| OpenMS 2.5.0

PercolatorOutfile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/MSExperiment.h>
38 #include <OpenMS/METADATA/PeptideIdentification.h>
39 #include <OpenMS/METADATA/ProteinIdentification.h>
40 #include <OpenMS/METADATA/SpectrumMetaDataLookup.h>
41
42 #include <vector>
43
44 namespace OpenMS
45 {
46
52 class OPENMS_DLLAPI PercolatorOutfile
53 {
54
55 public:
56
58 enum ScoreType { QVALUE, POSTERRPROB, SCORE, SIZE_OF_SCORETYPE };
59
61 static const std::string score_type_names[SIZE_OF_SCORETYPE];
62
64 static enum ScoreType getScoreType(String score_type_name);
65
67 PercolatorOutfile();
68
70 void load(const String& filename, ProteinIdentification& proteins,
71 std::vector<PeptideIdentification>& peptides,
72 SpectrumMetaDataLookup& lookup,
73 enum ScoreType output_score = QVALUE);
74
75 private:
77 void getPeptideSequence_(String peptide, AASequence& seq) const;
78
80 void resolveMisassignedNTermMods_(String& peptide) const;
81 };
82
83 } // namespace OpenMS
84
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::PercolatorOutfile
Class for reading Percolator tab-delimited output files.
Definition: PercolatorOutfile.h:52
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
SpectrumMetaDataLookup.h
OpenMS::SpectrumMetaDataLookup
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:142
MSExperiment.h
OpenMS::PercolatorOutfile::ScoreType
ScoreType
Types of Percolator scores.
Definition: PercolatorOutfile.h:58