Classes | Namespaces | Typedefs | Enumerations | Functions | Variables
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.


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...


namespace  pwiz
namespace  pwiz::msdata
namespace  pwiz::msdata::IO
namespace  pwiz::msdata::id


typedef boost::shared_ptr
< SourceFile > 
 Description of the source file, including location and type.
typedef boost::shared_ptr< Sample > pwiz::msdata::SamplePtr
typedef boost::shared_ptr
< Software > 
typedef boost::shared_ptr
< ScanSettings > 
typedef boost::shared_ptr
< InstrumentConfiguration > 
typedef boost::shared_ptr
< ProcessingMethod > 
typedef boost::shared_ptr
< DataProcessing > 
typedef boost::shared_ptr
< BinaryDataArray > 
typedef boost::shared_ptr
< Spectrum > 
typedef boost::shared_ptr
< Chromatogram > 
typedef boost::shared_ptr
< SpectrumList > 
typedef boost::shared_ptr
< SpectrumListSimple > 
typedef boost::shared_ptr
< ChromatogramList > 
typedef boost::shared_ptr
< ChromatogramListSimple > 
typedef boost::shared_ptr< MSData > pwiz::msdata::MSDataPtr


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 }


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")


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