OpenMS
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  const String& tmp,
75  boost::shared_ptr<ExperimentalSettings>& exp_meta,
76  const 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(const String& file,
102  const String& tmp,
103  boost::shared_ptr<ExperimentalSettings>& exp_meta,
104  const String& readoptions = "normal");
105 
107  std::vector<OpenSwath::SwathMap> loadSqMass(const 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  const 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 
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.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
File adapter for Swath files.
Definition: SwathFile.h:69
std::vector< OpenSwath::SwathMap > loadMzML(const String &file, const String &tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, const String &readoptions="normal", Interfaces::IMSDataConsumer *plugin_consumer=nullptr)
Loads a Swath run from a single mzML file.
std::vector< OpenSwath::SwathMap > loadSqMass(const String &file, boost::shared_ptr< ExperimentalSettings > &)
Loads a Swath run from a single sqMass file.
boost::shared_ptr< PeakMap > populateMetaData_(const String &file)
Only read the meta data from a file and use it to populate exp_meta.
std::vector< OpenSwath::SwathMap > loadSplit(StringList file_list, const String &tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, const String &readoptions="normal")
Loads a Swath run from a list of split mzML files.
OpenSwath::SpectrumAccessPtr doCacheFile_(const String &in, const String &tmp, const String &tmp_fname, const boost::shared_ptr< PeakMap > &experiment_metadata)
Cache a file to disk.
void countScansInSwath_(const std::vector< MSSpectrum > &exp, std::vector< int > &swath_counter, int &nr_ms1_spectra, std::vector< OpenSwath::SwathMap > &known_window_boundaries)
Counts the number of scans in a full Swath file (e.g. concatenated non-split file)
std::vector< OpenSwath::SwathMap > loadMzXML(const String &file, const String &tmp, boost::shared_ptr< ExperimentalSettings > &exp_meta, const String &readoptions="normal")
Loads a Swath run from a single mzXML file.
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
IMSDataConsumer IMSDataConsumer
Definition: IMSDataConsumer.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:87