OpenMS
ConsensusIDAlgorithmPEPMatrix.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Hendrik Weisser $
6 // $Authors: Andreas Bertsch, Marc Sturm, Sven Nahnsen, Hendrik Weisser $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
13 
14 namespace OpenMS
15 {
25  class OPENMS_DLLAPI ConsensusIDAlgorithmPEPMatrix :
27  {
28  public:
31 
32 
33  private:
34 
37 
40 
43 
45  double getSimilarity_(AASequence seq1, AASequence seq2) override;
46 
47  // Docu in base class
48  void updateMembers_() override;
49  };
50 
51 } // namespace OpenMS
52 
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
Calculates a consensus from multiple ID runs based on PEPs and sequence similarities.
Definition: ConsensusIDAlgorithmPEPMatrix.h:27
ConsensusIDAlgorithmPEPMatrix & operator=(const ConsensusIDAlgorithmPEPMatrix &)
Not implemented.
double getSimilarity_(AASequence seq1, AASequence seq2) override
Sequence similarity based on substitution matrix (ignores PTMs)
void updateMembers_() override
Docu in base class.
ConsensusIDAlgorithmPEPMatrix(const ConsensusIDAlgorithmPEPMatrix &)
Not implemented.
NeedlemanWunsch alignment_
object for alignment score calculation
Definition: ConsensusIDAlgorithmPEPMatrix.h:36
ConsensusIDAlgorithmPEPMatrix()
Default constructor.
Abstract base class for ConsensusID algorithms that take peptide similarity into account.
Definition: ConsensusIDAlgorithmSimilarity.h:30
This class contains functions that are used to calculate the global alignment score of two amino acid...
Definition: NeedlemanWunsch.h:21
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19