33 #include "boost/iostreams/positioning.hpp" 146 PWIZ_API_DECL void read(std::istream& is,
Precursor& precursor,
const std::map<std::string,std::string>* legacyIdRefToNativeId = 0);
177 void write(minimxml::XMLWriter& writer,
const Spectrum& spectrum,
const MSData& msd,
178 const BinaryDataEncoder::Config& config = BinaryDataEncoder::Config());
180 void read(std::istream& is, Spectrum& spectrum,
183 const std::map<std::string,std::string>* legacyIdRefToNativeId = 0,
184 const MSData* msd = 0,
185 const SpectrumIdentityFromXML *
id = 0);
189 void write(minimxml::XMLWriter& writer,
const Chromatogram& chromatogram,
190 const BinaryDataEncoder::Config& config = BinaryDataEncoder::Config());
192 void read(std::istream& is, Chromatogram& chromatogram,
197 void write(minimxml::XMLWriter& writer,
const SpectrumList& spectrumList,
const MSData& msd,
198 const BinaryDataEncoder::Config& config = BinaryDataEncoder::Config(),
199 std::vector<boost::iostreams::stream_offset>* spectrumPositions = 0,
201 PWIZ_API_DECL void read(std::istream& is, SpectrumListSimple& spectrumListSimple);
205 void write(minimxml::XMLWriter& writer,
const ChromatogramList& chromatogramList,
206 const BinaryDataEncoder::Config& config = BinaryDataEncoder::Config(),
207 std::vector<boost::iostreams::stream_offset>* chromatogramPositions = 0,
209 PWIZ_API_DECL void read(std::istream& is, ChromatogramListSimple& chromatogramListSimple);
216 void write(minimxml::XMLWriter& writer,
const Run& run,
const MSData& msd,
217 const BinaryDataEncoder::Config& config = BinaryDataEncoder::Config(),
218 std::vector<boost::iostreams::stream_offset>* spectrumPositions = 0,
219 std::vector<boost::iostreams::stream_offset>* chromatogramPositions = 0,
222 void read(std::istream& is, Run& run,
227 void write(minimxml::XMLWriter& writer,
const MSData& msd,
228 const BinaryDataEncoder::Config& config = BinaryDataEncoder::Config(),
229 std::vector<boost::iostreams::stream_offset>* spectrumPositions = 0,
230 std::vector<boost::iostreams::stream_offset>* chromatogramPositions = 0,
233 void read(std::istream& is, MSData& msd,
This summarizes the different types of spectra that can be expected in the file. This is expected to ...
The type and energy level used for activation.
PWIZ_API_DECL const CV & cv(const std::string &prefix)
returns a CV object for the specified namespace (prefix); currently supported namespaces are: MS UO ...
The XMLWriter class provides simple, tag-level XML syntax writing.
Description of the way in which a particular software was used.
Description of the source file, including location and type.
Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile...
The method of precursor ion selection and activation.
A component of an instrument corresponding to a source (i.e. ion source), an analyzer (i...
Information about an ontology or CV source and a short 'lookup' tag to refer to.
boost::iostreams::stream_offset sourceFilePositionForBinarySpectrumData
for efficient read of peak lists after previous read of scan header in mzML and mzXML - avoids repars...
SpectrumIdentityFromXML()
Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead.
PWIZ_API_DECL void read(std::istream &is, TraData &td)
Description of the default peak processing method. This element describes the base method used in the...
Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
unsigned int peaksCount
for efficient read of peak lists after previous read of scan header in mzXML - avoids reparsing the h...
List with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified.
SpectrumIdentityFromMzXML()
This element captures the isolation (or 'selection') window configured to isolate one or more precurs...
Identifying information for a spectrum as read from mzML or mzXML subclassed to add private informati...
A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML doc...
Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST ha...
The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style...
Identifying information for a spectrum.
encoding/decoding configuration
handles registration of IterationListeners and broadcast of update messages
Description of the acquisition settings of the instrument prior to the start of the run...
List and descriptions of scans.
Expansible description of the sample used to generate the dataset, named in sampleName.
Identifying information for a spectrum subclassed to add private information for faster file IO in mz...
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const Configuration &x)
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
represents a tag-value pair, where the tag comes from the controlled vocabulary