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pwiz::msdata Namespace Reference

Namespaces

namespace  examples
namespace  IO
namespace  id
namespace  mz5
namespace  References
 functions for resolving references from objects into the internal MSData lists
namespace  detail

Classes

class  BinaryDataEncoder
 binary-to-text encoding More...
class  ChromatogramList_mz5
 implementation of ChromatogramList, backed by an mz5 file More...
class  ChromatogramList_mzML
 implementation of ChromatogramList, backed by an mzML file More...
class  ChromatogramListBase
 common functionality for base ChromatogramList implementations More...
class  Reader_mzML
class  Reader_mzXML
class  Reader_MGF
class  Reader_MSn
class  Reader_BTDX
class  Reader_mz5
class  DefaultReaderList
 default Reader list More...
struct  DiffConfig
 configuration struct for diffing MSData types More...
struct  Index_mzML
struct  SpectrumIdentityFromXML
 Identifying information for a spectrum subclassed to add private information for faster file IO in mzML and mzXML. 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...
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  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  SourceFile
 Description of the source file, including location and type. 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  FileDescription
 Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here. More...
struct  Sample
 Expansible description of the sample used to generate the dataset, named in sampleName. 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  Software
 A piece of software. More...
struct  Target
 TODO. More...
struct  ScanSettings
 Description of the acquisition settings of the instrument prior to the start of the run. More...
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  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  DataProcessing
 Description of the way in which a particular software was used. More...
struct  IsolationWindow
 This element captures the isolation (or 'selection') window configured to isolate one or more precursors. More...
struct  SelectedIon
 TODO. More...
struct  Activation
 The type and energy level used for activation. More...
struct  Precursor
 The method of precursor ion selection and activation. More...
struct  Product
 product ion information More...
struct  ScanWindow
 TODO. 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  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  MZIntensityPair
 The data point type of a mass spectrum. More...
struct  TimeIntensityPair
 The data point type of a chromatogram. More...
struct  SpectrumIdentity
 Identifying information for a spectrum. More...
struct  ChromatogramIdentity
 Identifying information for a chromatogram. More...
struct  Spectrum
 The structure that captures the generation of a peak list (including the underlying acquisitions) More...
struct  Chromatogram
 A single chromatogram. More...
class  IndexList
class  SpectrumList
 Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...
struct  SpectrumListSimple
 Simple writeable in-memory implementation of SpectrumList. More...
class  ChromatogramList
 Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...
struct  ChromatogramListSimple
 Simple writeable in-memory implementation of ChromatogramList. More...
struct  Run
 A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument. 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
class  RAMPAdapter
 adapter to provide RAMP-friendly access to MSData library More...
class  Reader
 interface for file readers More...
class  ReaderFail
class  ReaderList
 Reader container (composite pattern). More...
class  Serializer_MGF
 MSData <-> MGF stream serialization. More...
class  Serializer_MSn
 MSData <-> MSn stream serialization. More...
class  Serializer_mz5
 MSData <-> MZ5 file serialization. More...
class  Serializer_mzML
 MSData <-> mzML stream serialization. More...
class  Serializer_mzXML
 MSData <-> mzXML stream serialization. More...
class  SHA1OutputObserver
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_BTDX
 SpectrumList backed by a Bruker BioTools DataExchange XML file. More...
class  SpectrumList_MGF
 implementation of SpectrumList, backed by an MGF file More...
struct  MSnHeader
class  SpectrumList_MSn
 implementation of SpectrumList, backed by an MGF file More...
class  SpectrumList_mz5
 implementation of SpectrumList, backed by an mz5 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  SpectrumListWrapper
 Inheritable pass-through implementation for wrapping a SpectrumList. More...
class  TextWriter
struct  Version
class  Reader_ABI
class  Reader_ABI_T2D
class  Reader_Agilent
class  Reader_Bruker
class  ExtendedReaderList
 default ReaderList, extended to include vendor readers More...
class  Reader_Thermo
class  Reader_Waters

Typedefs

typedef boost::shared_ptr
< Index_mzML
Index_mzML_Ptr
typedef boost::shared_ptr
< SourceFile
SourceFilePtr
 Description of the source file, including location and type.
typedef boost::shared_ptr< SampleSamplePtr
typedef boost::shared_ptr
< Software
SoftwarePtr
typedef boost::shared_ptr
< ScanSettings
ScanSettingsPtr
typedef boost::shared_ptr
< InstrumentConfiguration
InstrumentConfigurationPtr
typedef boost::shared_ptr
< ProcessingMethod
ProcessingMethodPtr
typedef boost::shared_ptr
< DataProcessing
DataProcessingPtr
typedef boost::shared_ptr
< BinaryDataArray
BinaryDataArrayPtr
typedef boost::shared_ptr
< Spectrum
SpectrumPtr
typedef boost::shared_ptr
< Chromatogram
ChromatogramPtr
typedef boost::shared_ptr
< SpectrumList
SpectrumListPtr
typedef boost::shared_ptr
< SpectrumListSimple
SpectrumListSimplePtr
typedef boost::shared_ptr
< ChromatogramList
ChromatogramListPtr
typedef boost::shared_ptr
< ChromatogramListSimple
ChromatogramListSimplePtr
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
PWIZ_API_DECL void calculateSHA1Checksums (const MSData &msd)
 Iterate and calculate SHA-1 for all source files.
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
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
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 size_t IDENTITY_INDEX_NONE = (size_t)-1

Typedef Documentation

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

Definition at line 61 of file Index_mzML.hpp.

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

Description of the source file, including location and type.

Definition at line 74 of file MSData.hpp.

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

Definition at line 116 of file MSData.hpp.

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

Definition at line 196 of file MSData.hpp.

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

Definition at line 223 of file MSData.hpp.

Definition at line 248 of file MSData.hpp.

Definition at line 267 of file MSData.hpp.

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

Definition at line 286 of file MSData.hpp.

Definition at line 415 of file MSData.hpp.

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

Definition at line 564 of file MSData.hpp.

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

Definition at line 615 of file MSData.hpp.

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

Definition at line 705 of file MSData.hpp.

Definition at line 725 of file MSData.hpp.

Definition at line 779 of file MSData.hpp.

Definition at line 799 of file MSData.hpp.

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

Definition at line 902 of file MSData.hpp.

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

Definition at line 112 of file Reader.hpp.


Enumeration Type Documentation

Enumerator:
ComponentType_Unknown 
ComponentType_Source 
ComponentType_Analyzer 
ComponentType_Detector 

Definition at line 119 of file MSData.hpp.

Enumerator:
DetailLevel_InstantMetadata 
DetailLevel_FastMetadata 
DetailLevel_FullMetadata 
DetailLevel_FullData 

Definition at line 621 of file MSData.hpp.

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

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const BinaryDataEncoder::Config &  config 
)
PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const pwiz::data::Diff< MSData, DiffConfig > &  diff 
)
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 void pwiz::msdata::calculateSourceFileSHA1 ( SourceFile &  sourceFile)

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

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

Iterate and calculate SHA-1 for all source files.

PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
MSDataFile::Format  format 
)
PWIZ_API_DECL std::ostream& pwiz::msdata::operator<< ( std::ostream &  os,
const MSDataFile::WriteConfig &  config 
)
PWIZ_API_DECL ReaderList pwiz::msdata::operator+ ( const ReaderPtr &  lhs,
const ReaderPtr &  rhs 
)

returns a list containing the lhs and rhs as readers

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().

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

Variable Documentation

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

Definition at line 465 of file MSData.hpp.