| OpenMS 2.5.0

XQuestResultXMLFile.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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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: Eugen Netz $
32 // $Authors: Lukas Zimmermann, Eugen Netz $
33 // --------------------------------------------------------------------------
34 #pragma once
35
36 #include <OpenMS/FORMAT/XMLFile.h>
37 #include <OpenMS/CONCEPT/ProgressLogger.h>
38 #include <OpenMS/METADATA/PeptideIdentification.h>
39 #include <OpenMS/METADATA/ProteinIdentification.h>
40 #include <OpenMS/ANALYSIS/XLMS/OPXLDataStructs.h>
41
42 namespace OpenMS
43 {
44
55 class OPENMS_DLLAPI XQuestResultXMLFile :
56 public Internal::XMLFile,
57 public ProgressLogger
58 {
59 public:
60 XQuestResultXMLFile();
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);
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);
126
127
128
129 private:
130
136 static String getxQuestBase64EncodedSpectrum_(const PeakSpectrum& spec, String header);
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
ProteinIdentification.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
XMLFile.h
OPXLDataStructs.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
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
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::XQuestResultXMLFile::n_hits_
int n_hits_
Total number of hits within the result file.
Definition: XQuestResultXMLFile.h:146
ProgressLogger.h
OpenMS::OPXLDataStructs::PreprocessedPairSpectra
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:303
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
OpenMS::XQuestResultXMLFile
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:55
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::XQuestResultXMLFile::max_score_
double max_score_
Maximum score encountered in file.
Definition: XQuestResultXMLFile.h:148