MSData.hpp File Reference

#include "pwiz/utility/misc/Export.hpp"
#include "pwiz/data/common/ParamTypes.hpp"
#include "boost/shared_ptr.hpp"
#include "boost/iostreams/positioning.hpp"
#include <vector>
#include <string>
#include <map>

Go to the source code of this file.

Classes
struct	pwiz::msdata::FileContent
	This summarizes the different types of spectra that can be expected in the file. This is expected to aid processing software in skipping files that do not contain appropriate spectrum types for it. More...
struct	pwiz::msdata::SourceFile
	Description of the source file, including location and type. More...
struct	pwiz::msdata::Contact
	Structure allowing the use of a controlled (cvParam) or uncontrolled vocabulary (userParam), or a reference to a predefined set of these in this mzML file (paramGroupRef). More...
struct	pwiz::msdata::FileDescription
	Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here. More...
struct	pwiz::msdata::Sample
	Expansible description of the sample used to generate the dataset, named in sampleName. More...
struct	pwiz::msdata::Component
	A component of an instrument corresponding to a source (i.e. ion source), an analyzer (i.e. mass analyzer), or a detector (i.e. ion detector) More...
struct	pwiz::msdata::ComponentList
	List with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified. More...
struct	pwiz::msdata::Software
	A piece of software. More...
struct	pwiz::msdata::Target
	TODO. More...
struct	pwiz::msdata::ScanSettings
	Description of the acquisition settings of the instrument prior to the start of the run. More...
struct	pwiz::msdata::InstrumentConfiguration
	Description of a particular hardware configuration of a mass spectrometer. Each configuration MUST have one (and only one) of the three different components used for an analysis. For hybrid instruments, such as an LTQ-FT, there MUST be one configuration for each permutation of the components that is used in the document. For software configuration, reference the appropriate ScanSettings element. More...
struct	pwiz::msdata::ProcessingMethod
	Description of the default peak processing method. This element describes the base method used in the generation of a particular mzML file. Variable methods should be described in the appropriate acquisition section - if no acquisition-specific details are found, then this information serves as the default. More...
struct	pwiz::msdata::DataProcessing
	Description of the way in which a particular software was used. More...
struct	pwiz::msdata::IsolationWindow
	This element captures the isolation (or 'selection') window configured to isolate one or more precursors. More...
struct	pwiz::msdata::SelectedIon
	TODO. More...
struct	pwiz::msdata::Activation
	The type and energy level used for activation. More...
struct	pwiz::msdata::Precursor
	The method of precursor ion selection and activation. More...
struct	pwiz::msdata::Product
	product ion information More...
struct	pwiz::msdata::ScanWindow
	TODO. More...
struct	pwiz::msdata::Scan
	Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile. More...
struct	pwiz::msdata::ScanList
	List and descriptions of scans. More...
struct	pwiz::msdata::BinaryDataArray
	The structure into which encoded binary data goes. Byte ordering is always little endian (Intel style). Computers using a different endian style MUST convert to/from little endian when writing/reading mzML. More...
struct	pwiz::msdata::MZIntensityPair
	The data point type of a mass spectrum. More...
struct	pwiz::msdata::TimeIntensityPair
	The data point type of a chromatogram. More...
struct	pwiz::msdata::SpectrumIdentity
	Identifying information for a spectrum. More...
struct	pwiz::msdata::ChromatogramIdentity
	Identifying information for a chromatogram. More...
struct	pwiz::msdata::Spectrum
	The structure that captures the generation of a peak list (including the underlying acquisitions) More...
struct	pwiz::msdata::Chromatogram
	A single chromatogram. More...
class	pwiz::msdata::IndexList
class	pwiz::msdata::SpectrumList
	Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...
struct	pwiz::msdata::SpectrumListSimple
	Simple writeable in-memory implementation of SpectrumList. More...
class	pwiz::msdata::ChromatogramList
	Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...
struct	pwiz::msdata::ChromatogramListSimple
	Simple writeable in-memory implementation of ChromatogramList. More...
struct	pwiz::msdata::Run
	A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument. More...
struct	pwiz::msdata::MSData
	This is the root element of ProteoWizard; it represents the mzML element, defined as: intended to capture the use of a mass spectrometer, the data generated, and the initial processing of that data (to the level of the peak list). More...

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

Typedefs
typedef boost::shared_ptr < SourceFile >	pwiz::msdata::SourceFilePtr
	Description of the source file, including location and type.
typedef boost::shared_ptr< Sample >	pwiz::msdata::SamplePtr
typedef boost::shared_ptr < Software >	pwiz::msdata::SoftwarePtr
typedef boost::shared_ptr < ScanSettings >	pwiz::msdata::ScanSettingsPtr
typedef boost::shared_ptr < InstrumentConfiguration >	pwiz::msdata::InstrumentConfigurationPtr
typedef boost::shared_ptr < ProcessingMethod >	pwiz::msdata::ProcessingMethodPtr
typedef boost::shared_ptr < DataProcessing >	pwiz::msdata::DataProcessingPtr
typedef boost::shared_ptr < BinaryDataArray >	pwiz::msdata::BinaryDataArrayPtr
typedef boost::shared_ptr < Spectrum >	pwiz::msdata::SpectrumPtr
typedef boost::shared_ptr < Chromatogram >	pwiz::msdata::ChromatogramPtr
typedef boost::shared_ptr < SpectrumList >	pwiz::msdata::SpectrumListPtr
typedef boost::shared_ptr < SpectrumListSimple >	pwiz::msdata::SpectrumListSimplePtr
typedef boost::shared_ptr < ChromatogramList >	pwiz::msdata::ChromatogramListPtr
typedef boost::shared_ptr < ChromatogramListSimple >	pwiz::msdata::ChromatogramListSimplePtr
typedef boost::shared_ptr< MSData >	pwiz::msdata::MSDataPtr

Enumerations
enum	pwiz::msdata::ComponentType { pwiz::msdata::ComponentType_Unknown = -1, pwiz::msdata::ComponentType_Source = 0, pwiz::msdata::ComponentType_Analyzer, pwiz::msdata::ComponentType_Detector }
enum	pwiz::msdata::DetailLevel { pwiz::msdata::DetailLevel_InstantMetadata, pwiz::msdata::DetailLevel_FastMetadata, pwiz::msdata::DetailLevel_FullMetadata, pwiz::msdata::DetailLevel_FullData }

Functions
PWIZ_API_DECL std::vector< CV >	pwiz::msdata::defaultCVList ()
PWIZ_API_DECL std::ostream &	pwiz::msdata::operator<< (std::ostream &os, const MZIntensityPair &mzi)
PWIZ_API_DECL std::ostream &	pwiz::msdata::operator<< (std::ostream &os, const TimeIntensityPair &ti)
PWIZ_API_DECL std::map < std::string, std::string >	pwiz::msdata::id::parse (const std::string &id)
	parses an id string into a map<string,string>
PWIZ_API_DECL std::string	pwiz::msdata::id::value (const std::string &id, const std::string &name)
	convenience function to extract a named value from an id string
template<typename value_type >
value_type	pwiz::msdata::id::valueAs (const std::string &id, const std::string &name)
	templated convenience function to extract a named value from an id string
PWIZ_API_DECL CVID	pwiz::msdata::id::getDefaultNativeIDFormat (const MSData &msd)
	returns the nativeID format from the defaultSourceFilePtr if set, or from sourceFilePtrs[0] if the list isn't empty, or CVID_Unknown
PWIZ_API_DECL std::string	pwiz::msdata::id::translateScanNumberToNativeID (CVID nativeIDFormat, const std::string &scanNumber)
	translates a "scan number" to a string that is correct for the given nativeID format; semantic validity requires that scanNumber be parseable as an integer; some nativeID formats cannot be translated to and will always return an empty string currently supported formats: Thermo, Bruker/Agilent YEP, Bruker BAF, mzXML, MGF, and mzData
PWIZ_API_DECL std::string	pwiz::msdata::id::translateNativeIDToScanNumber (CVID nativeIDFormat, const std::string &id)
	translates a nativeID in the given nativeID format to a simple integer "scan number"; some nativeID formats cannot be translated from and will always return an empty string currently supported formats: Thermo, Bruker/Agilent YEP, Bruker BAF, mzXML, MGF, and mzData
PWIZ_API_DECL std::string	pwiz::msdata::id::abbreviate (const std::string &id, char delimiter= '.')
	abbreviates a nativeID ("name1=value1 name2=value2" translates to "value1.value2")

Variables
const size_t	pwiz::msdata::IDENTITY_INDEX_NONE = (size_t)-1