OpenMS  3.0.0
ChromatogramSettings.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 2002-2022.
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: Andreas Bertsch $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
44 
45 #include <map>
46 #include <vector>
47 
48 namespace OpenMS
49 {
50 
59  class OPENMS_DLLAPI ChromatogramSettings :
60  public MetaInfoInterface
61  {
62 
63 public:
64 
68  {
69  MASS_CHROMATOGRAM = 0,
78  SIZE_OF_CHROMATOGRAM_TYPE // last entry!
79  };
80 
82  static const char * const ChromatogramNames[SIZE_OF_CHROMATOGRAM_TYPE+1]; // avoid string[], since it gets copied onto heap on initialization
83 
87  ChromatogramSettings(const ChromatogramSettings &) = default;
91  virtual ~ChromatogramSettings();
92 
93  // Assignment operator
94  ChromatogramSettings & operator=(const ChromatogramSettings &) = default;
96  ChromatogramSettings& operator=(ChromatogramSettings&&) & = default;
97 
99  bool operator==(const ChromatogramSettings & rhs) const;
101  bool operator!=(const ChromatogramSettings & rhs) const;
102 
104  const String & getNativeID() const;
106  void setNativeID(const String & native_id);
107 
109  const String & getComment() const;
111  void setComment(const String & comment);
112 
114  const InstrumentSettings & getInstrumentSettings() const;
116  InstrumentSettings & getInstrumentSettings();
118  void setInstrumentSettings(const InstrumentSettings & instrument_settings);
119 
121  const AcquisitionInfo & getAcquisitionInfo() const;
123  AcquisitionInfo & getAcquisitionInfo();
125  void setAcquisitionInfo(const AcquisitionInfo & acquisition_info);
126 
128  const SourceFile & getSourceFile() const;
130  SourceFile & getSourceFile();
132  void setSourceFile(const SourceFile & source_file);
133 
135  const Precursor & getPrecursor() const;
137  Precursor & getPrecursor();
139  void setPrecursor(const Precursor & precursor);
140 
142  const Product & getProduct() const;
144  Product & getProduct();
146  void setProduct(const Product & product);
147 
149  ChromatogramType getChromatogramType() const;
150 
152  void setChromatogramType(ChromatogramType type);
153 
155  void setDataProcessing(const std::vector< DataProcessingPtr > & data_processing);
156 
158  std::vector< DataProcessingPtr > & getDataProcessing();
159 
161  const std::vector< boost::shared_ptr<const DataProcessing > > getDataProcessing() const;
162 
163 protected:
164 
172  std::vector< DataProcessingPtr > data_processing_;
174  };
175 
177  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const ChromatogramSettings & spec);
178 
179 } // namespace OpenMS
180 
OpenMS::InstrumentSettings
Description of the settings a MS Instrument was run with.
Definition: InstrumentSettings.h:47
OpenMS::AcquisitionInfo
Description of the combination of raw data to a single spectrum.
Definition: AcquisitionInfo.h:52
OpenMS::ChromatogramSettings::BASEPEAK_CHROMATOGRAM
Definition: ChromatogramSettings.h:72
OpenMS::ChromatogramSettings::ABSORPTION_CHROMATOGRAM
Definition: ChromatogramSettings.h:76
OpenMS::String
A more convenient string class.
Definition: String.h:58
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::ChromatogramSettings::comment_
String comment_
Definition: ChromatogramSettings.h:166
Product.h
OpenMS::ChromatogramSettings::type_
ChromatogramType type_
Definition: ChromatogramSettings.h:173
OpenMS::Precursor
Precursor meta information.
Definition: Precursor.h:58
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ChromatogramSettings
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:59
OpenMS::ChromatogramSettings::precursor_
Precursor precursor_
Definition: ChromatogramSettings.h:170
DataProcessing.h
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::ChromatogramSettings::native_id_
String native_id_
Definition: ChromatogramSettings.h:165
OpenMS::ChromatogramSettings::TOTAL_ION_CURRENT_CHROMATOGRAM
Definition: ChromatogramSettings.h:70
OpenMS::ChromatogramSettings::EMISSION_CHROMATOGRAM
Definition: ChromatogramSettings.h:77
OpenMS::ChromatogramSettings::ELECTROMAGNETIC_RADIATION_CHROMATOGRAM
Definition: ChromatogramSettings.h:75
OpenMS::ChromatogramSettings::source_file_
SourceFile source_file_
Definition: ChromatogramSettings.h:168
AcquisitionInfo.h
OpenMS::ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM
Definition: ChromatogramSettings.h:74
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::ChromatogramSettings::acquisition_info_
AcquisitionInfo acquisition_info_
Definition: ChromatogramSettings.h:169
Precursor.h
OpenMS::ChromatogramSettings::SELECTED_ION_MONITORING_CHROMATOGRAM
Definition: ChromatogramSettings.h:73
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::ChromatogramSettings::ChromatogramType
ChromatogramType
Definition: ChromatogramSettings.h:67
OpenMS::SourceFile
Description of a file location, used to store the origin of (meta) data.
Definition: SourceFile.h:46
String.h
InstrumentSettings.h
OpenMS::ChromatogramSettings::SELECTED_ION_CURRENT_CHROMATOGRAM
Definition: ChromatogramSettings.h:71
OpenMS::Product
Product meta information.
Definition: Product.h:48
OpenMS::ChromatogramSettings::data_processing_
std::vector< DataProcessingPtr > data_processing_
Definition: ChromatogramSettings.h:172
OpenMS::ChromatogramSettings::product_
Product product_
Definition: ChromatogramSettings.h:171
SourceFile.h
OpenMS::ChromatogramSettings::instrument_settings_
InstrumentSettings instrument_settings_
Definition: ChromatogramSettings.h:167