ProteoWizard
Classes | Namespaces | Functions | Variables
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

 pwiz
 
 pwiz::msdata
 
 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
 

Variable Documentation

§ IgnoreBinaryData

IgnoreBinaryData

Definition at line 173 of file IO.hpp.

§ ReadBinaryData

ReadBinaryData

Definition at line 173 of file IO.hpp.

Referenced by testChromatogram(), and testSpectrum().

§ IgnoreSpectrumList

IgnoreSpectrumList

Definition at line 212 of file IO.hpp.

Referenced by testRun().