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openms/include/OpenMS/INTERFACES/ISpectrumAccess.h
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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.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest, Witold Wolski $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/INTERFACES/DataStructures.h>
38
39 #include <vector>
40 #include <string>
41 #include <boost/shared_ptr.hpp>
42
43 namespace OpenMS
44 {
45 namespace Interfaces
46 {
47
51 class OPENMS_DLLAPI ISpectraReader
52 {
53 public:
54 virtual ~ISpectraReader() {}
56 virtual SpectrumPtr getSpectrumById(int id) const = 0;
58 virtual SpectrumPtr getSpectrumById(const std::string& id) const = 0;
60 virtual std::vector<std::size_t> getSpectraByRT(double RT, double deltaRT) const = 0;
62 virtual size_t getNrSpectra() const = 0;
64 virtual SpectrumMetaPtr getSpectrumMetaById(int id) const = 0;
65
66 /*
67 * Do we need an Iterator here?
68 * We would have to provide our own iterator wrapper class because we don't
69 * know whether all the spectra are loaded at any given timepoint
70 typedef SpectrumPtr const ConstSpectraIterator;
71 ConstSpectraIterator beginSpectra() const;
72 ConstSpectraIterator endSpectra() const;
73 */
74 };
75 typedef boost::shared_ptr<ISpectraReader> SpectraReaderPtr;
76
77
81 class OPENMS_DLLAPI IChromatogramsReader
82 {
83 public:
84 virtual ~IChromatogramsReader() {}
86 virtual ChromatogramPtr getChromatogramById(int id) const = 0;
88 virtual ChromatogramPtr getChromatogramById(const std::string& id) const = 0;
90 virtual std::vector<std::size_t> getChromatogramByPrecursorMZ(double mz, double deltaMZ) const = 0;
92 virtual std::size_t getNrChromatograms() const = 0;
94 virtual ChromatogramMetaPtr getChromatogramMetaById(int id) const = 0;
95
96 /*
97 * Do we need an Iterator here?
98 * We would have to provide our own iterator wrapper class because we don't
99 * know whether all the chromatograms are loaded at any given timepoint
100 ConstChromatogramIterator beginChromatograms() const;
101 ConstChromatogramIterator endChromatograms() const;
102 */
103 };
104 typedef boost::shared_ptr<IChromatogramsReader> ChromatogramsReaderPtr;
105
106
107 class OPENMS_DLLAPI ISpectraWriter
108 {
109 public:
110 virtual ~ISpectraWriter() {}
112 virtual void appendSpectrum(SpectrumPtr spectrum, bool write_through=false) = 0;
114 virtual void flush() = 0;
115 };
116 typedef boost::shared_ptr<ISpectraWriter> SpectraWriterPtr;
117
118
119 class OPENMS_DLLAPI IChromatogramsWriter
120 {
121 public:
122 virtual ~IChromatogramsWriter() {}
124 virtual void appendChromatogram(ChromatogramPtr chromatogram, bool write_through=false) = 0;
126 virtual void flush() = 0;
127 };
128 typedef boost::shared_ptr<IChromatogramsWriter> ChromatogramsWriterPtr;
129
130 } //end namespace Interfaces
131 } //end namespace OpenMS
132
OpenMS::Interfaces::ChromatogramMetaPtr
boost::shared_ptr< ChromatogramMeta > ChromatogramMetaPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:99
OpenMS::Interfaces::IChromatogramsWriter::~IChromatogramsWriter
virtual ~IChromatogramsWriter()
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:122
OpenMS::Interfaces::ISpectraReader::~ISpectraReader
virtual ~ISpectraReader()
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:54
OpenMS::Interfaces::SpectraWriterPtr
boost::shared_ptr< ISpectraWriter > SpectraWriterPtr
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:116
OpenMS::Interfaces::IChromatogramsReader::~IChromatogramsReader
virtual ~IChromatogramsReader()
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:84
OpenMS::Interfaces::ISpectraWriter
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:107
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Interfaces::SpectrumMetaPtr
boost::shared_ptr< SpectrumMeta > SpectrumMetaPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:179
OpenMS::Interfaces::ChromatogramsReaderPtr
boost::shared_ptr< IChromatogramsReader > ChromatogramsReaderPtr
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:104
OpenMS::Interfaces::IChromatogramsReader
The interface of read-access to a list of chromatograms.
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:81
OpenMS::Interfaces::ChromatogramsWriterPtr
boost::shared_ptr< IChromatogramsWriter > ChromatogramsWriterPtr
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:128
OpenMS::Interfaces::SpectraReaderPtr
boost::shared_ptr< ISpectraReader > SpectraReaderPtr
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:75
OpenMS::Interfaces::IChromatogramsWriter
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:119
OpenMS::Interfaces::ISpectraReader
The interface of read-access to a list of spectra.
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:51
OpenMS::Interfaces::ISpectraWriter::~ISpectraWriter
virtual ~ISpectraWriter()
Definition: openms/include/OpenMS/INTERFACES/ISpectrumAccess.h:110
OpenMS::Interfaces::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
OpenMS::Interfaces::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
DataStructures.h