDEWIKSIQAAVSVD",
    AlignmentType.LOCAL,
    new GapPenaltyDefinitionAffine(-14, -4),
    new SubstitutionMatrix("BLOSUM50", "C:\\eclipsews\\MDPA\\mtx\\BLOSUM50.txt"),
    10,
    0.202,
    0.045,
    0.01);   
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Examples of org.lightforge.bioinformatics.alignment.GapPenaltyDefinitionAffine

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    }
  }
 
  private void evaluateAffineGapPenalty() {
    EvaluationItem[] evalVector;
    GapPenaltyDefinitionAffine gapPenaltyDefinition = (GapPenaltyDefinitionAffine)_gapPenaltyDefinition;
    int oValue = gapPenaltyDefinition.get_openningValue();
    int eValue = gapPenaltyDefinition.get_extensionValue();
   
    if (isAffineInitCell()) {
      initializeAffineCells(oValue, eValue);
    } else if (checkPrerequisites()) {
      evalVector = buildEvalVectorAffineGapPenalty(oValue, eValue);
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