OpenMS  2.4.0
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 
80  OpenMS::Interfaces::SpectrumPtr decodeBinaryDataSpectrum_(std::vector<BinaryData> & data);
81 
82  void decodeBinaryDataMSSpectrum_(std::vector<BinaryData>& data, OpenMS::MSSpectrum& s);
83 
84  void decodeBinaryDataMSChrom_(std::vector<BinaryData>& data, OpenMS::MSChromatogram& c);
85 
93  OpenMS::Interfaces::ChromatogramPtr decodeBinaryDataChrom_(std::vector<BinaryData> & data);
94 
105  void handleBinaryDataArray_(xercesc::DOMNode * indexListNode, std::vector<BinaryData>& data);
106 
122  void domParseString_(const std::string& in, std::vector<BinaryData>& data);
123 
124  public:
125 
126  explicit MzMLSpectrumDecoder(bool skip_xml_checks = false) :
127  skip_xml_checks_(skip_xml_checks)
128  {}
129 
143  void domParseSpectrum(const std::string& in, OpenMS::Interfaces::SpectrumPtr & sptr);
144 
158  void domParseSpectrum(const std::string& in, MSSpectrum& s);
159 
173  void domParseChromatogram(const std::string& in, MSChromatogram& c);
174 
188  void domParseChromatogram(const std::string& in, OpenMS::Interfaces::ChromatogramPtr & cptr);
189 
191  void setSkipXMLChecks(bool only);
192  };
193 }
194 
195 
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:236
MzMLSpectrumDecoder(bool skip_xml_checks=false)
Definition: MzMLSpectrumDecoder.h:126
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:156
The representation of a chromatogram.
Definition: MSChromatogram.h:54
Binary data representation.
Definition: MzMLHandlerHelper.h:57
const double c
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool skip_xml_checks_
Definition: MzMLSpectrumDecoder.h:69
A class to decode input strings that contain an mzML chromatogram or spectrum tag.
Definition: MzMLSpectrumDecoder.h:65
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
Internal::MzMLHandlerHelper::BinaryData BinaryData
Definition: MzMLSpectrumDecoder.h:71