All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Modules Pages
PercolatorOutfile.h
Go to the documentation of this file.
1 // Copyright (c) 2002-present, OpenMS Inc. -- 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 
16 
17 #include <vector>
18 
19 namespace OpenMS
20 {
21 
27  class OPENMS_DLLAPI PercolatorOutfile
28  {
29 
30  public:
31 
33  enum ScoreType { QVALUE, POSTERRPROB, SCORE, SIZE_OF_SCORETYPE };
34 
36  static const std::string score_type_names[SIZE_OF_SCORETYPE];
37 
39  static enum ScoreType getScoreType(String score_type_name);
40 
43 
45  void load(const String& filename, ProteinIdentification& proteins,
46  PeptideIdentificationList& peptides,
47  SpectrumMetaDataLookup& lookup,
48  enum ScoreType output_score = QVALUE);
49 
50  private:
52  void getPeptideSequence_(String peptide, AASequence& seq) const;
53 
55  void resolveMisassignedNTermMods_(String& peptide) const;
56  };
57 
58 } // namespace OpenMS
59 
Representation of a peptide/protein sequence.
Definition: AASequence.h:86
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
Class for reading Percolator tab-delimited output files.
Definition: PercolatorOutfile.h:28
PercolatorOutfile()
Constructor.
void getPeptideSequence_(String peptide, AASequence &seq) const
Converts the peptide string to an 'AASequence' instance.
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:33
@ POSTERRPROB
Definition: PercolatorOutfile.h:33
void load(const String &filename, ProteinIdentification &proteins, PeptideIdentificationList &peptides, SpectrumMetaDataLookup &lookup, enum ScoreType output_score=QVALUE)
Loads a Percolator output file.
Representation of a protein identification run.
Definition: ProteinIdentification.h:51
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:118
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19