IO.hpp File Reference

#include "pwiz/utility/misc/Export.hpp"
#include "MSData.hpp"
#include "BinaryDataEncoder.hpp"
#include "pwiz/utility/minimxml/XMLWriter.hpp"
#include "pwiz/utility/misc/IterationListener.hpp"
#include "boost/iostreams/positioning.hpp"

Go to the source code of this file.

Classes
struct	pwiz::msdata::SpectrumIdentityFromXML
	Identifying information for a spectrum subclassed to add private information for faster file IO in mzML and mzXML. More...
struct	pwiz::msdata::SpectrumIdentityFromMzXML
	Identifying information for a spectrum as read from mzML or mzXML subclassed to add private information for faster file IO in mzXML. More...

Namespaces
namespace	pwiz
	AMTContainer.hpp.
namespace	pwiz::msdata
namespace	pwiz::msdata::IO

Functions
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const CV &cv)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, CV &cv)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const UserParam &userParam)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, UserParam &userParam)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const CVParam &cv)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, CVParam &cv)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const ParamGroup &paramGroup)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, ParamGroup &paramGroup)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const FileContent &fc)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, FileContent &fc)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const SourceFile &sf)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, SourceFile &sf)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Contact &c)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Contact &c)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const FileDescription &fd)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, FileDescription &fd)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Sample &sf)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Sample &sf)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Component &component)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Component &component)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const ComponentList &componentList)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, ComponentList &componentList)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Software &software)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Software &software)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const InstrumentConfiguration &instrumentConfiguration)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, InstrumentConfiguration &instrumentConfiguration)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const ProcessingMethod &processingMethod)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, ProcessingMethod &processingMethod)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const DataProcessing &dataProcessing)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, DataProcessing &dataProcessing)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Target &t)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Target &t)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const ScanSettings &scanSettings)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, ScanSettings &scanSettings)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const IsolationWindow &isolationWindow)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, IsolationWindow &isolationWindow)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const SelectedIon &selectedIon)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, SelectedIon &selectedIon)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Activation &activation)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Activation &activation)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Precursor &precursor)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Precursor &precursor, const std::map< std::string, std::string > *legacyIdRefToNativeId=0)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Product &product)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Product &product)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const ScanWindow &selectionWindow)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, ScanWindow &selectionWindow)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Scan &scan, const MSData &msd)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Scan &scan)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const ScanList &scanList, const MSData &msd)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, ScanList &scanList)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const BinaryDataArray &binaryDataArray, const BinaryDataEncoder::Config &config=BinaryDataEncoder::Config())
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, BinaryDataArray &binaryDataArray, const MSData *msd=0)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Spectrum &spectrum, const MSData &msd, const BinaryDataEncoder::Config &config=BinaryDataEncoder::Config())
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Spectrum &spectrum, BinaryDataFlag binaryDataFlag=IgnoreBinaryData, int version=0, const std::map< std::string, std::string > *legacyIdRefToNativeId=0, const MSData *msd=0, const SpectrumIdentityFromXML *id=0)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Chromatogram &chromatogram, const BinaryDataEncoder::Config &config=BinaryDataEncoder::Config())
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Chromatogram &chromatogram, BinaryDataFlag binaryDataFlag=IgnoreBinaryData)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const SpectrumList &spectrumList, const MSData &msd, const BinaryDataEncoder::Config &config=BinaryDataEncoder::Config(), std::vector< boost::iostreams::stream_offset > *spectrumPositions=0, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry=0)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, SpectrumListSimple &spectrumListSimple)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const ChromatogramList &chromatogramList, const BinaryDataEncoder::Config &config=BinaryDataEncoder::Config(), std::vector< boost::iostreams::stream_offset > *chromatogramPositions=0, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry=0)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, ChromatogramListSimple &chromatogramListSimple)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const Run &run, const MSData &msd, const BinaryDataEncoder::Config &config=BinaryDataEncoder::Config(), std::vector< boost::iostreams::stream_offset > *spectrumPositions=0, std::vector< boost::iostreams::stream_offset > *chromatogramPositions=0, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry=0)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, Run &run, SpectrumListFlag spectrumListFlag=IgnoreSpectrumList)
PWIZ_API_DECL void	pwiz::msdata::IO::write (minimxml::XMLWriter &writer, const MSData &msd, const BinaryDataEncoder::Config &config=BinaryDataEncoder::Config(), std::vector< boost::iostreams::stream_offset > *spectrumPositions=0, std::vector< boost::iostreams::stream_offset > *chromatogramPositions=0, const pwiz::util::IterationListenerRegistry *iterationListenerRegistry=0)
PWIZ_API_DECL void	pwiz::msdata::IO::read (std::istream &is, MSData &msd, SpectrumListFlag spectrumListFlag=IgnoreSpectrumList)

Variables
	IgnoreBinaryData
	ReadBinaryData
	IgnoreSpectrumList

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Variable Documentation

IgnoreBinaryData

Definition at line 173 of file IO.hpp.

ReadBinaryData

Definition at line 173 of file IO.hpp.

Referenced by testChromatogram(), and testSpectrum().

IgnoreSpectrumList

Definition at line 212 of file IO.hpp.

Referenced by testRun().