| OpenMS 2.5.0

SpectrumAccessOpenMSInMemory.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: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/KERNEL/MSSpectrum.h>
39 #include <OpenMS/KERNEL/MSChromatogram.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41
42 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
43
44 #include <boost/shared_ptr.hpp>
45 #include <algorithm> // std::lower_bound, std::upper_bound, std::sort
46
47 namespace OpenMS
48 {
74 class OPENMS_DLLAPI SpectrumAccessOpenMSInMemory :
75 public OpenSwath::ISpectrumAccess
76 {
77 public:
78 typedef OpenMS::PeakMap MSExperimentType;
79 typedef OpenMS::MSSpectrum MSSpectrumType;
80 typedef OpenMS::MSChromatogram MSChromatogramType;
81
83 explicit SpectrumAccessOpenMSInMemory(OpenSwath::ISpectrumAccess & origin);
84
86 ~SpectrumAccessOpenMSInMemory() override;
87
89 SpectrumAccessOpenMSInMemory(const SpectrumAccessOpenMSInMemory & rhs);
90
92 boost::shared_ptr<OpenSwath::ISpectrumAccess> lightClone() const override;
93
94 OpenSwath::SpectrumPtr getSpectrumById(int id) override;
95
96 OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const override;
97
98 std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const override;
99
100 size_t getNrSpectra() const override;
101
102 OpenSwath::ChromatogramPtr getChromatogramById(int id) override;
103
104 size_t getNrChromatograms() const override;
105
106 std::string getChromatogramNativeID(int id) const override;
107
108 private:
109
110 std::vector< OpenSwath::SpectrumPtr > spectra_;
111 std::vector< OpenSwath::SpectrumMeta > spectra_meta_;
112
113 std::vector< OpenSwath::ChromatogramPtr > chromatograms_;
114 std::vector< std::string > chromatogram_ids_;
115
116 };
117
118 } //end namespace OpenMS
119
OpenSwath::OSSpectrumMeta
Identifying information for a spectrum.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:175
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:54
OpenMS::SpectrumAccessOpenMSInMemory::spectra_
std::vector< OpenSwath::SpectrumPtr > spectra_
Definition: SpectrumAccessOpenMSInMemory.h:110
OpenMS::SpectrumAccessOpenMSInMemory::MSExperimentType
OpenMS::PeakMap MSExperimentType
Definition: SpectrumAccessOpenMSInMemory.h:78
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::SpectrumAccessOpenMSInMemory::MSChromatogramType
OpenMS::MSChromatogram MSChromatogramType
Definition: SpectrumAccessOpenMSInMemory.h:80
OpenMS::SpectrumAccessOpenMSInMemory::chromatogram_ids_
std::vector< std::string > chromatogram_ids_
Definition: SpectrumAccessOpenMSInMemory.h:114
StandardTypes.h
OpenMS::SpectrumAccessOpenMSInMemory
An implementation of the OpenSWATH Spectrum Access interface completely in memory.
Definition: SpectrumAccessOpenMSInMemory.h:74
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenSwath::ISpectrumAccess
The interface of a mass spectrometry experiment.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:50
MSSpectrum.h
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:292
MSChromatogram.h
OpenMS::SpectrumAccessOpenMSInMemory::chromatograms_
std::vector< OpenSwath::ChromatogramPtr > chromatograms_
Definition: SpectrumAccessOpenMSInMemory.h:113
ISpectrumAccess.h
OpenSwath::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:172
OpenMS::SpectrumAccessOpenMSInMemory::spectra_meta_
std::vector< OpenSwath::SpectrumMeta > spectra_meta_
Definition: SpectrumAccessOpenMSInMemory.h:111
OpenMS::SpectrumAccessOpenMSInMemory::MSSpectrumType
OpenMS::MSSpectrum MSSpectrumType
Definition: SpectrumAccessOpenMSInMemory.h:79