| OpenMS 2.5.0

MzMLFile.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, Chris Bielow, Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/FORMAT/XMLFile.h>
39 #include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
40 #include <OpenMS/CONCEPT/ProgressLogger.h>
41 #include <OpenMS/CONCEPT/Exception.h>
42
43 #include <OpenMS/DATASTRUCTURES/ListUtils.h> // StringList
44 #include <OpenMS/INTERFACES/IMSDataConsumer.h>
45
46 namespace OpenMS
47 {
55 class OPENMS_DLLAPI MzMLFile :
56 public Internal::XMLFile,
57 public ProgressLogger
58 {
59 public:
61 MzMLFile();
63 ~MzMLFile() override;
64
66 PeakFileOptions& getOptions();
67
69 const PeakFileOptions& getOptions() const;
70
72 void setOptions(const PeakFileOptions &);
73
83 void load(const String& filename, PeakMap& map);
84
93 void loadBuffer(const std::string& buffer, PeakMap& map);
94
105 void loadSize(const String & filename, Size& scount, Size& ccount);
106
114 void store(const String& filename, const PeakMap& map) const;
115
122 void storeBuffer(std::string & output, const PeakMap& map) const;
123
142 void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count = false, bool skip_first_pass = false);
143
158 void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, PeakMap& map, bool skip_full_count = false, bool skip_first_pass = false);
159
165 bool isValid(const String& filename, std::ostream& os = std::cerr);
166
176 bool isSemanticallyValid(const String& filename, StringList& errors, StringList& warnings);
177
178 protected:
179
181 void transformFirstPass_(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count);
182
184 void safeParse_(const String & filename, Internal::XMLHandler * handler);
185
186 private:
187
189 PeakFileOptions options_;
190
192 String indexed_schema_location_;
193 };
194
195 } // namespace OpenMS
196
197
OpenMS::String
A more convenient string class.
Definition: String.h:58
XMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
Exception.h
StandardTypes.h
OpenMS::MzMLFile::options_
PeakFileOptions options_
Options for loading / storing.
Definition: MzMLFile.h:189
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
ProgressLogger.h
IMSDataConsumer.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::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
PeakFileOptions.h
ListUtils.h
OpenMS::MzMLFile::indexed_schema_location_
String indexed_schema_location_
Location of indexed mzML schema.
Definition: MzMLFile.h:192
OpenMS::Internal::XMLHandler
Base class for XML handlers.
Definition: XMLHandler.h:151
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55