OpenMS  3.0.0
MzMLSpectrumDecoder.h
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
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34 
35 #pragma once
36 
37 #include <OpenMS/config.h>
38 #include <OpenMS/CONCEPT/Types.h>
41 #include <OpenMS/FORMAT/Base64.h>
44 
45 #include <string>
46 #include <xercesc/dom/DOMNode.hpp>
47 
51 
52 namespace OpenMS
53 {
54 
65  class OPENMS_DLLAPI MzMLSpectrumDecoder
66  {
67  protected:
68 
70 
72 
79  OpenMS::Interfaces::SpectrumPtr decodeBinaryDataSpectrum_(std::vector<BinaryData> & data) const;
80 
81  void decodeBinaryDataMSSpectrum_(std::vector<BinaryData>& data, OpenMS::MSSpectrum& s) const;
82 
83  void decodeBinaryDataMSChrom_(std::vector<BinaryData>& data, OpenMS::MSChromatogram& c) const;
84 
91  OpenMS::Interfaces::ChromatogramPtr decodeBinaryDataChrom_(std::vector<BinaryData> & data) const;
92 
103  void handleBinaryDataArray_(xercesc::DOMNode * indexListNode, std::vector<BinaryData>& data);
104 
120  std::string 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 
OpenMS::Interfaces::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
DataStructures.h
Types.h
OpenMS::Constants::c
const double c
Definition: Constants.h:209
OpenMS::Interfaces::ChromatogramPtr
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::Internal::MzMLHandlerHelper::BinaryData
Representation for binary data in mzML.
Definition: MzMLHandlerHelper.h:69
Exception.h
OpenMS::MzMLSpectrumDecoder::MzMLSpectrumDecoder
MzMLSpectrumDecoder(bool skip_xml_checks=false)
Definition: MzMLSpectrumDecoder.h:124
Base64.h
OpenMS::MzMLSpectrumDecoder
A class to decode input strings that contain an mzML chromatogram or spectrum tag.
Definition: MzMLSpectrumDecoder.h:65
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
MSChromatogram.h
OpenMS::MSChromatogram
The representation of a chromatogram.
Definition: MSChromatogram.h:53
String.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
MSSpectrum.h
MetaInfoDescription.h
MzMLHandlerHelper.h