ProteoWizard
|
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< Sample > | SamplePtr |
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< MSData > | MSDataPtr |
typedef boost::shared_ptr< Reader > | ReaderPtr |
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< CV > | defaultCVList () |
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 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.
typedef boost::shared_ptr<InstrumentConfiguration> pwiz::msdata::InstrumentConfigurationPtr |
Definition at line 248 of file MSData.hpp.
typedef boost::shared_ptr<ProcessingMethod> pwiz::msdata::ProcessingMethodPtr |
Definition at line 267 of file MSData.hpp.
typedef boost::shared_ptr<DataProcessing> pwiz::msdata::DataProcessingPtr |
Definition at line 286 of file MSData.hpp.
typedef boost::shared_ptr<BinaryDataArray> pwiz::msdata::BinaryDataArrayPtr |
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.
typedef boost::shared_ptr<SpectrumListSimple> pwiz::msdata::SpectrumListSimplePtr |
Definition at line 725 of file MSData.hpp.
typedef boost::shared_ptr<ChromatogramList> pwiz::msdata::ChromatogramListPtr |
Definition at line 779 of file MSData.hpp.
typedef boost::shared_ptr<ChromatogramListSimple> pwiz::msdata::ChromatogramListSimplePtr |
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.
ComponentType_Unknown | |
ComponentType_Source | |
ComponentType_Analyzer | |
ComponentType_Detector |
Definition at line 119 of file MSData.hpp.
DetailLevel_InstantMetadata | |
DetailLevel_FastMetadata | |
DetailLevel_FullMetadata | |
DetailLevel_FullData |
Definition at line 621 of file MSData.hpp.
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.
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 | ||
) |
const size_t pwiz::msdata::IDENTITY_INDEX_NONE = (size_t)-1 |
Definition at line 465 of file MSData.hpp.