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struct | Activation |
| The type and energy level used for activation. More...
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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...
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class | BinaryDataEncoder |
| binary-to-text encoding More...
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struct | Chromatogram |
| A single chromatogram. More...
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struct | ChromatogramIdentity |
| Identifying information for a chromatogram. More...
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class | ChromatogramList |
| Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...
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class | ChromatogramList_mzML |
| implementation of ChromatogramList, backed by an mzML file More...
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class | ChromatogramListBase |
| common functionality for base ChromatogramList implementations More...
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struct | ChromatogramListSimple |
| Simple writeable in-memory implementation of ChromatogramList. More...
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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...
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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...
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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...
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struct | DataProcessing |
| Description of the way in which a particular software was used. More...
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class | DefaultReaderList |
| default Reader list More...
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struct | DiffConfig |
| configuration struct for diffing MSData types More...
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class | ExtendedReaderList |
| default ReaderList, extended to include vendor readers More...
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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...
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struct | FileDescription |
| Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here. More...
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struct | Index_mzML |
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class | IndexList |
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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...
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struct | IsolationWindow |
| This element captures the isolation (or 'selection') window configured to isolate one or more precursors. More...
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class | LegacyAdapter_Instrument |
| interface for legacy access to Instrument More...
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class | LegacyAdapter_Software |
| interface for legacy access to Software More...
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class | MemoryMRUCache |
| an MRU cache for SpectrumPtrs or ChromatogramPtrs More...
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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...
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struct | MSDataFile |
| MSData object plus file I/O. More...
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struct | MSDataMerger |
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struct | MSnHeader |
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struct | MZIntensityPair |
| The data point type of a mass spectrum. More...
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struct | Precursor |
| The method of precursor ion selection and activation. More...
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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...
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struct | Product |
| product ion information More...
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class | Reader |
| interface for file readers More...
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class | Reader_ABI |
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class | Reader_ABI_T2D |
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class | Reader_Agilent |
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class | Reader_Bruker |
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class | Reader_BTDX |
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class | Reader_MGF |
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class | Reader_MSn |
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class | Reader_mz5 |
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class | Reader_mzML |
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class | Reader_mzXML |
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class | Reader_Shimadzu |
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class | Reader_Thermo |
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class | Reader_UIMF |
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class | Reader_Waters |
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class | ReaderFail |
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class | ReaderList |
| Reader container (composite pattern). More...
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struct | Run |
| A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument. More...
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struct | Sample |
| Expansible description of the sample used to generate the dataset, named in sampleName. More...
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struct | Scan |
| Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile. More...
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struct | ScanList |
| List and descriptions of scans. More...
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struct | ScanSettings |
| Description of the acquisition settings of the instrument prior to the start of the run. More...
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struct | ScanWindow |
| TODO. More...
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struct | SelectedIon |
| TODO. More...
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class | Serializer_MGF |
| MSData <-> MGF stream serialization. More...
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class | Serializer_MSn |
| MSData <-> MSn stream serialization. More...
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class | Serializer_mzML |
| MSData <-> mzML stream serialization. More...
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class | Serializer_mzXML |
| MSData <-> mzXML stream serialization. More...
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class | SHA1OutputObserver |
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struct | Software |
| A piece of software. More...
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struct | SourceFile |
| Description of the source file, including location and type. More...
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struct | Spectrum |
| The structure that captures the generation of a peak list (including the underlying acquisitions) More...
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struct | SpectrumIdentity |
| Identifying information for a spectrum. More...
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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...
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struct | SpectrumIdentityFromXML |
| Identifying information for a spectrum subclassed to add private information for faster file IO in mzML and mzXML. More...
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struct | SpectrumInfo |
| simple structure for holding Spectrum info More...
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class | SpectrumIterator |
| SpectrumIterator provides convenient iteration through a set of scans in a SpectrumList. More...
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class | SpectrumList |
| Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML). More...
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class | SpectrumList_BTDX |
| SpectrumList backed by a Bruker BioTools DataExchange XML file. More...
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class | SpectrumList_MGF |
| implementation of SpectrumList, backed by an MGF file More...
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class | SpectrumList_MSn |
| implementation of SpectrumList, backed by an MGF file More...
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class | SpectrumList_mzML |
| implementation of SpectrumList, backed by an mzML file More...
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class | SpectrumList_mzXML |
| implementation of SpectrumList, backed by an mzXML file More...
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class | SpectrumListBase |
| common functionality for base SpectrumList implementations More...
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class | SpectrumListCache |
| adds a level of flexible MRU caching to a SpectrumList processor chain More...
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struct | SpectrumListSimple |
| Simple writeable in-memory implementation of SpectrumList. More...
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class | SpectrumListWrapper |
| Inheritable pass-through implementation for wrapping a SpectrumList. More...
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class | SpectrumWorkerThreads |
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struct | Target |
| TODO. More...
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class | TextWriter |
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struct | TimeIntensityPair |
| The data point type of a chromatogram. More...
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struct | Version |
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PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const BinaryDataEncoder::Config &config) |
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PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const pwiz::data::Diff< MSData, DiffConfig > &diff) |
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PWIZ_API_DECL std::vector< CV > | defaultCVList () |
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PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const MZIntensityPair &mzi) |
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PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const TimeIntensityPair &ti) |
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PWIZ_API_DECL void | calculateSourceFileSHA1 (SourceFile &sourceFile) |
| calculates and adds a CV term for the SHA1 checksum of a source file element More...
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PWIZ_API_DECL void | calculateSHA1Checksums (const MSData &msd) |
| Iterate and calculate SHA-1 for all source files. More...
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PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, MSDataFile::Format format) |
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PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const MSDataFile::WriteConfig &config) |
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PWIZ_API_DECL ReaderList | operator+ (const ReaderPtr &lhs, const ReaderPtr &rhs) |
| returns a list containing the lhs and rhs as readers More...
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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...
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PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const Serializer_mzML::Config &config) |
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PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const Serializer_mzXML::Config &config) |
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