OpenMS
PercolatorOutfile.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
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34 
35 #pragma once
36 
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 
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 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Class for reading Percolator tab-delimited output files.
Definition: PercolatorOutfile.h:53
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:58
@ POSTERRPROB
Definition: PercolatorOutfile.h:58
Representation of a protein identification run.
Definition: ProteinIdentification.h:76
Helper class for looking up spectrum meta data.
Definition: SpectrumMetaDataLookup.h:143
A more convenient string class.
Definition: String.h:60
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48