OpenMS  3.0.0
SwathFile.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
42 
43 #include <vector>
44 #include <boost/shared_ptr.hpp>
45 
46 namespace OpenMS
47 {
48  class ExperimentalSettings;
49  namespace Interfaces
50  {
51  class IMSDataConsumer;
52  }
53 
54 
67  class OPENMS_DLLAPI SwathFile :
68  public ProgressLogger
69  {
70 public:
71 
73  std::vector<OpenSwath::SwathMap> loadSplit(StringList file_list,
74  String tmp,
75  boost::shared_ptr<ExperimentalSettings>& exp_meta,
76  String readoptions = "normal");
77 
94  std::vector<OpenSwath::SwathMap> loadMzML(const String& file,
95  const String& tmp,
96  boost::shared_ptr<ExperimentalSettings>& exp_meta,
97  const String& readoptions = "normal",
98  Interfaces::IMSDataConsumer* plugin_consumer = nullptr);
99 
101  std::vector<OpenSwath::SwathMap> loadMzXML(String file,
102  String tmp,
103  boost::shared_ptr<ExperimentalSettings>& exp_meta,
104  String readoptions = "normal");
105 
107  std::vector<OpenSwath::SwathMap> loadSqMass(String file, boost::shared_ptr<ExperimentalSettings>& /* exp_meta */);
108 
109 protected:
110 
112  OpenSwath::SpectrumAccessPtr doCacheFile_(const String& in, const String& tmp, const String& tmp_fname,
113  boost::shared_ptr<PeakMap > experiment_metadata);
114 
116  boost::shared_ptr< PeakMap > populateMetaData_(const String& file);
117 
119  void countScansInSwath_(const std::vector<MSSpectrum>& exp,
120  std::vector<int>& swath_counter, int& nr_ms1_spectra,
121  std::vector<OpenSwath::SwathMap>& known_window_boundaries);
122 
123  };
124 }
125 
SwathMap.h
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
OpenMS::String
A more convenient string class.
Definition: String.h:58
ListUtils.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::Interfaces::IMSDataConsumer
IMSDataConsumer IMSDataConsumer
Definition: IMSDataConsumer.h:127
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:87
OpenMS::SwathFile
File adapter for Swath files.
Definition: SwathFile.h:67
String.h
StandardTypes.h