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33 #include "boost/iostreams/positioning.hpp"
183 const std::map<std::string,std::string>* legacyIdRefToNativeId = 0,
199 std::vector<boost::iostreams::stream_offset>* spectrumPositions = 0,
207 std::vector<boost::iostreams::stream_offset>* chromatogramPositions = 0,
218 std::vector<boost::iostreams::stream_offset>* spectrumPositions = 0,
219 std::vector<boost::iostreams::stream_offset>* chromatogramPositions = 0,
229 std::vector<boost::iostreams::stream_offset>* spectrumPositions = 0,
230 std::vector<boost::iostreams::stream_offset>* chromatogramPositions = 0,
Uncontrolled user parameters (essentially allowing free text). Before using these,...
This element captures the isolation (or 'selection') window configured to isolate one or more precurs...
The XMLWriter class provides simple, tag-level XML syntax writing.
Simple writeable in-memory implementation of ChromatogramList.
Identifying information for a spectrum.
The structure that captures the generation of a peak list (including the underlying acquisitions)
Information about an ontology or CV source and a short 'lookup' tag to refer to.
Description of the default peak processing method. This element describes the base method used in the...
Description of the source file, including location and type.
A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument.
List and descriptions of scans.
List with the different components used in the mass spectrometer. At least one source,...
A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML doc...
The type and energy level used for activation.
unsigned int peaksCount
for efficient read of peak lists after previous read of scan header in mzXML - avoids reparsing the h...
PWIZ_API_DECL void read(std::istream &is, CV &cv)
boost::iostreams::stream_offset sourceFilePositionForBinarySpectrumData
for efficient read of peak lists after previous read of scan header in mzML and mzXML - avoids repars...
Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is sto...
Identifying information for a spectrum subclassed to add private information for faster file IO in mz...
handles registration of IterationListeners and broadcast of update messages
A component of an instrument corresponding to a source (i.e. ion source), an analyzer (i....
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
Description of the acquisition settings of the instrument prior to the start of the run.
Simple writeable in-memory implementation of SpectrumList.
Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile.
Identifying information for a spectrum as read from mzML or mzXML subclassed to add private informati...
This summarizes the different types of spectra that can be expected in the file. This is expected to ...
Expansible description of the sample used to generate the dataset, named in sampleName.
The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style...
Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST ha...
This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to cap...
Description of the way in which a particular software was used.
Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW,...
The method of precursor ion selection and activation.
SpectrumIdentityFromMzXML()
represents a tag-value pair, where the tag comes from the controlled vocabulary
SpectrumIdentityFromXML()
Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW,...
PWIZ_API_DECL void write(minimxml::XMLWriter &writer, const CV &cv)
encoding/decoding configuration