OpenMS  2.8.0
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:
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 
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
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:49
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
Used to load and store xQuest result files.
Definition: XQuestResultXMLFile.h:58
int n_hits_
Total number of hits within the result file.
Definition: XQuestResultXMLFile.h:146
double getMinScore() const
Returns minimum score among the hits in the file.
static void wrap_(const String &input, Size width, String &output)
A helper function, that takes one string containing one line and wraps it into several lines of a giv...
double max_score_
Maximum score encountered in file.
Definition: XQuestResultXMLFile.h:148
void load(const String &filename, std::vector< PeptideIdentification > &pep_ids, std::vector< ProteinIdentification > &prot_ids)
Load the content of the xquest.xml file into the provided data structures.
static void writeXQuestXMLSpec(const String &out_file, const String &base_name, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra)
Writes spec.xml output containing spectra for visualization. This version of the function is meant to...
static String getxQuestBase64EncodedSpectrum_(const PeakSpectrum &spec, String header)
Transforms a PeakSpectrum into a base64 encoded string, which is the format used in spec....
static void writeXQuestXMLSpec(const String &out_file, const String &base_name, const OPXLDataStructs::PreprocessedPairSpectra &preprocessed_pair_spectra, const std::vector< std::pair< Size, Size > > &spectrum_pairs, const std::vector< std::vector< OPXLDataStructs::CrossLinkSpectrumMatch > > &all_top_csms, const PeakMap &spectra)
Writes spec.xml output containing matching peaks between heavy and light spectra after comparing and ...
double min_score_
Minimum score encountered in file.
Definition: XQuestResultXMLFile.h:147
void store(const String &filename, const std::vector< ProteinIdentification > &poid, const std::vector< PeptideIdentification > &peid) const
Stores the identifications in a xQuest XML file.
int getNumberOfHits() const
Returns the total number of hits in the file.
double getMaxScore() const
Returns maximum score among the hits in the file.
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
The PreprocessedPairSpectra struct represents the result of comparing a light and a heavy labeled spe...
Definition: OPXLDataStructs.h:304