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MzMLSpectrumDecoder.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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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 $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/config.h>
38 #include <OpenMS/CONCEPT/Types.h>
39 #include <OpenMS/CONCEPT/Exception.h>
40 #include <OpenMS/DATASTRUCTURES/String.h>
41 #include <OpenMS/FORMAT/Base64.h>
42 #include <OpenMS/INTERFACES/DataStructures.h>
43 #include <OpenMS/METADATA/MetaInfoDescription.h>
44
45 #include <string>
46 #include <xercesc/dom/DOMNode.hpp>
47
48 #include <OpenMS/FORMAT/HANDLERS/MzMLHandlerHelper.h>
49 #include <OpenMS/KERNEL/MSSpectrum.h>
50 #include <OpenMS/KERNEL/MSChromatogram.h>
51
52 namespace OpenMS
53 {
54
65 class OPENMS_DLLAPI MzMLSpectrumDecoder
66 {
67 protected:
68
69 bool skip_xml_checks_;
70
71 typedef Internal::MzMLHandlerHelper::BinaryData BinaryData;
72
79 OpenMS::Interfaces::SpectrumPtr decodeBinaryDataSpectrum_(std::vector<BinaryData> & data);
80
81 void decodeBinaryDataMSSpectrum_(std::vector<BinaryData>& data, OpenMS::MSSpectrum& s);
82
83 void decodeBinaryDataMSChrom_(std::vector<BinaryData>& data, OpenMS::MSChromatogram& c);
84
91 OpenMS::Interfaces::ChromatogramPtr decodeBinaryDataChrom_(std::vector<BinaryData> & data);
92
103 void handleBinaryDataArray_(xercesc::DOMNode * indexListNode, std::vector<BinaryData>& data);
104
120 void domParseString_(const std::string& in, std::vector<BinaryData>& data);
121
122 public:
123
124 explicit MzMLSpectrumDecoder(bool skip_xml_checks = false) :
125 skip_xml_checks_(skip_xml_checks)
126 {}
127
141 void domParseSpectrum(const std::string& in, OpenMS::Interfaces::SpectrumPtr & sptr);
142
156 void domParseSpectrum(const std::string& in, MSSpectrum& s);
157
171 void domParseChromatogram(const std::string& in, MSChromatogram& c);
172
186 void domParseChromatogram(const std::string& in, OpenMS::Interfaces::ChromatogramPtr & cptr);
187
189 void setSkipXMLChecks(bool only);
190 };
191 }
192
193
Base64.h
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:54
OpenMS::MzMLSpectrumDecoder
A class to decode input strings that contain an mzML chromatogram or spectrum tag.
Definition: MzMLSpectrumDecoder.h:65
Exception.h
MzMLHandlerHelper.h
Types.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
OpenMS::Internal::MzMLHandlerHelper::BinaryData
Representation for binary data in mzML.
Definition: MzMLHandlerHelper.h:69
String.h
OpenMS::MzMLSpectrumDecoder::MzMLSpectrumDecoder
MzMLSpectrumDecoder(bool skip_xml_checks=false)
Definition: MzMLSpectrumDecoder.h:124
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSSpectrum.h
OpenMS::Constants::c
const double c
MetaInfoDescription.h
MSChromatogram.h
OpenMS::MzMLSpectrumDecoder::skip_xml_checks_
bool skip_xml_checks_
Whether to skip some XML checks (e.g. removing whitespace inside base64 arrays) and be fast instead...
Definition: MzMLSpectrumDecoder.h:69
OpenMS::MzMLSpectrumDecoder::BinaryData
Internal::MzMLHandlerHelper::BinaryData BinaryData
Definition: MzMLSpectrumDecoder.h:71
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