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IndexedMzMLFile.h
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34 
35 #ifndef OPENMS_FORMAT_INDEXEDMZMLFILE_H
36 #define OPENMS_FORMAT_INDEXEDMZMLFILE_H
37 
38 #include <OpenMS/config.h>
39 #include <OpenMS/CONCEPT/Types.h>
43 
44 #include <string>
45 #include <fstream>
46 
47 //#define DEBUG_READER
48 
49 namespace OpenMS
50 {
51 
70  class OPENMS_DLLAPI IndexedMzMLFile
71  {
75  std::vector< std::pair<std::string, std::streampos> > spectra_offsets_;
77  std::vector< std::pair<std::string, std::streampos> > chromatograms_offsets_;
79  std::streampos index_offset_;
83  std::ifstream filestream_;
86 
88 
95  void parseFooter_(String filename);
96 
97  public:
98 
103 
109  explicit IndexedMzMLFile(String filename);
110 
112  IndexedMzMLFile(const IndexedMzMLFile & source);
113 
115  ~IndexedMzMLFile();
116 
122  void openFile(String filename);
123 
133  bool getParsingSuccess() const;
134 
136  size_t getNrSpectra() const;
137 
139  size_t getNrChromatograms() const;
140 
149  OpenMS::Interfaces::SpectrumPtr getSpectrumById(int id);
150 
159  OpenMS::Interfaces::ChromatogramPtr getChromatogramById(int id);
160 
162  void setSkipXMLChecks(bool skip)
163  {
164  skip_xml_checks_ = skip;
165  }
166 
167  };
168 }
169 
170 #endif
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:237
bool parsing_success_
Whether parsing the indexedmzML file was successful.
Definition: IndexedMzMLFile.h:85
void setSkipXMLChecks(bool skip)
sets whether to skip some XML checks and be fast instead
Definition: IndexedMzMLFile.h:162
boost::shared_ptr< Chromatogram > ChromatogramPtr
Definition: openms/include/OpenMS/INTERFACES/DataStructures.h:157
A more convenient string class.
Definition: String.h:57
bool skip_xml_checks_
Definition: IndexedMzMLFile.h:87
bool spectra_before_chroms_
Whether spectra are written before chromatograms in this file.
Definition: IndexedMzMLFile.h:81
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
A class to read an indexedmzML file.
Definition: IndexedMzMLFile.h:70
std::streampos index_offset_
offset to the <indexList> element
Definition: IndexedMzMLFile.h:79
std::ifstream filestream_
The current filestream (opened by openFile)
Definition: IndexedMzMLFile.h:83
std::vector< std::pair< std::string, std::streampos > > spectra_offsets_
Binary offsets to all spectra.
Definition: IndexedMzMLFile.h:75
std::vector< std::pair< std::string, std::streampos > > chromatograms_offsets_
Binary offsets to all chromatograms.
Definition: IndexedMzMLFile.h:77
IndexedMzMLFile()
Constructor.
Definition: IndexedMzMLFile.h:102
String filename_
Name of the file.
Definition: IndexedMzMLFile.h:73

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11