OpenMS  3.0.0
XQuestResultXMLFile.h
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31 // $Maintainer: Eugen Netz $
32 // $Authors: Lukas Zimmermann, Eugen Netz $
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34 #pragma once
35 
36 #include <OpenMS/FORMAT/XMLFile.h>
41 
42 namespace OpenMS
43 {
44 
55  class OPENMS_DLLAPI XQuestResultXMLFile :
56  public Internal::XMLFile,
57  public ProgressLogger
58  {
59 public:
61  ~XQuestResultXMLFile() override;
62 
69  void load(const String & filename,
70  std::vector< PeptideIdentification > & pep_ids,
71  std::vector< ProteinIdentification > & prot_ids
72  );
73 
79  void store(const String& filename,
80  const std::vector<ProteinIdentification>& poid,
81  const std::vector<PeptideIdentification>& peid) const;
82 
87  int getNumberOfHits() const;
88 
93  double getMinScore() const;
94 
99  double getMaxScore() const;
100 
110  static void writeXQuestXMLSpec(const String& out_file, const String& base_name,
111  const OPXLDataStructs::PreprocessedPairSpectra& preprocessed_pair_spectra,
112  const std::vector< std::pair<Size, Size> >& spectrum_pairs,
113  const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms,
114  const PeakMap& spectra, const bool& test_mode = false);
115 
123  static void writeXQuestXMLSpec(const String& out_file, const String& base_name,
124  const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > >& all_top_csms,
125  const PeakMap& spectra, const bool& test_mode = false);
126 
127 
128 
129 private:
130 
136  static String getxQuestBase64EncodedSpectrum_(const PeakSpectrum& spec, String header, const bool& test_mode = false);
137 
144  static void wrap_(const String& input, Size width, String& output);
145 
146  int n_hits_;
147  double min_score_;
148  double max_score_;
149  };
150 } // namespace OpenMS
XMLFile.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::XQuestResultXMLFile::n_hits_
int n_hits_
Total number of hits within the result file.
Definition: XQuestResultXMLFile.h:146
OpenMS::OPXLDataStructs::PreprocessedPairSpectra
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:303
OPXLDataStructs.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::XQuestResultXMLFile
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
ProteinIdentification.h
OpenMS::XQuestResultXMLFile::max_score_
double max_score_
Maximum score encountered in file.
Definition: XQuestResultXMLFile.h:148
OpenMS::XQuestResultXMLFile::min_score_
double min_score_
Minimum score encountered in file.
Definition: XQuestResultXMLFile.h:147
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
PeptideIdentification.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66