OpenMS  2.6.0
MzDataFile.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Marc Sturm $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/FORMAT/XMLFile.h>
41 #include <OpenMS/KERNEL/Peak1D.h>
45 
46 namespace OpenMS
47 {
53  class OPENMS_DLLAPI MzDataFile :
54  public Internal::XMLFile,
55  public ProgressLogger
56  {
57  typedef PeakMap MapType;
58 
59 public:
60 
62  MzDataFile();
64  ~MzDataFile() override;
65 
67  PeakFileOptions & getOptions();
68 
70  const PeakFileOptions & getOptions() const;
71 
73  void setOptions(const PeakFileOptions &);
74 
83  void load(const String & filename, MapType & map);
84 
92  void store(const String & filename, const MapType & map) const;
93 
103  bool isSemanticallyValid(const String & filename, StringList & errors, StringList & warnings);
104 
105 private:
106 
109  };
110 
111 } // namespace OpenMS
112 
113 
OpenMS::MzDataFile::MapType
PeakMap MapType
Definition: MzDataFile.h:57
OpenMS::MzDataFile
File adapter for MzData files.
Definition: MzDataFile.h:53
XMLFile.h
DocumentIdentifier.h
OpenMS::String
A more convenient string class.
Definition: String.h:59
Peak1D.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
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
ProgressLogger.h
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
PeakFileOptions.h
MSExperiment.h
OpenMS::MzDataFile::options_
PeakFileOptions options_
Options for loading / storing.
Definition: MzDataFile.h:108
OpenMS::PeakFileOptions
Options for loading files containing peak data.
Definition: PeakFileOptions.h:47
OpenMS::Internal::XMLFile
Base class for loading/storing XML files that have a handler derived from XMLHandler.
Definition: XMLFile.h:48
StandardTypes.h
MzDataHandler.h