| OpenMS 2.5.0

SqMassFile.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.
6 //
7 // This software is released under a three-clause BSD license:
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10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
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15 // without specific prior written permission.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/MSExperiment.h>
38
39 #include <OpenMS/INTERFACES/IMSDataConsumer.h>
40
41 namespace OpenMS
42 {
43
52 class OPENMS_DLLAPI SqMassFile
53 {
54 public:
55
61 struct OPENMS_DLLAPI SqMassConfig
62 {
63 bool write_full_meta;
64 bool use_lossy_numpress;
65 double linear_fp_mass_acc;
66
67 SqMassConfig () :
68 write_full_meta(true),
69 use_lossy_numpress(false),
70 linear_fp_mass_acc(-1) {}
71 };
72
73 typedef MSExperiment MapType;
74
78 SqMassFile();
80
82 ~SqMassFile();
84
88
89 void load(const String& filename, MapType& map);
90
91 void store(const String& filename, MapType& map);
92
93 void transform(const String& filename_in, Interfaces::IMSDataConsumer * consumer, bool skip_full_count = false, bool skip_first_pass = false);
94
95 void setConfig(SqMassConfig config)
96 {
97 config_ = config;
98 }
99
100 // maybe later ...
101 // static inline void readSpectrumFast(OpenSwath::BinaryDataArrayPtr data1,
102 // OpenSwath::BinaryDataArrayPtr data2, std::ifstream& ifs, int& ms_level,
103 // double& rt)
104
105 // static inline void readChromatogramFast(OpenSwath::BinaryDataArrayPtr data1,
106 // OpenSwath::BinaryDataArrayPtr data2, std::ifstream& ifs)
107
108 protected:
109
110 SqMassConfig config_;
111
112 };
113 }
114
115
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SqMassFile::SqMassConfig::write_full_meta
bool write_full_meta
write full meta data
Definition: SqMassFile.h:63
OpenMS::SqMassFile::SqMassConfig::linear_fp_mass_acc
double linear_fp_mass_acc
desired mass accuracy for numpress linear encoding (-1 no effect, use 0.0001 for 0.2 ppm accuracy @ 500 m/z)
Definition: SqMassFile.h:65
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::SqMassFile::setConfig
void setConfig(SqMassConfig config)
Definition: SqMassFile.h:95
OpenMS::SqMassFile::SqMassConfig::SqMassConfig
SqMassConfig()
Definition: SqMassFile.h:67
OpenMS::SqMassFile::SqMassConfig
Configuration class for SqMassFile.
Definition: SqMassFile.h:61
IMSDataConsumer.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::SqMassFile::MapType
MSExperiment MapType
Definition: SqMassFile.h:73
OpenMS::SqMassFile::config_
SqMassConfig config_
Definition: SqMassFile.h:110
OpenMS::SqMassFile::SqMassConfig::use_lossy_numpress
bool use_lossy_numpress
use lossy numpress compression
Definition: SqMassFile.h:64
OpenMS::Interfaces::IMSDataConsumer
The interface of a consumer of spectra and chromatograms.
Definition: IMSDataConsumer.h:69
OpenMS::SqMassFile
An class that uses on-disk SQLite database to read and write spectra and chromatograms.
Definition: SqMassFile.h:52