  pwiz::data::pepxml::AlternativeProtein | |
| pwiz::data::pepxml::AminoAcidModification | |
| pwiz::eharmony::AMTContainer | |
 pwiz::eharmony::AMTDatabase | |
  pwiz::eharmony::IslandizedDatabase | |
| pwiz::identdata::AnalysisCollection | Implementation of AnalysisCollectionType from the mzIdentML schema |
| pwiz::identdata::AnalysisData | Implementation of AnalysisDataType from the mzIdentML schema |
| pwiz::identdata::AnalysisProtocolCollection | Implementation of AnalysisProtocolCollectionType from the mzIdentML schema |
| pwiz::data::pepxml::AnalysisResult | |
| pwiz::identdata::AnalysisSampleCollection | Implementation of AnalysisSampleCollectionType from mzIdentML schema |
| pwiz::data::pepxml::AnalysisSummary | |
| pwiz::data::pepxml::AnalysisTimestamp | Reference for analysis applied to current run (time corresponds with analysis_summary/, id corresponds with analysis_result/) |
| pwiz::analysis::analyzer_strings< analyzer_type > | This auxilliary class should be specialized for MSDataAnalyzers whose instantiation is controlled by user-supplied strings (via command line, config file, etc.) |
| pwiz::analysis::analyzer_strings< MetadataReporter > | |
| pwiz::analysis::analyzer_strings< Pseudo2DGel > | |
| pwiz::analysis::analyzer_strings< RegionSIC > | |
| pwiz::analysis::analyzer_strings< RegionSlice > | |
| pwiz::analysis::analyzer_strings< RegionTIC > | |
| pwiz::analysis::analyzer_strings< RunSummary > | |
| pwiz::analysis::analyzer_strings< SpectrumBinaryData > | |
| pwiz::analysis::analyzer_strings< SpectrumTable > | |
| pwiz::minimxml::SAXParser::Handler::Attributes::attribute | |
| pwiz::minimxml::SAXParser::Handler::Attributes | |
| pwiz::minimxml::XMLWriter::Attributes | Vector of name/value pairs to be written as XML attributes |
| auto_vector< T >::auto_lvalue | |
| auto_vector< T > | |
| pwiz::data::BaseDiffConfig | |
| pwiz::identdata::DiffConfig | |
| pwiz::msdata::DiffConfig | Configuration struct for diffing MSData types |
| pwiz::proteome::DiffConfig | Configuration struct for diffs |
| pwiz::tradata::DiffConfig | Configuration struct for diffs |
| pwiz::minimxml::basic_charcounter< Ch > | |
| pwiz::Bin< T > | |
| pwiz::msdata::BinaryDataEncoder | Binary-to-text encoding |
| pwiz::msdata::mz5::BinaryDataMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#binaryDataArray but without raw data |
| pwiz::data::CalibrationParameters | |
| pwiz::calibration::Calibrator | Calibrates using EM algorithm using peptide mass database |
| pwiz::calibration::CalibratorLog | |
| pwiz::calibration::CalibratorTrial | |
| pwiz::minimxml::basic_charcounter< Ch >::category | |
| pwiz::util::CharIndexedVector< T > | Wrapper for boost::array that is indexable by character; supports indexes 0-127 |
| pwiz::util::CharIndexedVectorConstIterator< T > | Const_iterator for CharIndexedVector |
| pwiz::util::CharIndexedVectorIterator< T > | Iterator for CharIndexedVector |
| pwiz::analysis::ChromatogramDataFilter | |
| pwiz::msdata::ChromatogramIdentity | Identifying information for a chromatogram |
| pwiz::msdata::Chromatogram | A single chromatogram |
| pwiz::msdata::ChromatogramList | Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML) |
| pwiz::analysis::ChromatogramListWrapper | Inheritable pass-through implementation for wrapping a ChromatogramList |
| pwiz::analysis::ChromatogramList_SavitzkyGolaySmoother | ChromatogramList implementation to return native centroided chromatogram data |
| pwiz::msdata::ChromatogramListBase | Common functionality for base ChromatogramList implementations |
| MyBase | |
| pwiz::msdata::ChromatogramList_mz5 | Implementation of ChromatogramList, backed by an mz5 file |
| pwiz::msdata::ChromatogramList_mzML | Implementation of ChromatogramList, backed by an mzML file |
| pwiz::msdata::detail::ChromatogramList_ABI | |
| pwiz::msdata::detail::ChromatogramList_Agilent | |
| pwiz::msdata::detail::ChromatogramList_Bruker | |
| pwiz::msdata::detail::ChromatogramList_Thermo | |
| pwiz::msdata::detail::ChromatogramList_Waters | |
| pwiz::msdata::ChromatogramListSimple | Simple writeable in-memory implementation of ChromatogramList |
| pwiz::msdata::mz5::ChromatogramMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#chromatogram but without binary data element |
| pwiz::util::ClickwrapPrompter | Barrier to force end users to agree/disagree to a prompt before continuing |
| pwiz::util::Image::Color | Struct for holding rgb values (in [0,255]) |
| pwiz::util::COMInitializer | Singleton used to initialize and uninitialize COM once per thread |
| 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 |
| pwiz::msdata::mz5::ComponentListMZ5 | List of components |
| pwiz::msdata::mz5::ComponentMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#source http://www.peptideatlas.org/tmp/mzML1.1.0.html#analyzer http://www.peptideatlas.org/tmp/mzML1.1.0.html#detector |
| pwiz::msdata::mz5::ComponentsMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#componentList |
| pwiz::analysis::Pseudo2DGel::Config | Holds the configuration for an instance of Pseudo2DGel |
| pwiz::analysis::SpectrumBinaryData::Config | |
| pwiz::msdata::BinaryDataEncoder::Config | Encoding/decoding configuration |
| pwiz::analysis::FeatureDetectorPeakel::Config | Convenience construction |
| pwiz::analysis::NoiseCalculator_2Pass::Config | |
| pwiz::analysis::PeakelGrower_Proximity::Config | |
| pwiz::analysis::PeakelPicker_Basic::Config | |
| pwiz::analysis::PeakFamilyDetectorFT::Config | |
| pwiz::analysis::PeakFinder_SNR::Config | |
| pwiz::analysis::PeakFitter_Parabola::Config | |
| pwiz::msdata::Reader::Config | Reader configuration |
| pwiz::msdata::Serializer_mzML::Config | Serializer_mzML configuration |
| pwiz::analysis::MS2Deisotoper::Config | PrecursorMassFilter's parameters |
| pwiz::msdata::Serializer_mzXML::Config | Serializer_mzXML configuration |
| pwiz::msdata::SpectrumIterator::Config | SpectrumIterator configuration – note that constructors allow automatic conversion from IntegerSet or Sieve to Config |
| pwiz::analysis::MS2NoiseFilter::Config | MS2NoiseFilter's parameters |
| pwiz::analysis::PrecursorMassFilter::Config | PrecursorMassFilter's parameters |
| pwiz::analysis::PrecursorRecalculatorDefault::Config | |
| pwiz::proteome::Digestion::Config | Sets constraints for valid peptides produced by iterating the digestion |
| pwiz::proteome::Reader_FASTA::Config | Reader_FASTA configuration |
| pwiz::proteome::Serializer_FASTA::Config | Serializer_FASTA configuration |
| pwiz::chemistry::IsotopeEnvelopeEstimator::Config | |
| pwiz::minimxml::XMLWriter::Config | Initial configuration of the XMLWriter |
| pwiz::frequency::FrequencyEstimatorPhysicalModel::Config | |
| pwiz::frequency::PeakDetectorMatchedFilter::Config | Structure for holding configuration |
| pwiz::identdata::Reader::Config | HACK: provide an option to read only file-level metadata; once we have an enumerable ResultList implementation this will be deprecated |
| Reader1::Config | |
| Reader2::Config | |
| pwiz::identdata::Serializer_mzIdentML::Config | Serializer_mzIdentML configuration |
| pwiz::identdata::Serializer_pepXML::Config | Serializer_pepXML configuration |
| pwiz::identdata::Serializer_protXML::Config | Serializer_protXML configuration |
| pwiz::identdata::Serializer_Text::Config | < Controls the format of the text file |
| pwiz::analysis::MSDataCache::Config | MSDataCache configuration |
| pwiz::analysis::PepxmlRecordReader::Config | |
| pwiz::calibration::CalibratorTrial::Configuration | |
| pwiz::msdata::mz5::Configuration_mz5 | Configuration class for mz5 im- and export |
| pwiz::msdata::mz5::Connection_mz5 | This class is used for reading and writing information to a mz5 file |
| pwiz::proteome::Digestion::const_iterator | Forward-only, read-only iteration to enumerate peptides |
| pwiz::msdata::mz5::ContVocabMZ5Data | |
| pwiz::msdata::mz5::ContVocabMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#cv |
| pwiz::math::MatchedFilter::Correlation< Y > | |
| CSHA1 | |
| CustomPair | |
| pwiz::cv::CV | Information about an ontology or CV source and a short 'lookup' tag to refer to |
| pwiz::identdata::CVMap | |
| pwiz::identdata::CVIDMatchCVMap | |
| pwiz::identdata::RegexCVMap | |
| pwiz::identdata::StringMatchCVMap | |
| pwiz::data::CVParam | Tag-value pair, where the tag comes from the controlled vocabulary |
| pwiz::identdata::ContactRole | Implementation of ContactRoleType from the mzIdentML schema |
| pwiz::identdata::IonType | Implementation of IonTypeType from the mzIdentML schema |
| pwiz::data::CVParamIs | Functor for finding CVParam with specified exact CVID in a collection of CVParams: |
| pwiz::data::CVParamIsChildOf | Functor for finding children of a specified CVID in a collection of CVParams: |
| pwiz::msdata::mz5::CVParamMZ5Data | |
| pwiz::msdata::mz5::CVParamMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#cvParam |
| pwiz::msdata::mz5::CVRefMZ5Data | |
| pwiz::msdata::mz5::CVRefMZ5 | This class will be referenced from CVParamMZ5 and UserParamMZ5 to reduce storage size |
| pwiz::cv::CVTermInfo | Structure for holding CV term info |
| pwiz::data::CVTranslator | Translates text to CV terms |
| pwiz::eharmony::DatabaseQuery | |
| pwiz::identdata::DatabaseTranslation | Implementation of DatabaseTranslationType from the mzIdentML schema |
| pwiz::identdata::DataCollection | Implementation of DataCollectionType from the mzIdentML schema |
| pwiz::eharmony::DataFetcherContainer | |
| pwiz::data::pepxml::DataFilter | |
| pwiz::analysis::MSDataAnalyzer::DataInfo | Information about the data to be analyzed |
| pwiz::msdata::DataProcessing | Description of the way in which a particular software was used |
| pwiz::msdata::mz5::DataProcessingMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#dataProcessing |
| pwiz::data::pepxml::DatasetDerivation | Source and filtering criteria used to generate dataset |
| Datum | |
| pwiz::identdata::dbsequence_p | |
| DeletePtr< T > | |
| pwiz::identdata::DelimWriter | |
| pwiz::data::Diff< object_type, config_type, object_result_type > | Calculate diffs of objects in a ProteoWizard data model hierarchy |
| DigestedPeptideLessThan | |
| pwiz::proteome::Digestion | Enumerates the peptides from proteolytic digestion of a polypeptide or protein; |
| pwiz::eharmony::DistanceAttribute | |
| pwiz::eharmony::EditDistance | |
| pwiz::eharmony::HammingDistance | |
| pwiz::eharmony::NumberOfMS2IDs | |
| pwiz::eharmony::RandomDistance | |
| pwiz::eharmony::RTDiffDistribution | |
| pwiz::eharmony::WeightedHammingDistance | |
| pwiz::data::pepxml::DistributionPoint | |
| pwiz::chemistry::detail::Element | |
| pwiz::calibration::MassDatabase::Entry | |
| pwiz::data::Index::Entry | Generic type identifying an indexed item by string id, ordinal index, and stream offset |
| pwiz::data::pepxml::EnzymaticSearchConstraint | |
| EnzymePtr_missedCleavages | |
| EnzymePtr_specificity | |
| pwiz::identdata::Enzymes | Implementation of EnzymesType from the mzIdentML schema |
| pwiz::calibration::ErrorEstimator | |
| pwiz::frequency::ParametrizedFunction< value_type >::ErrorFunction | |
| pwiz::data::pepxml::ErrorPoint | |
| pwiz::eharmony::Exporter | |
| pwiz::analysis::ExtraZeroSamplesFilter | Removes (most) zero samples in signal profiles, except those flanking nonzero samples simply looks for runs of 0 values, removes all but start and end of run |
| pwiz::data::peakdata::Feature | |
| pwiz::eharmony::Feature2PeptideMatcher | |
| pwiz::eharmony::Feature_dataFetcher | |
| pwiz::analysis::FeatureDetector | |
| pwiz::analysis::FeatureDetectorPeakel | FeatureDetectorPeakel implements a 'template method', delegating to 'strategies' encapsulated by the following interfaces: PeakExtractor PeakelGrower PeakelPicker |
| pwiz::analysis::FeatureDetectorSimple | FeatureDetectorSimple detects 'rectangular' features, ie number of peaks in isotope envelope is the same for each scan included in the feature |
| pwiz::data::peakdata::FeatureFile | |
| pwiz::analysis::FeatureModeler | Interface for fitting and scoring Feature data to a model |
| pwiz::analysis::FeatureModeler_Gaussian | Gaussian implementation |
| pwiz::eharmony::FeatureSequenced | |
| Fifth | |
| pwiz::msdata::FileDescription | Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here |
| pwiz::msdata::mz5::FileInformationMZ5Data | General mz5 file information |
| pwiz::msdata::mz5::FileInformationMZ5 | |
| pwiz::identdata::Filter | Implementation of FilterType from the mzIdentML schema |
| First | |
| pwiz::peptideid::FlatRecordBuilder | |
| pwiz::peptideid::MSInspectRecordBuilder | |
| pwiz::chemistry::Formula | Class to represent a chemical formula |
| pwiz::identdata::FragmentArray | Implementation of FragmentArrayType from the mzIdentML schema |
| pwiz::proteome::Fragmentation | Fragment ion masses for a peptide |
| pwiz::data::FrequencyData | Class for binary storage of complex frequency data |
| pwiz::frequency::FrequencyEstimator | Interface for frequency estimator modules |
| pwiz::frequency::FrequencyEstimatorPhysicalModel | Physical model implementation of the FrequencyEstimator interface |
| pwiz::frequency::FrequencyEstimatorSimple | Simple implementation of the FrequencyEstimator interface |
| pwiz::eharmony::IslandizedDatabase::Gaussian | |
| glob_t | |
| Goober | |
| pwiz::minimxml::SAXParser::Handler | SAX event handler interface |
| AnotherRootHandler | |
| FifthHandler | |
| FirstHandler | |
| NestedHandler | |
| PrintEventHandler | |
| pwiz::data::peakdata::HandlerFeature | |
| pwiz::data::peakdata::HandlerPeak | |
| pwiz::data::peakdata::HandlerPeakel | |
| RootHandler | |
| SecondHandler | |
| pwiz::data::diff_impl::HasID< object_type > | |
| pwiz::identdata::id_p< T > | |
| pwiz::identdata::Identifiable | Parent class representing extensions of the IdentifiableType from the mzIdentML schema |
| pwiz::identdata::AnalysisSoftware | Implementation of AnalysisSoftwareType from the mzIdentML schema |
| pwiz::identdata::BibliographicReference | Implementation for the BibliographicReferenceType tag in the mzIdentML schema |
| pwiz::identdata::Enzyme | Implementation of EnzymeType from the mzIdentML schema |
| pwiz::identdata::IdentData | Implementation of the MzIdentMLType from the mzIdentML schema |
| pwiz::identdata::IdentDataFile | IdentData object plus file I/O |
| pwiz::identdata::ProteinDetection | Implementation of ProteinDetectionType from the mzIdentML schema |
| pwiz::identdata::ProteinDetectionProtocol | Implementation of ProteinDetectionProtocolType from the mzIdentML schema |
| pwiz::identdata::Provider | Implementation of ProviderType from the mzIdentML schema |
| pwiz::identdata::SpectraData | Implementation of SpectraDataType from the mzIdentML schema |
| pwiz::identdata::SpectrumIdentification | Implementation of SpectrumIdentificationType from the mzIdentML schema |
| pwiz::identdata::SpectrumIdentificationList | Implementation of SpectrumIdentificationListType from the mzIdentML schema |
| pwiz::identdata::SpectrumIdentificationProtocol | Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema |
| pwiz::util::Image | Wrapper class for using 'gd' graphics library |
| pwiz::data::Index | Generic interface for creating and using an index on a stream of serialized objects |
| pwiz::data::BinaryIndexStream | Index implementation in a stream (intended for fstreams but any iostream works); find(string id) is O(logN); find(ordinal index) is O(1); memory footprint is negligible |
| pwiz::data::MemoryIndex | Index implementation in memory; find(string id) is O(logN); find(ordinal index) is O(1); memory footprint is basically (number of entries * 2) |
| pwiz::msdata::Index_mzML | |
| pwiz::msdata::SpectrumList_mzXML::index_not_found | Exception thrown if create(*,*,true) is called and the mzXML index cannot be found |
| pwiz::msdata::IndexList | |
| pwiz::proteome::IndexList | |
| pwiz::identdata::Inputs | Implementation of the InputsType from the mzIdentML schema |
| pwiz::msdata::mz5::InstrumentConfigurationMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#instrumentConfiguration |
| InstrumentStruct | |
| pwiz::util::IntegerSet | Virtual container of integers, accessible via an iterator interface, stored as union of intervals |
| pwiz::util::IntegerSet::Interval | Single closed interval of integers |
| pwiz::proteome::IPIFASTADatabase | Class for accessing data in ipi.*.fasta files |
| IsFS | |
| IsInt | |
| pwiz::eharmony::IslandizedDatabase::Island | |
| pwiz::IsObject< T > | |
| pwiz::chemistry::detail::Isotope | |
| pwiz::chemistry::IsotopeCalculator | |
| pwiz::chemistry::IsotopeEnvelopeEstimator | Class used for calculating a theoretical isotope envelope for a given mass, based on an estimate of the elemental composition for that mass |
| pwiz::chemistry::IsotopeTable | Class representing a table of isotope distributions for collections of multiple atoms of a single element; the table is computed on instantiation, based on the element's mass distribution, a maximum atom count, and abundance cutoff value |
| IsSQ | |
| pwiz::util::IterationListener | Interface to be implemented by clients who want progress callbacks |
| BadListener | |
| CancelListener | |
| TestIterationListener | |
| TestIterationListener_WithCancel | |
| TestListener | |
| pwiz::util::IterationListenerRegistry | Handles registration of IterationListeners and broadcast of update messages |
| pwiz::peptideid::PeptideID::Iterator | Iterator for |
| pwiz::util::IntegerSet::Iterator | Forward iterator providing readonly access to the virtual container |
| pwiz::peptideid::PeptideID::IteratorInternal | Interface for |
| pwiz::math::MatchedFilter::KernelTraits< Kernel > | |
| pwiz::math::MatchedFilter::KernelTraitsBase< Kernel > | |
| pwiz::math::MatchedFilter::KernelTraitsBase< Y(*)(X)> | |
| pwiz::eharmony::KeyLessThan | |
| pwiz::calibration::LeastSquaresCalibrator | |
| pwiz::msdata::LegacyAdapter_Instrument | Interface for legacy access to Instrument |
| pwiz::msdata::LegacyAdapter_Software | Interface for legacy access to Software |
| pwiz::math::LinearLeastSquares< LinearLeastSquaresType_LU > | |
| pwiz::math::LinearLeastSquares< LinearLeastSquaresType_QR > | |
| pwiz::math::LinearSolver< LinearSolverType_LU > | |
| pwiz::math::LinearSolver< LinearSolverType_QR > | |
| pwiz::peptideid::PeptideID::Location | |
| pwiz::peptideid::location_less | |
| LU | |
| pwiz::frequency::MagnitudeLorentzian | |
| pwiz::chemistry::MassAbundance | Struct for holding isotope information |
| pwiz::calibration::MassDatabase | |
| pwiz::calibration::MassSpread | |
| pwiz::identdata::MassTable | Implementation of MassTableType from the mzIdentML schema |
| pwiz::data::pepxml::Match | |
| pwiz::data::pepxml::MatchData | |
| pwiz::eharmony::Matcher | |
| pwiz::eharmony::Matrix | |
| pwiz::eharmony::NeighborJoiner | |
| pwiz::calibration::Calibrator::Measurement | Structure for holding frequency-charge pairs |
| pwiz::data::pepxml::MixtureModel | |
| pwiz::data::pepxml::ModAminoAcidMass | |
| pwiz::proteome::Modification | Post-translational modification (PTM) modification formula or masses must be provided at instantiation |
| pwiz::data::pepxml::ModificationInfo | |
| pwiz::proteome::ModificationList | List of modifications on a single amino acid |
| pwiz::eharmony::ModificationStateEntry | |
| pwiz::util::mru_list< Item, KeyExtractor > | |
| pwiz::util::mru_list< PtrType, KeyExtractor > | |
| pwiz::msdata::MemoryMRUCache< PtrType, KeyExtractor > | MRU cache for SpectrumPtrs or ChromatogramPtrs |
| 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) |
| MSDataWithSettableVersion | |
| pwiz::msdata::MSDataFile | MSData object plus file I/O |
| pwiz::msdata::MSDataMerger | |
| pwiz::analysis::MSDataAnalyzer | Interface for MSData analyzers |
| EvenRequester | |
| pwiz::analysis::MetadataReporter | Writes file-level metadata to a file |
| pwiz::analysis::MSDataAnalyzerContainer | Container of MSDataAnalyzer (composite pattern) |
| pwiz::analysis::MSDataCache | Simple memory cache for common MSData info |
| pwiz::analysis::Pseudo2DGel | Creates pseudo-2D-gel images from survey scan data |
| pwiz::analysis::RegionAnalyzer | Analyzes a rectangular region of m/z-time space |
| pwiz::analysis::RegionSIC | Writes data samples from a single rectangular region |
| pwiz::analysis::RegionSlice | Writes data samples from a single rectangular region |
| pwiz::analysis::RegionTIC | Writes data samples from a single rectangular region |
| pwiz::analysis::RunSummary | Writes table of spectrum metadata to a file |
| pwiz::analysis::SpectrumBinaryData | Writes table of spectrum metadata to a file |
| pwiz::analysis::SpectrumTable | Writes table of spectrum metadata to a file |
| SimpleAnalyzer | |
| pwiz::analysis::MSDataAnalyzerDriver | Event generator for MSDataAnalyzer |
| pwiz::eharmony::MSIAMTData | |
| pwiz::data::pepxml::MSMSPipelineAnalysis | |
| pwiz::data::pepxml::MSMSRunSummary | |
| pwiz::msdata::MSnHeader | |
| MyPred | |
| pwiz::msdata::MZIntensityPair | The data point type of a mass spectrum |
| mzrtEqual | |
| pwiz::analysis::MZRTField< T > | MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT |
| pwiz::chemistry::MZTolerance | Struct for expressing m/z tolerance in either amu or ppm |
| pwiz::peptideid::nativeID_less | |
| pwiz::analysis::PeakFamilyDetectorFT::NoDataException | FT-specific exception |
| pwiz::analysis::Noise | |
| pwiz::analysis::NoiseCalculator | |
| pwiz::analysis::NoiseCalculator_2Pass | |
| pwiz::data::OBO | Represents a selectively parsed OBO file |
| pwiz::eharmony::Observation | |
| pwiz::util::once_flag_proxy | |
| OneMinusAbs | |
| pwiz::math::OrderedPair | |
| pwiz::math::OrderedPairContainerRef | Wrapper class for accessing contiguous data as a container of OrderedPairs; note that it does not own the underlying data |
| pwiz::identdata::organization_p | |
| pwiz::minimxml::XMLWriter::OutputObserver | Interface to allow outside observation of data sent to output stream |
| pwiz::msdata::SHA1OutputObserver | |
| TestOutputObserver | |
| pwiz::calibration::MassSpread::Pair | |
| pwiz::math::Parabola | |
| pwiz::data::ParamContainer | The base class for elements that may contain cvParams, userParams, or paramGroup references |
| pwiz::data::ParamGroup | A collection of CVParam and UserParam elements that can be referenced from elsewhere in this mzML document by using the 'paramGroupRef' element in that location to reference the 'id' attribute value of this element |
| pwiz::identdata::AmbiguousResidue | Implementation of AmbiguousResidueType from the mzIdentML schema |
| pwiz::identdata::IdentifiableParamContainer | Parent class of all Identifiable objects that have ParamGroups |
| pwiz::identdata::Contact | Implementation of ContactType from mzIdentML |
| pwiz::identdata::Organization | Implementation of AbstractOrganizationType from the mzIdentML schema |
| pwiz::identdata::Person | Implementation of PersonType from the mzIdentML schema |
| pwiz::identdata::DBSequence | Implementation of DBSequenceType from the mzIdentML schema |
| pwiz::identdata::Measure | Implementation of MeasureType from the mzIdentML schema |
| pwiz::identdata::Peptide | Implementation of PeptideType from the mzIdentML schema |
| pwiz::identdata::PeptideEvidence | Implementation of PeptideEvidenceType from the mzIdentML schema |
| pwiz::identdata::ProteinAmbiguityGroup | Implementation of ProteinAmbiguityGroupType from the mzIdentML schema |
| pwiz::identdata::ProteinDetectionHypothesis | Implementation of ProteinDetectionHypothesisType from the mzIdentML schema |
| pwiz::identdata::ProteinDetectionList | Implementation of ProteinDetectionListType from the mzIdentML schema |
| pwiz::identdata::Sample | Implementation of the SampleType from the mzIdentML schema |
| pwiz::identdata::SearchDatabase | Implementation of SearchDatabaseType from the mzIdentML schema |
| pwiz::identdata::SourceFile | Implementation of SourceFileType from the mzIdentML schema |
| pwiz::identdata::SpectrumIdentificationItem | Implementation of SpectrumIdentificationItemType from the mzIdentML schema |
| pwiz::identdata::SpectrumIdentificationResult | Implementation of SpectrumIdentificationResultType from the mzIdentML schema |
| pwiz::identdata::TranslationTable | Implementation of TranslationTableType from the mzIdentML schema |
| pwiz::identdata::Modification | Implementation of ModificationType from the mzIdentML schema |
| pwiz::identdata::SearchModification | Implementation of SearchModificationType from the mzIdentML schema |
| pwiz::msdata::Activation | The type and energy level used for activation |
| 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 |
| pwiz::msdata::Chromatogram | A single chromatogram |
| 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) |
| 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) |
| 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 |
| 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 |
| pwiz::msdata::IsolationWindow | This element captures the isolation (or 'selection') window configured to isolate one or more precursors |
| pwiz::msdata::Precursor | The method of precursor ion selection and activation |
| 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 |
| pwiz::msdata::Run | A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument |
| pwiz::msdata::Sample | Expansible description of the sample used to generate the dataset, named in sampleName |
| pwiz::msdata::Scan | Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile |
| pwiz::msdata::ScanList | List and descriptions of scans |
| pwiz::msdata::ScanWindow | TODO |
| pwiz::msdata::SelectedIon | TODO |
| pwiz::msdata::Software | A piece of software |
| pwiz::msdata::SourceFile | Description of the source file, including location and type |
| pwiz::msdata::Spectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
| pwiz::msdata::Target | TODO |
| pwiz::tradata::Compound | Chemical compound other than a peptide for which one or more transitions |
| pwiz::tradata::Configuration | Instrument configuration used in the validation or optimization of the transitions |
| pwiz::tradata::Contact | |
| pwiz::tradata::Evidence | Information about empirical mass spectrometer observations of the peptide |
| pwiz::tradata::Instrument | Instrument on which transitions are validated |
| pwiz::tradata::Interpretation | A possible interpration of the product ion for a transition |
| pwiz::tradata::Modification | A molecule modification specification |
| pwiz::tradata::Peptide | Peptide for which one or more transitions are intended to identify |
| pwiz::tradata::Precursor | Precursor (Q1) of the transition |
| pwiz::tradata::Prediction | Information about a prediction for a suitable transition using some software |
| pwiz::tradata::Product | Product (Q3) of the transition |
| pwiz::tradata::Protein | |
| pwiz::tradata::Publication | |
| pwiz::tradata::RetentionTime | |
| pwiz::tradata::Software | |
| pwiz::tradata::Target | A peptide or compound that is to be included or excluded from a target list of precursor m/z values |
| pwiz::tradata::TargetList | List of precursor m/z targets to include or exclude |
| pwiz::tradata::Transition | |
| pwiz::tradata::Validation | Information about the state of validation of a transition on a given instrument model |
| pwiz::data::peakdata::Software::Parameter | |
| pwiz::data::pepxml::Parameter | |
| pwiz::data::pepxml::SearchScore | |
| pwiz::frequency::ParameterEstimator | |
| pwiz::frequency::ParametrizedFunction< value_type > | |
| pwiz::frequency::ParametrizedFunction< double > | |
| ParametrizedCosine | |
| pwiz::frequency::ParametrizedFunction< std::complex< double > > | |
| pwiz::frequency::TruncatedLorentzian | |
| pwiz::msdata::mz5::ParamGroupMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#referenceableParamGroup |
| pwiz::msdata::mz5::ParamListMZ5Data | |
| pwiz::msdata::mz5::ParamListMZ5 | This class represents a pwiz::msdata::ParamContainer but only stores start and end indices for CVParams, UserParams and ParamGroups |
| pwiz::msdata::mz5::ParamListsMZ5 | This class is used as a generalized container for Targets, SelectedIons, Products and ScanWindows |
| pwiz::msaux::Path | |
| pwiz::data::peakdata::Peak | |
| pwiz::analysis::Peak | Some generic metadata about a peak detected in a signal |
| pwiz::data::peakdata::PeakData | |
| pwiz::analysis::PeakDetector | |
| pwiz::analysis::LocalMaximumPeakDetector | |
| pwiz::frequency::PeakDetector | Interface for finding peaks in frequency data |
| pwiz::frequency::PeakDetectorMatchedFilter | MatchedFilter implementation of the PeakDetector interface |
| pwiz::frequency::PeakDetectorNaive | Naive implementation of the PeakDetector interface |
| pwiz::data::peakdata::Peakel | Struct for an eluted peak (PEAK ELution) |
| pwiz::analysis::PeakelGrower | Interface for growing Peakels |
| pwiz::analysis::PeakelGrower_Proximity | Simple PeakelGrower implementation, based on proximity of Peaks |
| pwiz::analysis::PeakelPicker | Interface for picking Peakels and arranging into Features; note: Peakels are actually removed from the PeakelField |
| pwiz::analysis::PeakelPicker_Basic | Basic implementation |
| pwiz::analysis::PeakExtractor | Class for extracting Peak objects from an array of ordered pairs; in design pattern lingo, this is a "template method" delegating peak finding and peak fitting to "strategies" |
| pwiz::data::peakdata::PeakFamily | |
| pwiz::analysis::PeakFamilyDetector | Interface for peak family (isotope envelope) detection |
| pwiz::analysis::PeakFamilyDetectorFT | FT-specific implementation of PeakFamilyDetector |
| pwiz::analysis::PeakFinder | Interface for finding peaks in an array of ordered pairs |
| pwiz::analysis::PeakFinder_SNR | PeakFinder implementation based on signal-to-noise ratio |
| pwiz::analysis::PeakFitter | Interface for fitting peaks in an array of ordered pairs |
| pwiz::analysis::PeakFitter_Parabola | PeakFitter implementation based on fitting a parabola |
| pwiz::identdata::Pep2MzIdent | Translates data from a MinimumPepXML object into a IdentData object tree when a translation is known |
| pwiz::proteome::Peptide | Peptide or polypeptide (a sequence of amino acids) |
| pwiz::proteome::DigestedPeptide | Peptide subclass that contains extra metadata provided by digestion |
| pwiz::proteome::Protein | |
| pwiz::proteome::PeptideDatabase | |
| pwiz::proteome::PeptideDatabaseFormula | |
| pwiz::proteome::PeptideDatabaseRecord | |
| pwiz::eharmony::PeptideEntry | |
| pwiz::identdata::PeptideHypothesis | Implementation of PeptideHypothesisType from the mzIdentML schema |
| pwiz::peptideid::PeptideID | This is an interface for classes that allow access to data sources of identified peptides |
| pwiz::peptideid::PeptideID_flat | This class allows access to peptides listed in a flat tab delimited text file |
| pwiz::peptideid::PeptideID_pepXml | This class allows access to identified proteins in PeptideProphet files |
| pwiz::peptideid::PeptideIDMap | |
| pwiz::eharmony::PeptideID_dataFetcher | |
| pwiz::eharmony::PeptideMatcher | |
| pwiz::data::pepxml::PeptideProphetResult | |
| pwiz::data::pepxml::PeptideProphetSummary | |
| pwiz::analysis::PepxmlRecordReader | |
| pwiz::identdata::PepXMLSpecificity | |
| pwiz::identdata::person_p | |
| pwiz::util::Image::Point | Struct for holding pixel coordinates |
| PointsToSame | |
| pwiz::msdata::SpectrumInfo::PrecursorInfo | Structure for Precursor info |
| pwiz::analysis::PrecursorRecalculator::PrecursorInfo | |
| pwiz::analysis::SpectrumList_PrecursorRefine::PrecursorInfo | |
| pwiz::msdata::mz5::PrecursorListMZ5 | Variable length precursor list |
| pwiz::msdata::mz5::PrecursorMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#precursor |
| pwiz::analysis::PrecursorRecalculator | |
| pwiz::analysis::PrecursorRecalculatorDefault | |
| pwiz::analysis::ProteinList_DecoyGenerator::Predicate | Client-implemented generator predicate – called during construction of ProteinList_DecoyGenerator to create a decoy protein from a target protein |
| pwiz::analysis::ProteinList_DecoyGeneratorPredicate_Reversed | Creates a reversed copy of every target protein with the specified decoy string prefixed to the id |
| pwiz::analysis::ProteinList_DecoyGeneratorPredicate_Shuffled | Creates a randomly shuffled copy of every target protein with the specified decoy string prefixed to the id |
| pwiz::analysis::ProteinList_Filter::Predicate | Client-implemented filter predicate – called during construction of ProteinList_Filter to create the filtered list of proteins |
| pwiz::analysis::ProteinList_FilterPredicate_IdSet | |
| pwiz::analysis::ProteinList_FilterPredicate_IndexSet | |
| SelectedIndexPredicate | |
| pwiz::analysis::SpectrumList_Filter::Predicate | Client-implemented filter predicate – called during construction of SpectrumList_Filter to create the filtered list of spectra |
| EvenMS2Predicate | |
| EvenPredicate | |
| HasBinaryDataPredicate | |
| pwiz::analysis::SpectrumList_FilterPredicate_ActivationType | |
| pwiz::analysis::SpectrumList_FilterPredicate_AnalyzerType | |
| pwiz::analysis::SpectrumList_FilterPredicate_DefaultArrayLengthSet | |
| pwiz::analysis::SpectrumList_FilterPredicate_IndexSet | |
| pwiz::analysis::SpectrumList_FilterPredicate_MSLevelSet | |
| pwiz::analysis::SpectrumList_FilterPredicate_Polarity | |
| pwiz::analysis::SpectrumList_FilterPredicate_PrecursorMzSet | |
| pwiz::analysis::SpectrumList_FilterPredicate_ScanEventSet | |
| pwiz::analysis::SpectrumList_FilterPredicate_ScanNumberSet | |
| pwiz::analysis::SpectrumList_FilterPredicate_ScanTimeRange | |
| SelectedIndexPredicate | |
| pwiz::analysis::SpectrumList_Sorter::Predicate | Client-implemented sort predicate – called during construction of SpectrumList_Sorter to sort the underlying spectrum list |
| DefaultArrayLengthSorter | |
| MSLevelSorter | |
| pwiz::analysis::SpectrumList_SorterPredicate_ScanStartTime | |
| PrintAttribute | |
| pwiz::msdata::mz5::ProcessingMethodListMZ5 | Variable length processing method list |
| pwiz::msdata::mz5::ProcessingMethodMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#processingMethod |
| pwiz::msdata::Product | Product ion information |
| pwiz::math::MatchedFilter::ProductSpace< X, Y > | |
| pwiz::analysis::MSDataAnalyzerDriver::ProgressCallback | Progress callback interface |
| CancelProgressCallback | |
| SimpleProgressCallback | |
| pwiz::proteome::ProteinList | |
| pwiz::proteome::ProteinListSimple | |
 pwiz::proteome::ProteinListWrapper | Inheritable pass-through implementation for wrapping a ProteinList |
 FilterWrapper | |
| MyWrapper | |
| pwiz::analysis::ProteinList_DecoyGenerator | ProteinList decoy generator for creating decoy proteins on the fly |
| pwiz::analysis::ProteinList_Filter | ProteinList filter, for creating Protein sub-lists |
| pwiz::proteome::ProteinListCache | Adds a level of flexible MRU caching to a ProteinList processor chain |
| pwiz::analysis::ProteinListFactory | Factory for instantiating and wrapping ProteinLists |
| pwiz::proteome::ProteomeData | |
| pwiz::proteome::ProteomeDataFile | ProteomeData object plus file I/O |
| pwiz_RAMPAdapter | SWIG-friendly wrapper to provide RAMP-friendly access to MSData library |
| pwiz::data::pepxml::Q3RatioResult | |
| pwiz::msdata::RAMPAdapter | Adapter to provide RAMP-friendly access to MSData library |
| RAMPFILE | |
| pwiz::math::Random | |
| pwiz::util::random_access_compressed_ifstream | |
| RawMassDatum | |
| pwiz::identdata::Reader | Interface for file readers |
| pwiz::identdata::DelimReader | |
| pwiz::identdata::MascotReader | |
| pwiz::identdata::ReaderList | Reader container (composite pattern) |
| pwiz::identdata::DefaultReaderList | Default Reader list |
| pwiz::proteome::Reader | Interface for file readers |
| pwiz::proteome::Reader_FASTA | FASTA -> ProteomeData stream serialization |
| pwiz::proteome::ReaderList | Reader container (composite pattern) |
| pwiz::proteome::DefaultReaderList | Default Reader list |
| pwiz::tradata::DefaultReaderList | Default Reader list |
| pwiz::tradata::ReaderList | Reader container (composite pattern) |
| TestReader | |
| TestReader | |
| pwiz::tradata::Reader | Interface for file readers |
| Reader1 | |
| Reader1 | |
| Reader1 | |
| Reader1 | |
| Reader2 | |
| Reader2 | |
| Reader2 | |
| Reader2 | |
| pwiz::msdata::Reader | Interface for file readers |
| pwiz::msdata::Reader_ABI | |
| pwiz::msdata::Reader_ABI_T2D | |
| pwiz::msdata::Reader_Agilent | |
| pwiz::msdata::Reader_Bruker | |
| pwiz::msdata::Reader_BTDX | |
| pwiz::msdata::Reader_MGF | |
| pwiz::msdata::Reader_MSn | |
| pwiz::msdata::Reader_mz5 | |
| pwiz::msdata::Reader_mzML | |
| pwiz::msdata::Reader_mzXML | |
| pwiz::msdata::Reader_Thermo | |
| pwiz::msdata::Reader_Waters | |
| pwiz::msdata::ReaderList | Reader container (composite pattern) |
| pwiz::msdata::DefaultReaderList | Default Reader list |
| pwiz::msdata::ExtendedReaderList | Default ReaderList, extended to include vendor readers |
| Reader1::ReaderConfig | |
| Reader2::ReaderConfig | |
| pwiz::msdata::ReaderFail | |
| pwiz::proteome::ReaderFail | |
| pwiz::tradata::ReaderFail | |
| pwiz::identdata::ReaderFail | |
| pwiz::utility::MSIHandler::Record | |
| pwiz::peptideid::PeptideID::Record | |
| pwiz::proteome::AminoAcid::Info::Record | Struct for holding data for a single amino acid |
| pwiz::chemistry::Element::Info::Record | |
| pwiz::proteome::IPIFASTADatabase::Record | Structure for holding peptide info |
| pwiz::analysis::PepxmlRecordReader::record | |
| pwiz::msdata::mz5::ReferenceRead_mz5 | This class is a helper class to read and convert a mz5 file to a MSData object |
| pwiz::msdata::mz5::ReferenceWrite_mz5 | This class is a helper class for converting and writing mz5 files in mz5 format |
| pwiz::msdata::mz5::RefListMZ5Data | |
| pwiz::msdata::mz5::RefListMZ5 | Variable length list of references |
| pwiz::msdata::mz5::RefMZ5Data | |
| pwiz::msdata::mz5::RefMZ5 | Is used as a general reference for different tags |
| pwiz::identdata::Residue | Implementation of ResidueType from the mzIdentML schema |
| pwiz::calibration::CalibratorTrial::Results | |
| pwiz::data::pepxml::RocDataPoint | |
| Root | |
| pwiz::analysis::RTMatches_Any< T > | Predicate always returns true |
| pwiz::analysis::RTMatches_Contains< T > | Predicate returns true iff the object's retention time range contains the specified retention time |
| pwiz::analysis::RTMatches_IsContainedIn< T > | Predicate returns true iff the object's retention time range is completely contained within the range of the specified reference object, up to the specified tolerance |
| RunHeaderStruct | |
| pwiz::msdata::mz5::RunMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#run but without spectrum and chromatogram elements |
| pwiz::data::diff_impl::Same< object_type, config_type > | |
| pwiz::data::diff_impl::SameDeep< object_type, config_type > | |
| pwiz::data::SampleDatum< abscissa_type, ordinate_type > | |
| pwiz::math::MatchedFilter::SampledData< space_type > | |
| pwiz::data::pepxml::SampleEnzyme | |
| pwiz::msdata::mz5::SampleMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#sample |
| pwiz::minimxml::SAXParser::saxstring | |
| pwiz::data::peakdata::Scan | |
| ScanCacheStruct | |
| ScanHeaderStruct | |
| pwiz::msdata::mz5::ScanListMZ5 | Variable length scan list |
| pwiz::msdata::mz5::ScanMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#scan |
| pwiz::msdata::mz5::ScanSettingMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#scanSettings |
| pwiz::msdata::ScanSettings | Description of the acquisition settings of the instrument prior to the start of the run |
| pwiz::msdata::mz5::ScansMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.htmlscanList |
| pwiz::frequency::PeakDetectorMatchedFilter::Score | Structure for holding the matched filter calculation results |
| pwiz::data::pepxml::SearchDatabase | |
| pwiz::data::pepxml::SearchHit | |
| pwiz::eharmony::SearchNeighborhoodCalculator | |
| pwiz::eharmony::NormalDistributionSearch | |
| pwiz::data::pepxml::SearchResult | |
| pwiz::data::pepxml::SearchSummary | Database search settings |
| Second | |
| pwiz::SecondIs< T > | |
| pwiz::identdata::seq_p | |
| pwiz::identdata::sequence_p | |
| pwiz::identdata::SequenceCollection | Implementation of SequenceCollectionType from the mzIdentML schema |
| pwiz::proteome::Serializer_FASTA | ProteomeData <-> FASTA stream serialization |
| pwiz::msdata::Serializer_MGF | MSData <-> MGF stream serialization |
| pwiz::msdata::Serializer_MSn | MSData <-> MSn stream serialization |
| pwiz::msdata::Serializer_mz5 | MSData <-> MZ5 file serialization |
| pwiz::identdata::Serializer_mzIdentML | MZIDData <-> mzIdentML stream serialization |
| pwiz::msdata::Serializer_mzML | MSData <-> mzML stream serialization |
| pwiz::msdata::Serializer_mzXML | MSData <-> mzXML stream serialization |
| pwiz::identdata::Serializer_pepXML | MZIDData <-> pepXML stream serialization |
| pwiz::identdata::Serializer_protXML | MZIDData <-> pepXML stream serialization |
| pwiz::identdata::Serializer_Text | Serializer_Text reads in and writes out an id file in tab format |
| pwiz::tradata::Serializer_traML | TraData <-> traML stream serialization |
| SetRetentionTime | |
| pwiz::util::SHA1_ostream | Ostream filter for calculating a SHA-1 hash of data on the fly |
| SHA1_WORKSPACE_BLOCK | |
| pwiz::util::SHA1Calculator | |
| pwiz::util::SHA1Filter | Model of boost::iostreams::Filter |
| pwiz::util::SHA1SymmetricFilter | Model of boost::iostreams::SymmetricFilter |
| pwiz::util::shared_map< keyT, valueT, _Pr, _Alloc > | Copy semantics of shared_ptr<map<K,V> > with a std::map interface |
| pwiz::msdata::SpectrumIterator::Sieve | Interface for filtering based on ScanInfo |
| FTSieve | |
| Simple | |
| pwiz::analysis::Smoother | Interface for a one-dimensional smoothing algorithm |
| pwiz::analysis::SavitzkyGolaySmoother< T > | |
| pwiz::analysis::WhittakerSmoother | |
| pwiz::data::peakdata::Software | |
| pwiz::identdata::software_p | |
| pwiz::msdata::mz5::SoftwareMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#software |
| pwiz::msdata::mz5::SourceFileMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#sourceFile |
| pwiz::data::pepxml::Specificity | |
| pwiz::analysis::SpectrumDataFilter | |
| pwiz::analysis::MS2Deisotoper | |
| pwiz::analysis::MS2NoiseFilter | |
| pwiz::analysis::PrecursorMassFilter | |
| pwiz::analysis::ThresholdFilter | |
| pwiz::msdata::SpectrumIdentity | Identifying information for a spectrum |
| pwiz::msdata::Spectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
| pwiz::msdata::SpectrumIdentityFromXML | Identifying information for a spectrum subclassed to add private information for faster file IO in mzML and mzXML |
| pwiz::msdata::SpectrumIdentityFromMzXML | Identifying information for a spectrum as read from mzML or mzXML subclassed to add private information for faster file IO in mzXML |
| pwiz::msdata::SpectrumInfo | Simple structure for holding Spectrum info |
| pwiz::msdata::SpectrumIterator | SpectrumIterator provides convenient iteration through a set of scans in a SpectrumList |
| pwiz::msdata::SpectrumList | Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML) |
| pwiz::msdata::SpectrumListBase | Common functionality for base SpectrumList implementations |
| MyBase | |
| pwiz::msdata::detail::SpectrumList_ABI | |
| pwiz::msdata::detail::SpectrumList_ABI_T2D | |
| pwiz::msdata::detail::SpectrumList_Agilent | |
| pwiz::msdata::detail::SpectrumList_Bruker | |
| pwiz::msdata::detail::SpectrumList_Thermo | |
| pwiz::msdata::detail::SpectrumList_Waters | |
| pwiz::msdata::SpectrumList_BTDX | SpectrumList backed by a Bruker BioTools DataExchange XML file |
| pwiz::msdata::SpectrumList_MGF | Implementation of SpectrumList, backed by an MGF file |
| pwiz::msdata::SpectrumList_MSn | Implementation of SpectrumList, backed by an MGF file |
| pwiz::msdata::SpectrumList_mz5 | Implementation of SpectrumList, backed by an mz5 file |
| pwiz::msdata::SpectrumList_mzML | Implementation of SpectrumList, backed by an mzML file |
| pwiz::msdata::SpectrumList_mzXML | Implementation of SpectrumList, backed by an mzXML file |
| pwiz::msdata::SpectrumListSimple | Simple writeable in-memory implementation of SpectrumList |
| pwiz::msdata::SpectrumListWrapper | Inheritable pass-through implementation for wrapping a SpectrumList |
| pwiz::analysis::SpectrumList_ChargeStateCalculator | SpectrumList implementation that assigns (probable) charge states to tandem mass spectra |
| pwiz::analysis::SpectrumList_Filter | SpectrumList filter, for creating Spectrum sub-lists |
| pwiz::analysis::SpectrumList_MetadataFixer | SpectrumList implementation to add (or replace) base peak and total ion metadata with new values calculated from the current binary data |
| pwiz::analysis::SpectrumList_MZWindow | SpectrumList filter, for creating Spectrum sub-lists |
| pwiz::analysis::SpectrumList_PeakFilter | SpectrumList implementation that returns spectra with the specified SpectrumDataFilter operation applied |
| pwiz::analysis::SpectrumList_PeakPicker | SpectrumList implementation to replace peak profiles with picked peaks |
| pwiz::analysis::SpectrumList_PrecursorRecalculator | SpectrumList wrapper that recalculates precursor info on spectrum() requests |
| pwiz::analysis::SpectrumList_PrecursorRefine | SpectrumList wrapper that recalculates precursor info on spectrum() requests |
| pwiz::analysis::SpectrumList_Smoother | SpectrumList implementation to return smoothed spectral data |
| pwiz::analysis::SpectrumList_Sorter | Provides a custom-sorted spectrum list |
| pwiz::analysis::SpectrumList_TitleMaker | SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user-specified format |
| pwiz::analysis::SpectrumList_ZeroSamplesFilter | SpectrumList implementation to return spectra with or without extra zero samples |
| pwiz::msdata::SpectrumListCache | Adds a level of flexible MRU caching to a SpectrumList processor chain |
| pwiz::analysis::SpectrumListFactory | Factory for instantiating and wrapping SpectrumLists |
| pwiz::msdata::mz5::SpectrumMZ5 | *http://www.peptideatlas.org/tmp/mzML1.1.0.html#spectrum but without binary data elements |
| pwiz::data::pepxml::SpectrumQuery | |
| pwiz::analysis::RegionAnalyzer::SpectrumStats | |
| pwiz::calibration::CalibratorTrial::State | |
| pwiz::analysis::RegionAnalyzer::Stats | |
| pwiz::math::Stats | |
| pwiz::minimxml::SAXParser::Handler::Status | Handler returns the Status struct as a means of changing the parser's behavior |
| pwiz::identdata::SubstitutionModification | Implementation of SubstitutionModificationType from the mzIdentML schema |
| pwiz::utility::TabHandler | |
| pwiz::utility::DefaultTabHandler | |
| pwiz::utility::MSIHandler | |
| pwiz::utility::VectorTabHandler | |
| pwiz::utility::TabReader | |
| pwiz::analysis::TabularConfig | |
| pwiz::analysis::RegionAnalyzer::Config | |
| pwiz::analysis::RegionSlice::Config | |
| pwiz::analysis::RegionSIC::Config | |
| pwiz::analysis::RegionTIC::Config | |
| pwiz::analysis::RunSummary::Config | |
| pwiz::analysis::SpectrumTable::Config | |
| pwiz::data::Term | Single controlled vocabulary term |
| TestAminoAcid | |
| TestChargeStateCalculator | |
| TestData | |
| TestDatum | |
| TestDeisotoper | |
| TestETDMassFilter | |
| TestFormula | |
| TestFragmentation | |
| TestInfo | |
| TestMetadataFixer | |
| TestModification | |
| TestModifiedPeptide | |
| TestMS2Denoise | |
| TestOperator | |
| TestPair | |
| TestPathmask | |
| pwiz::util::TestPathPredicate | Test implementations derive from this to define which paths should be tested |
| Is_T2D_Directory | |
| IsDirectory | |
| IsDirectory | |
| IsRawData | |
| IsRawFile | |
| IsWiffFile | |
| TestPeptide | |
| TestSpectrumInfo | |
| TestThresholder | |
| pwiz::identdata::TextWriter | |
| pwiz::msdata::TextWriter | |
| pwiz::tradata::TextWriter | |
| pwiz::proteome::TextWriter | |
| ThreadStatus | |
| pwiz::msdata::TimeIntensityPair | The data point type of a chromatogram |
| pwiz::util::Timer | |
| pwiz::tradata::TraData | |
| pwiz::tradata::TraDataFile | TraData object plus file I/O |
| pwiz::msdata::mz5::Translator_mz5 | Helper class to translate mz values |
| pwiz::frequency::TruncatedLorentzianEstimator | |
| pwiz::frequency::TruncatedLorentzianParameters | Struct for holding parameters for a Truncated Lorentzian function |
| pwiz::util::IterationListener::UpdateMessage | |
| pwiz::util::usage_exception | |
| pwiz::util::user_error | |
| pwiz::data::UserParam | Uncontrolled user parameters (essentially allowing free text). Before using these, one should verify whether there is an appropriate CV term available, and if so, use the CV term instead |
| pwiz::msdata::mz5::UserParamMZ5Data | |
| pwiz::msdata::mz5::UserParamMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#userParam |
| pwiz::frequency::DerivativeTest::VectorFunction< value_type > | |
| pwiz::frequency::DerivativeTest::ParametrizedDerivativeSlice< value_type > | |
| pwiz::frequency::DerivativeTest::ParametrizedFunctionSlice< value_type > | |
| pwiz::frequency::DerivativeTest::VectorFunction< double > | |
| pwiz::frequency::DerivativeTest::AdaptedErrorDerivative< value_type > | |
| pwiz::frequency::DerivativeTest::AdaptedErrorFunction< value_type > | |
| pwiz::Version | |
| pwiz::msdata::Version | |
| pwiz::tradata::Version | |
| pwiz::proteome::Version | |
| pwiz::identdata::Version | |
| pwiz::analysis::Version | |
| pwiz::util::virtual_map< keyT, valueT, _Pr, _Alloc > | Wrapper for std::map that will behave properly with polymorphism |
| pwiz::util::virtual_map< int, ModificationList > | |
| pwiz::proteome::ModificationMap | Maps peptide/protein sequence indexes (0-based) to a modification list |
| pwiz::eharmony::WarpFunction | |
| pwiz::eharmony::LinearWarpFunction | |
| pwiz::eharmony::PiecewiseLinearWarpFunction | |
| pwiz::eharmony::SplineWarpFunction | |
| pwiz::msdata::MSDataFile::WriteConfig | Configuration for write() |
| pwiz::proteome::ProteomeDataFile::WriteConfig | Configuration for write() |
| pwiz::tradata::TraDataFile::WriteConfig | Configuration for write() |
| pwiz::identdata::IdentDataFile::WriteConfig | Configuration for write() |
| WriteCVParam | |
| pwiz::minimxml::XMLWriter | Simple, tag-level XML syntax writing |
| pwiz::analysis::ZeroSampleFiller | Fills in missing zero samples around signal profiles |
1.8.1.1