OpenMS  2.4.0
MSPGenericFile.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 2002-2018.
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: Douglas McCloskey, Pasquale Domenico Colaianni $
32 // $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
37 #include <OpenMS/config.h> // OPENMS_DLLAPI
41 
42 namespace OpenMS
43 {
67  class OPENMS_DLLAPI MSPGenericFile :
68  public DefaultParamHandler
69  {
70 public:
73 
75  MSPGenericFile(const String& filename, MSExperiment& library);
76 
78  ~MSPGenericFile() = default;
79 
81  void getDefaultParameters(Param& params);
82 
84  friend class MSPGenericFile_friend;
85 
94  void load(const String& filename, MSExperiment& library);
95 
96 private:
98  void updateMembers_();
99 
114  void addSpectrumToLibrary(
115  MSSpectrum& spectrum,
116  MSExperiment& library
117  );
118 
120  std::set<String> loaded_spectra_names_;
121 
122  /*
123  The synonyms of a spectrum are collected into this variable and,
124  when `addSpectrumtoLibrary()` is called, the elements are concatenated
125  and the result is saved as a "Synon" metaValue.
126  The synonyms are separated by `synonyms_separator_`.
127  */
128  std::vector<String> synonyms_;
129 
132  };
133 
135  {
136 public:
137  MSPGenericFile_friend() = default;
138  ~MSPGenericFile_friend() = default;
139 
141  MSSpectrum& spectrum,
142  MSExperiment& library
143  )
144  {
145  return msp_.addSpectrumToLibrary(spectrum, library);
146  }
147 
149  };
150 }
Load MSP text file and save it into an `MSExperiment`.
Definition: MSPGenericFile.h:67
std::set< String > loaded_spectra_names_
To keep track of which spectra have already been loaded and avoid duplicates.
Definition: MSPGenericFile.h:120
A more convenient string class.
Definition: String.h:57
String synonyms_separator_
The separator to be used in "Synon" metaValue.
Definition: MSPGenericFile.h:131
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
std::vector< String > synonyms_
Definition: MSPGenericFile.h:128
Definition: MSPGenericFile.h:134
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
MSPGenericFile msp_
Definition: MSPGenericFile.h:148
Management and storage of parameters / INI files.
Definition: Param.h:74
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
void addSpectrumToLibrary(MSSpectrum &spectrum, MSExperiment &library)
void addSpectrumToLibrary(MSSpectrum &spectrum, MSExperiment &library)
Definition: MSPGenericFile.h:140
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91