| OpenMS 2.5.0

SwathFile.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: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
38 #include <OpenMS/CONCEPT/ProgressLogger.h>
39 #include <OpenMS/DATASTRUCTURES/String.h>
40 #include <OpenMS/DATASTRUCTURES/ListUtils.h>
41 #include <OpenMS/KERNEL/StandardTypes.h>
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
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Interfaces::IMSDataConsumer
IMSDataConsumer IMSDataConsumer
Definition: IMSDataConsumer.h:127
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
StandardTypes.h
String.h
ProgressLogger.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::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
OpenMS::SwathFile
File adapter for Swath files.
Definition: SwathFile.h:67
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
SwathMap.h
ListUtils.h