OpenMS  3.0.0
TransitionPQPFile.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: George Rosenberger $
32 // $Authors: George Rosenberger, Hannes Roest $
33 // --------------------------------------------------------------------------
34 
35 #pragma once
36 
38 
39 namespace OpenMS
40 {
41 
215  class OPENMS_DLLAPI TransitionPQPFile :
216  public TransitionTSVFile
217  {
218 
219 private:
220 
228  void readPQPInput_(const char* filename, std::vector<TSVTransition>& transition_list, bool legacy_traml_id = false);
229 
235  void writePQPOutput_(const char* filename, OpenMS::TargetedExperiment& targeted_exp);
236 
237 public:
238 
242 
244  ~TransitionPQPFile() override;
246 
253  void convertTargetedExperimentToPQP(const char* filename, OpenMS::TargetedExperiment& targeted_exp);
254 
262  void convertPQPToTargetedExperiment(const char* filename, OpenMS::TargetedExperiment& targeted_exp, bool legacy_traml_id = false);
263 
271  void convertPQPToTargetedExperiment(const char* filename, OpenSwath::LightTargetedExperiment& targeted_exp, bool legacy_traml_id = false);
272 
273  };
274 }
275 
276 
OpenMS::TransitionTSVFile
This class supports reading and writing of OpenSWATH transition lists.
Definition: TransitionTSVFile.h:144
OpenMS::TransitionPQPFile
This class supports reading and writing of PQP files.
Definition: TransitionPQPFile.h:215
TransitionTSVFile.h
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:218
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64