OpenMS
PercolatorOutfile.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: Hendrik Weisser $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
15 
16 #include <vector>
17 
18 namespace OpenMS
19 {
20 
26  class OPENMS_DLLAPI PercolatorOutfile
27  {
28 
29  public:
30 
32  enum ScoreType { QVALUE, POSTERRPROB, SCORE, SIZE_OF_SCORETYPE };
33 
35  static const std::string score_type_names[SIZE_OF_SCORETYPE];
36 
38  static enum ScoreType getScoreType(String score_type_name);
39 
42 
44  void load(const String& filename, ProteinIdentification& proteins,
45  std::vector<PeptideIdentification>& peptides,
46  SpectrumMetaDataLookup& lookup,
47  enum ScoreType output_score = QVALUE);
48 
49  private:
51  void getPeptideSequence_(String peptide, AASequence& seq) const;
52 
54  void resolveMisassignedNTermMods_(String& peptide) const;
55  };
56 
57 } // namespace OpenMS
58 
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
Class for reading Percolator tab-delimited output files.
Definition: PercolatorOutfile.h:27
PercolatorOutfile()
Constructor.
void getPeptideSequence_(String peptide, AASequence &seq) const
Converts the peptide string to an 'AASequence' instance.
void load(const String &filename, ProteinIdentification &proteins, std::vector< PeptideIdentification > &peptides, SpectrumMetaDataLookup &lookup, enum ScoreType output_score=QVALUE)
Loads a Percolator output file.
void resolveMisassignedNTermMods_(String &peptide) const
Resolve cases where N-terminal modifications may be misassigned to the first residue (for X!...
ScoreType
Types of Percolator scores.
Definition: PercolatorOutfile.h:32
@ POSTERRPROB
Definition: PercolatorOutfile.h:32
Representation of a protein identification run.
Definition: ProteinIdentification.h:50
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:117
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19