Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
SpectrumAccessOpenMSCached.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 2002-2013.
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 #ifndef OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_SPECTRUMACCESSOPENMSCACHED_H
36 #define OPENMS_ANALYSIS_OPENSWATH_DATAACCESS_SPECTRUMACCESSOPENMSCACHED_H
37 
41 
44 
45 namespace OpenMS
46 {
47 
56  class OPENMS_DLLAPI SpectrumAccessOpenMSCached :
58  {
59 
60 public:
63 
64  explicit SpectrumAccessOpenMSCached(String filename);
65 
67 
68  OpenSwath::SpectrumPtr getSpectrumById(int id) const;
69 
70  OpenSwath::SpectrumMeta getSpectrumMetaById(int id) const;
71 
72  std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const;
73 
74  size_t getNrSpectra() const;
75 
76  SpectrumSettings getSpectraMetaInfo(int id) const;
77 
78  OpenSwath::ChromatogramPtr getChromatogramById(int id) const;
79 
80  // FEATURE ?
81  // ChromatogramPtr getChromatogramByPrecursorMZ(double mz, double deltaMZ);
82 
83  size_t getNrChromatograms() const;
84 
85  ChromatogramSettings getChromatogramMetaInfo(int id) const;
86 
87  std::string getChromatogramNativeID(int id) const;
88 
89 private:
91  std::ifstream ifs_;
95  };
96 
97 } //end namespace
98 
99 #endif
OpenMS::MSExperiment< Peak1D > MSExperimentType
Definition: SpectrumAccessOpenMSCached.h:61
MSExperimentType meta_ms_experiment_
Definition: SpectrumAccessOpenMSCached.h:90
A more convenient string class.
Definition: String.h:56
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:152
Representation of 1D spectrum settings.
Definition: SpectrumSettings.h:64
CachedmzML cache_
Definition: SpectrumAccessOpenMSCached.h:92
Identifying information for a spectrum.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:155
OPENSWATHALGO_DLLAPI typedef boost::shared_ptr< Spectrum > SpectrumPtr
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/DataStructures.h:227
OpenMS::MSSpectrum< Peak1D > MSSpectrumType
Definition: SpectrumAccessOpenMSCached.h:62
String filename_cached_
Definition: SpectrumAccessOpenMSCached.h:94
Representation of chromatogram settings, e.g. SRM/MRM chromatograms.
Definition: ChromatogramSettings.h:59
std::ifstream ifs_
Definition: SpectrumAccessOpenMSCached.h:91
An class that uses on-disk caching to read and write spectra and chromatograms.
Definition: CachedmzML.h:60
An implementation of the OpenSWATH Spectrum Access interface using Disk caching.
Definition: SpectrumAccessOpenMSCached.h:56
The interface of a mass spectrometry experiment.
Definition: ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:50
String filename_
Definition: SpectrumAccessOpenMSCached.h:93

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:21 using doxygen 1.8.5