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pwiz::msdata Namespace Reference

Namespaces

 detail
 
 examples
 
 id
 
 IO
 
 MSNumpress
 
 References
 functions for resolving references from objects into the internal MSData lists
 

Classes

struct  Activation
 The type and energy level used for activation. More...
 
struct  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...
 
class  BinaryDataEncoder
 binary-to-text encoding More...
 
struct  Chromatogram
 A single chromatogram. More...
 
struct  ChromatogramIdentity
 Identifying information for a chromatogram. More...
 
class  ChromatogramList
 Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...
 
class  ChromatogramList_mzML
 implementation of ChromatogramList, backed by an mzML file More...
 
class  ChromatogramListBase
 common functionality for base ChromatogramList implementations More...
 
struct  ChromatogramListSimple
 Simple writeable in-memory implementation of ChromatogramList. More...
 
struct  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  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  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  DataProcessing
 Description of the way in which a particular software was used. More...
 
class  DefaultReaderList
 default Reader list More...
 
struct  DiffConfig
 configuration struct for diffing MSData types More...
 
class  ExtendedReaderList
 default ReaderList, extended to include vendor readers More...
 
struct  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  FileDescription
 Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here. More...
 
struct  Index_mzML
 
class  IndexList
 
struct  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  IsolationWindow
 This element captures the isolation (or 'selection') window configured to isolate one or more precursors. More...
 
class  LegacyAdapter_Instrument
 interface for legacy access to Instrument More...
 
class  LegacyAdapter_Software
 interface for legacy access to Software More...
 
class  MemoryMRUCache
 an MRU cache for SpectrumPtrs or ChromatogramPtrs More...
 
struct  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...
 
struct  MSDataFile
 MSData object plus file I/O. More...
 
struct  MSDataMerger
 
struct  MSnHeader
 
struct  MZIntensityPair
 The data point type of a mass spectrum. More...
 
struct  Precursor
 The method of precursor ion selection and activation. More...
 
struct  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  Product
 product ion information More...
 
class  Reader
 interface for file readers More...
 
class  Reader_ABI
 
class  Reader_ABI_T2D
 
class  Reader_Agilent
 
class  Reader_Bruker
 
class  Reader_BTDX
 
class  Reader_MGF
 
class  Reader_MSn
 
class  Reader_mz5
 
class  Reader_mzML
 
class  Reader_mzXML
 
class  Reader_Shimadzu
 
class  Reader_Thermo
 
class  Reader_UIMF
 
class  Reader_UNIFI
 
class  Reader_Waters
 
class  ReaderFail
 
class  ReaderList
 Reader container (composite pattern). More...
 
struct  Run
 A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument. More...
 
struct  Sample
 Expansible description of the sample used to generate the dataset, named in sampleName. More...
 
struct  Scan
 Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile. More...
 
struct  ScanList
 List and descriptions of scans. More...
 
struct  ScanSettings
 Description of the acquisition settings of the instrument prior to the start of the run. More...
 
struct  ScanWindow
 TODO. More...
 
struct  SelectedIon
 TODO. More...
 
class  Serializer_MGF
 MSData <-> MGF stream serialization. More...
 
class  Serializer_MSn
 MSData <-> MSn stream serialization. More...
 
class  Serializer_mzML
 MSData <-> mzML stream serialization. More...
 
class  Serializer_mzXML
 MSData <-> mzXML stream serialization. More...
 
class  SHA1OutputObserver
 
struct  Software
 A piece of software. More...
 
struct  SourceFile
 Description of the source file, including location and type. More...
 
struct  Spectrum
 The structure that captures the generation of a peak list (including the underlying acquisitions) More...
 
struct  SpectrumIdentity
 Identifying information for a spectrum. More...
 
struct  SpectrumIdentityFromMzXML
 Identifying information for a spectrum as read from mzML or mzXML subclassed to add private information for faster file IO in mzXML. More...
 
struct  SpectrumIdentityFromXML
 Identifying information for a spectrum subclassed to add private information for faster file IO in mzML and mzXML. More...
 
struct  SpectrumInfo
 simple structure for holding Spectrum info More...
 
class  SpectrumIterator
 SpectrumIterator provides convenient iteration through a set of scans in a SpectrumList. More...
 
class  SpectrumList
 Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...
 
class  SpectrumList_BTDX
 SpectrumList backed by a Bruker BioTools DataExchange XML file. More...
 
class  SpectrumList_MGF
 implementation of SpectrumList, backed by an MGF file More...
 
class  SpectrumList_MSn
 implementation of SpectrumList, backed by an MGF file More...
 
class  SpectrumList_mzML
 implementation of SpectrumList, backed by an mzML file More...
 
class  SpectrumList_mzXML
 implementation of SpectrumList, backed by an mzXML file More...
 
class  SpectrumListBase
 common functionality for base SpectrumList implementations More...
 
class  SpectrumListCache
 adds a level of flexible MRU caching to a SpectrumList processor chain More...
 
class  SpectrumListIonMobilityBase
 
struct  SpectrumListSimple
 Simple writeable in-memory implementation of SpectrumList. More...
 
class  SpectrumListWrapper
 Inheritable pass-through implementation for wrapping a SpectrumList. More...
 
class  SpectrumWorkerThreads
 
struct  Target
 TODO. More...
 
class  TextWriter
 
struct  TimeIntensityPair
 The data point type of a chromatogram. More...
 
struct  Version
 

Typedefs

typedef boost::shared_ptr< const msdata::SpectrumListSpectrumList_const_ptr
 
typedef boost::shared_ptr< const msdata::SpectrumSpectrum_const_ptr
 
typedef boost::shared_ptr< const BinaryDataArrayBinaryDataArray_const_ptr
 
typedef boost::shared_ptr< Index_mzMLIndex_mzML_Ptr
 
typedef boost::shared_ptr< SourceFileSourceFilePtr
 Description of the source file, including location and type. More...
 
typedef boost::shared_ptr< SampleSamplePtr
 
typedef boost::shared_ptr< SoftwareSoftwarePtr
 
typedef boost::shared_ptr< ScanSettingsScanSettingsPtr
 
typedef boost::shared_ptr< InstrumentConfigurationInstrumentConfigurationPtr
 
typedef boost::shared_ptr< ProcessingMethodProcessingMethodPtr
 
typedef boost::shared_ptr< DataProcessingDataProcessingPtr
 
typedef boost::shared_ptr< BinaryDataArrayBinaryDataArrayPtr
 
typedef boost::shared_ptr< SpectrumSpectrumPtr
 
typedef boost::shared_ptr< ChromatogramChromatogramPtr
 
typedef boost::shared_ptr< SpectrumListSpectrumListPtr
 
typedef boost::shared_ptr< SpectrumListSimpleSpectrumListSimplePtr
 
typedef boost::shared_ptr< ChromatogramListChromatogramListPtr
 
typedef boost::shared_ptr< ChromatogramListSimpleChromatogramListSimplePtr
 
typedef boost::shared_ptr< MSDataMSDataPtr
 
typedef boost::shared_ptr< ReaderReaderPtr
 

Enumerations

enum  ComponentType { ComponentType_Unknown = -1, ComponentType_Source = 0, ComponentType_Analyzer, ComponentType_Detector }
 
enum  DetailLevel { DetailLevel_InstantMetadata, DetailLevel_FastMetadata, DetailLevel_FullMetadata, DetailLevel_FullData }
 
enum  MSn_Type {
  MSn_Type_UNKNOWN, MSn_Type_BMS1, MSn_Type_CMS1, MSn_Type_BMS2,
  MSn_Type_CMS2, MSn_Type_MS1, MSn_Type_MS2
}
 

Functions

PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const BinaryDataEncoder::Config &config)
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const pwiz::data::Diff< MSData, DiffConfig > &diff)
 
PWIZ_API_DECL std::vector< CVdefaultCVList ()
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const MZIntensityPair &mzi)
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const TimeIntensityPair &ti)
 
PWIZ_API_DECL void calculateSourceFileSHA1 (SourceFile &sourceFile)
 calculates and adds a CV term for the SHA1 checksum of a source file element More...
 
PWIZ_API_DECL void calculateSHA1Checksums (const MSData &msd)
 Iterate and calculate SHA-1 for all source files. More...
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, MSDataFile::Format format)
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const MSDataFile::WriteConfig &config)
 
PWIZ_API_DECL ReaderList operator+ (const ReaderPtr &lhs, const ReaderPtr &rhs)
 returns a list containing the lhs and rhs as readers More...
 
PWIZ_API_DECL CVID identifyFileFormat (const ReaderPtr &reader, const std::string &filepath)
 tries to identify a filepath using the provided Reader or ReaderList; returns the CVID file format of the specified filepath, or CVID_Unknown if the file format has no CV term or the filepath doesn't exist More...
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const Serializer_mzML::Config &config)
 
PWIZ_API_DECL std::ostream & operator<< (std::ostream &os, const Serializer_mzXML::Config &config)
 

Variables

const double BinaryDataEncoder_default_numpressSlofErrorTolerance = 0.0002
 
const double BinaryDataEncoder_default_numpressLinearErrorTolerance = 2e-9
 
const double BinaryDataEncoder_default_numpressPicErrorTolerance = 0.5
 
const size_t IDENTITY_INDEX_NONE = (size_t)-1
 

Typedef Documentation

◆ SpectrumList_const_ptr

Definition at line 28 of file DemuxTypes.hpp.

◆ Spectrum_const_ptr

typedef boost::shared_ptr<const msdata::Spectrum> pwiz::msdata::Spectrum_const_ptr

Definition at line 29 of file DemuxTypes.hpp.

◆ BinaryDataArray_const_ptr

typedef boost::shared_ptr<const BinaryDataArray> pwiz::msdata::BinaryDataArray_const_ptr

Definition at line 30 of file DemuxTypes.hpp.

◆ Index_mzML_Ptr

typedef boost::shared_ptr<Index_mzML> pwiz::msdata::Index_mzML_Ptr

Definition at line 61 of file Index_mzML.hpp.

◆ SourceFilePtr

typedef boost::shared_ptr<SourceFile> pwiz::msdata::SourceFilePtr

Description of the source file, including location and type.

Definition at line 76 of file MSData.hpp.

◆ SamplePtr

typedef boost::shared_ptr<Sample> pwiz::msdata::SamplePtr

Definition at line 118 of file MSData.hpp.

◆ SoftwarePtr

typedef boost::shared_ptr<Software> pwiz::msdata::SoftwarePtr

Definition at line 198 of file MSData.hpp.

◆ ScanSettingsPtr

typedef boost::shared_ptr<ScanSettings> pwiz::msdata::ScanSettingsPtr

Definition at line 225 of file MSData.hpp.

◆ InstrumentConfigurationPtr

Definition at line 250 of file MSData.hpp.

◆ ProcessingMethodPtr

Definition at line 269 of file MSData.hpp.

◆ DataProcessingPtr

typedef boost::shared_ptr<DataProcessing> pwiz::msdata::DataProcessingPtr

Definition at line 288 of file MSData.hpp.

◆ BinaryDataArrayPtr

Definition at line 417 of file MSData.hpp.

◆ SpectrumPtr

typedef boost::shared_ptr<Spectrum> pwiz::msdata::SpectrumPtr

Definition at line 573 of file MSData.hpp.

◆ ChromatogramPtr

typedef boost::shared_ptr<Chromatogram> pwiz::msdata::ChromatogramPtr

Definition at line 624 of file MSData.hpp.

◆ SpectrumListPtr

typedef boost::shared_ptr<SpectrumList> pwiz::msdata::SpectrumListPtr

Definition at line 711 of file MSData.hpp.

◆ SpectrumListSimplePtr

Definition at line 731 of file MSData.hpp.

◆ ChromatogramListPtr

Definition at line 785 of file MSData.hpp.

◆ ChromatogramListSimplePtr

Definition at line 805 of file MSData.hpp.

◆ MSDataPtr

typedef boost::shared_ptr<MSData> pwiz::msdata::MSDataPtr

Definition at line 913 of file MSData.hpp.

◆ ReaderPtr

typedef boost::shared_ptr<Reader> pwiz::msdata::ReaderPtr

Definition at line 139 of file Reader.hpp.

Enumeration Type Documentation

◆ ComponentType

Enumerator
ComponentType_Unknown 
ComponentType_Source 
ComponentType_Analyzer 
ComponentType_Detector 

Definition at line 121 of file MSData.hpp.

◆ DetailLevel

Enumerator
DetailLevel_InstantMetadata 
DetailLevel_FastMetadata 
DetailLevel_FullMetadata 
DetailLevel_FullData 

Definition at line 630 of file MSData.hpp.

◆ MSn_Type

Enumerator
MSn_Type_UNKNOWN 
MSn_Type_BMS1 
MSn_Type_CMS1 
MSn_Type_BMS2 
MSn_Type_CMS2 
MSn_Type_MS1 
MSn_Type_MS2 

Definition at line 38 of file SpectrumList_MSn.hpp.

Function Documentation

◆ operator<<() [1/8]

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const BinaryDataEncoder::Config config 
)

◆ operator<<() [2/8]

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const pwiz::data::Diff< MSData, DiffConfig > &  diff 
)

◆ defaultCVList()

PWIZ_API_DECL std::vector<CV> pwiz::msdata::defaultCVList ( )

◆ operator<<() [3/8]

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const MZIntensityPair mzi 
)

◆ operator<<() [4/8]

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const TimeIntensityPair ti 
)

◆ calculateSourceFileSHA1()

PWIZ_API_DECL void pwiz::msdata::calculateSourceFileSHA1 ( SourceFile sourceFile)

calculates and adds a CV term for the SHA1 checksum of a source file element

◆ calculateSHA1Checksums()

PWIZ_API_DECL void pwiz::msdata::calculateSHA1Checksums ( const MSData msd)

Iterate and calculate SHA-1 for all source files.

◆ operator<<() [5/8]

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
MSDataFile::Format  format 
)

◆ operator<<() [6/8]

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const MSDataFile::WriteConfig config 
)

◆ operator+()

PWIZ_API_DECL ReaderList pwiz::msdata::operator+ ( const ReaderPtr lhs,
const ReaderPtr rhs 
)

returns a list containing the lhs and rhs as readers

◆ identifyFileFormat()

PWIZ_API_DECL CVID pwiz::msdata::identifyFileFormat ( const ReaderPtr reader,
const std::string &  filepath 
)

tries to identify a filepath using the provided Reader or ReaderList; returns the CVID file format of the specified filepath, or CVID_Unknown if the file format has no CV term or the filepath doesn't exist

Referenced by testIdentifyFileFormat().

◆ operator<<() [7/8]

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const Serializer_mzML::Config config 
)

◆ operator<<() [8/8]

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const Serializer_mzXML::Config config 
)

Variable Documentation

◆ BinaryDataEncoder_default_numpressSlofErrorTolerance

const double pwiz::msdata::BinaryDataEncoder_default_numpressSlofErrorTolerance = 0.0002

Definition at line 40 of file BinaryDataEncoder.hpp.

◆ BinaryDataEncoder_default_numpressLinearErrorTolerance

const double pwiz::msdata::BinaryDataEncoder_default_numpressLinearErrorTolerance = 2e-9

Definition at line 41 of file BinaryDataEncoder.hpp.

◆ BinaryDataEncoder_default_numpressPicErrorTolerance

const double pwiz::msdata::BinaryDataEncoder_default_numpressPicErrorTolerance = 0.5

Definition at line 42 of file BinaryDataEncoder.hpp.

◆ IDENTITY_INDEX_NONE

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

Definition at line 467 of file MSData.hpp.

pwiz::msdata::MSn_Type_BMS2
@ MSn_Type_BMS2
Definition: SpectrumList_MSn.hpp:38
pwiz::msdata::MSn_Type_MS1
@ MSn_Type_MS1
Definition: SpectrumList_MSn.hpp:38
pwiz::msdata::MSn_Type_CMS2
@ MSn_Type_CMS2
Definition: SpectrumList_MSn.hpp:38
pwiz::msdata::DetailLevel_FullMetadata
@ DetailLevel_FullMetadata
Definition: MSData.hpp:634
pwiz::msdata::DetailLevel_InstantMetadata
@ DetailLevel_InstantMetadata
Definition: MSData.hpp:632
pwiz::msdata::ComponentType_Detector
@ ComponentType_Detector
Definition: MSData.hpp:126
pwiz::msdata::ComponentType_Source
@ ComponentType_Source
Definition: MSData.hpp:124
pwiz::msdata::ComponentType_Unknown
@ ComponentType_Unknown
Definition: MSData.hpp:123
pwiz::msdata::ComponentType_Analyzer
@ ComponentType_Analyzer
Definition: MSData.hpp:125
pwiz::msdata::DetailLevel_FastMetadata
@ DetailLevel_FastMetadata
Definition: MSData.hpp:633
pwiz::msdata::DetailLevel_FullData
@ DetailLevel_FullData
Definition: MSData.hpp:635
pwiz::msdata::MSn_Type_CMS1
@ MSn_Type_CMS1
Definition: SpectrumList_MSn.hpp:38
pwiz::msdata::MSn_Type_BMS1
@ MSn_Type_BMS1
Definition: SpectrumList_MSn.hpp:38
pwiz::msdata::MSn_Type_UNKNOWN
@ MSn_Type_UNKNOWN
Definition: SpectrumList_MSn.hpp:38
pwiz::msdata::MSn_Type_MS2
@ MSn_Type_MS2
Definition: SpectrumList_MSn.hpp:38