| OpenMS 2.5.0

FileHandler.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: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/config.h>
38 #include <OpenMS/FORMAT/FileTypes.h>
39 #include <OpenMS/CONCEPT/ProgressLogger.h>
40 #include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
41
42 namespace OpenMS
43 {
44 class PeakFileOptions;
45 class MSSpectrum;
46 class MSExperiment;
47 class FeatureMap;
48
62 class OPENMS_DLLAPI FileHandler
63 {
64 public:
73 static FileTypes::Type getType(const String& filename);
74
75
77 static FileTypes::Type getTypeByFileName(const String& filename);
78
84 static bool hasValidExtension(const String& filename, const FileTypes::Type type);
85
91 static FileTypes::Type getTypeByContent(const String& filename);
92
94 static bool isSupported(FileTypes::Type type);
95
97 PeakFileOptions& getOptions();
98
100 const PeakFileOptions& getOptions() const;
101
103 void setOptions(const PeakFileOptions&);
104
120 bool loadExperiment(const String& filename, MSExperiment& exp, FileTypes::Type force_type = FileTypes::UNKNOWN, ProgressLogger::LogType log = ProgressLogger::NONE, const bool rewrite_source_file = true, const bool compute_hash = true);
121
133 void storeExperiment(const String& filename, const MSExperiment& exp, ProgressLogger::LogType log = ProgressLogger::NONE);
134
147 bool loadFeatures(const String& filename, FeatureMap& map, FileTypes::Type force_type = FileTypes::UNKNOWN);
148
154 static String computeFileHash(const String& filename);
155
156 private:
157 PeakFileOptions options_;
158
159 };
160
161 } //namespace
162
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
FileTypes.h
OpenMS::ProgressLogger::NONE
No progress logging.
Definition: ProgressLogger.h:74
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger::LogType
LogType
Possible log types.
Definition: ProgressLogger.h:70
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:58
OpenMS::FileHandler::options_
PeakFileOptions options_
Definition: FileHandler.h:157
PeakFileOptions.h
OpenMS::FileTypes::UNKNOWN
Unknown file extension.
Definition: FileTypes.h:60