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

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

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().