ProteoWizard
Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234]
oCpwiz::data::pepxml::AlternativeProtein
oCpwiz::data::pepxml::AminoAcidModification
oCpwiz::eharmony::AMTContainer
oCpwiz::eharmony::AMTDatabase
oCpwiz::identdata::AnalysisCollectionImplementation of AnalysisCollectionType from the mzIdentML schema
oCpwiz::identdata::AnalysisDataImplementation of AnalysisDataType from the mzIdentML schema
oCpwiz::identdata::AnalysisProtocolCollectionImplementation of AnalysisProtocolCollectionType from the mzIdentML schema
oCpwiz::data::pepxml::AnalysisResult
oCpwiz::identdata::AnalysisSampleCollectionImplementation of AnalysisSampleCollectionType from mzIdentML schema
oCpwiz::data::pepxml::AnalysisSummary
oCpwiz::data::pepxml::AnalysisTimestampReference for analysis applied to current run (time corresponds with analysis_summary/, id corresponds with analysis_result/)
oCpwiz::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.)
oCpwiz::analysis::analyzer_strings< MetadataReporter >
oCpwiz::analysis::analyzer_strings< Pseudo2DGel >
oCpwiz::analysis::analyzer_strings< RegionSIC >
oCpwiz::analysis::analyzer_strings< RegionSlice >
oCpwiz::analysis::analyzer_strings< RegionTIC >
oCpwiz::analysis::analyzer_strings< RunSummary >
oCpwiz::analysis::analyzer_strings< SpectrumBinaryData >
oCpwiz::analysis::analyzer_strings< SpectrumTable >
oCpwiz::minimxml::SAXParser::Handler::Attributes::attribute
oCpwiz::minimxml::SAXParser::Handler::Attributes
oCpwiz::minimxml::XMLWriter::AttributesVector of name/value pairs to be written as XML attributes
oCauto_vector< T >::auto_lvalue
oCauto_vector< T >
oCpwiz::data::BaseDiffConfig
oCpwiz::minimxml::basic_charcounter< Ch >
oCpwiz::Bin< T >
oCpwiz::msdata::BinaryDataEncoderBinary-to-text encoding
oCpwiz::msdata::mz5::BinaryDataMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#binaryDataArray but without raw data
oCpwiz::data::CalibrationParameters
oCpwiz::calibration::CalibratorCalibrates using EM algorithm using peptide mass database
oCpwiz::calibration::CalibratorLog
oCpwiz::calibration::CalibratorTrial
oCpwiz::minimxml::basic_charcounter< Ch >::category
oCpwiz::util::CharIndexedVector< T >Wrapper for boost::array that is indexable by character; supports indexes 0-127
oCpwiz::util::CharIndexedVectorConstIterator< T >Const_iterator for CharIndexedVector
oCpwiz::util::CharIndexedVectorIterator< T >Iterator for CharIndexedVector
oCpwiz::analysis::ChromatogramDataFilter
oCpwiz::msdata::ChromatogramIdentityIdentifying information for a chromatogram
oCpwiz::msdata::ChromatogramListInterface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML)
oCpwiz::msdata::mz5::ChromatogramMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#chromatogram but without binary data element
oCpwiz::util::ClickwrapPrompterBarrier to force end users to agree/disagree to a prompt before continuing
oCpwiz::util::Image::ColorStruct for holding rgb values (in [0,255])
oCpwiz::util::COMInitializerSingleton used to initialize and uninitialize COM once per thread
oCpwiz::msdata::ComponentListList with the different components used in the mass spectrometer. At least one source, one mass analyzer and one detector need to be specified
oCpwiz::msdata::mz5::ComponentListMZ5List of components
oCpwiz::msdata::mz5::ComponentMZ5Http://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
oCpwiz::msdata::mz5::ComponentsMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#componentList
oCpwiz::analysis::Pseudo2DGel::ConfigHolds the configuration for an instance of Pseudo2DGel
oCpwiz::analysis::SpectrumBinaryData::Config
oCpwiz::msdata::BinaryDataEncoder::ConfigEncoding/decoding configuration
oCpwiz::analysis::FeatureDetectorPeakel::ConfigConvenience construction
oCpwiz::analysis::NoiseCalculator_2Pass::Config
oCpwiz::analysis::PeakelGrower_Proximity::Config
oCpwiz::analysis::PeakelPicker_Basic::Config
oCpwiz::analysis::PeakFamilyDetectorFT::Config
oCpwiz::analysis::PeakFinder_SNR::Config
oCpwiz::analysis::PeakFitter_Parabola::Config
oCpwiz::msdata::Reader::ConfigReader configuration
oCpwiz::msdata::Serializer_mzML::ConfigSerializer_mzML configuration
oCpwiz::analysis::MS2Deisotoper::ConfigPrecursorMassFilter's parameters
oCpwiz::msdata::Serializer_mzXML::ConfigSerializer_mzXML configuration
oCpwiz::msdata::SpectrumIterator::ConfigSpectrumIterator configuration – note that constructors allow automatic conversion from IntegerSet or Sieve to Config
oCpwiz::analysis::MS2NoiseFilter::ConfigMS2NoiseFilter's parameters
oCpwiz::analysis::PrecursorMassFilter::ConfigPrecursorMassFilter's parameters
oCpwiz::analysis::PrecursorRecalculatorDefault::Config
oCpwiz::proteome::Digestion::ConfigSets constraints for valid peptides produced by iterating the digestion
oCpwiz::proteome::Reader_FASTA::ConfigReader_FASTA configuration
oCpwiz::proteome::Serializer_FASTA::ConfigSerializer_FASTA configuration
oCpwiz::chemistry::IsotopeEnvelopeEstimator::Config
oCpwiz::minimxml::XMLWriter::ConfigInitial configuration of the XMLWriter
oCpwiz::frequency::FrequencyEstimatorPhysicalModel::Config
oCpwiz::frequency::PeakDetectorMatchedFilter::ConfigStructure for holding configuration
oCpwiz::identdata::Reader::ConfigHACK: provide an option to read only file-level metadata; once we have an enumerable ResultList implementation this will be deprecated
oCReader1::Config
oCReader2::Config
oCpwiz::identdata::Serializer_mzIdentML::ConfigSerializer_mzIdentML configuration
oCpwiz::identdata::Serializer_pepXML::ConfigSerializer_pepXML configuration
oCpwiz::identdata::Serializer_protXML::ConfigSerializer_protXML configuration
oCpwiz::identdata::Serializer_Text::Config< Controls the format of the text file
oCpwiz::analysis::MSDataCache::ConfigMSDataCache configuration
oCpwiz::analysis::PepxmlRecordReader::Config
oCpwiz::calibration::CalibratorTrial::Configuration
oCpwiz::msdata::mz5::Configuration_mz5Configuration class for mz5 im- and export
oCpwiz::msdata::mz5::Connection_mz5This class is used for reading and writing information to a mz5 file
oCpwiz::proteome::Digestion::const_iteratorForward-only, read-only iteration to enumerate peptides
oCpwiz::msdata::mz5::ContVocabMZ5Data
oCpwiz::math::MatchedFilter::Correlation< Y >
oCCSHA1
oCCustomPair
oCpwiz::cv::CVInformation about an ontology or CV source and a short 'lookup' tag to refer to
oCpwiz::identdata::CVMap
oCpwiz::data::CVParamTag-value pair, where the tag comes from the controlled vocabulary
oCpwiz::data::CVParamIsFunctor for finding CVParam with specified exact CVID in a collection of CVParams:
oCpwiz::data::CVParamIsChildOfFunctor for finding children of a specified CVID in a collection of CVParams:
oCpwiz::msdata::mz5::CVParamMZ5Data
oCpwiz::msdata::mz5::CVRefMZ5Data
oCpwiz::cv::CVTermInfoStructure for holding CV term info
oCpwiz::data::CVTranslatorTranslates text to CV terms
oCpwiz::eharmony::DatabaseQuery
oCpwiz::identdata::DatabaseTranslationImplementation of DatabaseTranslationType from the mzIdentML schema
oCpwiz::identdata::DataCollectionImplementation of DataCollectionType from the mzIdentML schema
oCpwiz::eharmony::DataFetcherContainer
oCpwiz::data::pepxml::DataFilter
oCpwiz::analysis::MSDataAnalyzer::DataInfoInformation about the data to be analyzed
oCpwiz::msdata::DataProcessingDescription of the way in which a particular software was used
oCpwiz::msdata::mz5::DataProcessingMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#dataProcessing
oCpwiz::data::pepxml::DatasetDerivationSource and filtering criteria used to generate dataset
oCDatum
oCpwiz::identdata::dbsequence_p
oCDeletePtr< T >
oCpwiz::identdata::DelimWriter
oCpwiz::data::Diff< object_type, config_type, object_result_type >Calculate diffs of objects in a ProteoWizard data model hierarchy
oCDigestedPeptideLessThan
oCpwiz::proteome::DigestionEnumerates the peptides from proteolytic digestion of a polypeptide or protein;
oCpwiz::eharmony::DistanceAttribute
oCpwiz::data::pepxml::DistributionPoint
oCpwiz::chemistry::detail::Element
oCpwiz::calibration::MassDatabase::Entry
oCpwiz::data::Index::EntryGeneric type identifying an indexed item by string id, ordinal index, and stream offset
oCpwiz::data::pepxml::EnzymaticSearchConstraint
oCEnzymePtr_missedCleavages
oCEnzymePtr_specificity
oCpwiz::identdata::EnzymesImplementation of EnzymesType from the mzIdentML schema
oCpwiz::calibration::ErrorEstimator
oCpwiz::frequency::ParametrizedFunction< value_type >::ErrorFunction
oCpwiz::data::pepxml::ErrorPoint
oCpwiz::eharmony::Exporter
oCpwiz::analysis::ExtraZeroSamplesFilterRemoves (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
oCpwiz::data::peakdata::Feature
oCpwiz::eharmony::Feature2PeptideMatcher
oCpwiz::eharmony::Feature_dataFetcher
oCpwiz::analysis::FeatureDetector
oCpwiz::data::peakdata::FeatureFile
oCpwiz::analysis::FeatureModelerInterface for fitting and scoring Feature data to a model
oCpwiz::eharmony::FeatureSequenced
oCFifth
oCpwiz::msdata::FileDescriptionInformation pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here
oCpwiz::msdata::mz5::FileInformationMZ5DataGeneral mz5 file information
oCpwiz::identdata::FilterImplementation of FilterType from the mzIdentML schema
oCFirst
oCpwiz::peptideid::FlatRecordBuilder
oCpwiz::chemistry::FormulaClass to represent a chemical formula
oCpwiz::identdata::FragmentArrayImplementation of FragmentArrayType from the mzIdentML schema
oCpwiz::proteome::FragmentationFragment ion masses for a peptide
oCpwiz::data::FrequencyDataClass for binary storage of complex frequency data
oCpwiz::frequency::FrequencyEstimatorInterface for frequency estimator modules
oCpwiz::eharmony::IslandizedDatabase::Gaussian
oCglob_t
oCGoober
oCpwiz::minimxml::SAXParser::HandlerSAX event handler interface
oCpwiz::data::diff_impl::HasID< object_type >
oCpwiz::identdata::id_p< T >
oCpwiz::identdata::IdentifiableParent class representing extensions of the IdentifiableType from the mzIdentML schema
oCpwiz::util::ImageWrapper class for using 'gd' graphics library
oCpwiz::data::IndexGeneric interface for creating and using an index on a stream of serialized objects
oCpwiz::msdata::Index_mzML
oCpwiz::msdata::SpectrumList_mzXML::index_not_foundException thrown if create(*,*,true) is called and the mzXML index cannot be found
oCpwiz::msdata::IndexList
oCpwiz::proteome::IndexList
oCpwiz::identdata::InputsImplementation of the InputsType from the mzIdentML schema
oCpwiz::msdata::mz5::InstrumentConfigurationMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#instrumentConfiguration
oCInstrumentStruct
oCpwiz::util::IntegerSetVirtual container of integers, accessible via an iterator interface, stored as union of intervals
oCpwiz::util::IntegerSet::IntervalSingle closed interval of integers
oCpwiz::proteome::IPIFASTADatabaseClass for accessing data in ipi.*.fasta files
oCIsFS
oCIsInt
oCpwiz::eharmony::IslandizedDatabase::Island
oCpwiz::IsObject< T >
oCpwiz::chemistry::detail::Isotope
oCpwiz::chemistry::IsotopeCalculator
oCpwiz::chemistry::IsotopeEnvelopeEstimatorClass used for calculating a theoretical isotope envelope for a given mass, based on an estimate of the elemental composition for that mass
oCpwiz::chemistry::IsotopeTableClass 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
oCIsSQ
oCpwiz::util::IterationListenerInterface to be implemented by clients who want progress callbacks
oCpwiz::util::IterationListenerRegistryHandles registration of IterationListeners and broadcast of update messages
oCpwiz::peptideid::PeptideID::IteratorIterator for
oCpwiz::util::IntegerSet::IteratorForward iterator providing readonly access to the virtual container
oCpwiz::peptideid::PeptideID::IteratorInternalInterface for
oCpwiz::math::MatchedFilter::KernelTraits< Kernel >
oCpwiz::math::MatchedFilter::KernelTraitsBase< Kernel >
oCpwiz::math::MatchedFilter::KernelTraitsBase< Y(*)(X)>
oCpwiz::eharmony::KeyLessThan
oCpwiz::calibration::LeastSquaresCalibrator
oCpwiz::msdata::LegacyAdapter_InstrumentInterface for legacy access to Instrument
oCpwiz::msdata::LegacyAdapter_SoftwareInterface for legacy access to Software
oCpwiz::math::LinearLeastSquares< LinearLeastSquaresType_LU >
oCpwiz::math::LinearLeastSquares< LinearLeastSquaresType_QR >
oCpwiz::math::LinearSolver< LinearSolverType_LU >
oCpwiz::math::LinearSolver< LinearSolverType_QR >
oCpwiz::peptideid::PeptideID::Location
oCpwiz::peptideid::location_less
oCLU
oCpwiz::frequency::MagnitudeLorentzian
oCpwiz::chemistry::MassAbundanceStruct for holding isotope information
oCpwiz::calibration::MassDatabase
oCpwiz::calibration::MassSpread
oCpwiz::identdata::MassTableImplementation of MassTableType from the mzIdentML schema
oCpwiz::data::pepxml::Match
oCpwiz::data::pepxml::MatchData
oCpwiz::eharmony::Matcher
oCpwiz::eharmony::Matrix
oCpwiz::calibration::Calibrator::MeasurementStructure for holding frequency-charge pairs
oCpwiz::data::pepxml::MixtureModel
oCpwiz::data::pepxml::ModAminoAcidMass
oCpwiz::proteome::ModificationPost-translational modification (PTM) modification formula or masses must be provided at instantiation
oCpwiz::data::pepxml::ModificationInfo
oCpwiz::proteome::ModificationListList of modifications on a single amino acid
oCpwiz::eharmony::ModificationStateEntry
oCpwiz::util::mru_list< Item, KeyExtractor >
oCpwiz::util::mru_list< PtrType, KeyExtractor >
oCpwiz::msdata::MSDataThis 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)
oCpwiz::analysis::MSDataAnalyzerInterface for MSData analyzers
oCpwiz::analysis::MSDataAnalyzerDriverEvent generator for MSDataAnalyzer
oCpwiz::eharmony::MSIAMTData
oCpwiz::data::pepxml::MSMSPipelineAnalysis
oCpwiz::data::pepxml::MSMSRunSummary
oCpwiz::msdata::MSnHeader
oCMyPred
oCpwiz::msdata::MZIntensityPairThe data point type of a mass spectrum
oCmzrtEqual
oCpwiz::analysis::MZRTField< T >MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT
oCpwiz::chemistry::MZToleranceStruct for expressing m/z tolerance in either amu or ppm
oCpwiz::peptideid::nativeID_less
oCpwiz::analysis::PeakFamilyDetectorFT::NoDataExceptionFT-specific exception
oCpwiz::analysis::Noise
oCpwiz::analysis::NoiseCalculator
oCpwiz::data::OBORepresents a selectively parsed OBO file
oCpwiz::eharmony::Observation
oCpwiz::util::once_flag_proxy
oCOneMinusAbs
oCpwiz::math::OrderedPair
oCpwiz::math::OrderedPairContainerRefWrapper class for accessing contiguous data as a container of OrderedPairs; note that it does not own the underlying data
oCpwiz::identdata::organization_p
oCpwiz::minimxml::XMLWriter::OutputObserverInterface to allow outside observation of data sent to output stream
oCpwiz::calibration::MassSpread::Pair
oCpwiz::math::Parabola
oCpwiz::data::ParamContainerThe base class for elements that may contain cvParams, userParams, or paramGroup references
oCpwiz::data::peakdata::Software::Parameter
oCpwiz::data::pepxml::Parameter
oCpwiz::frequency::ParameterEstimator
oCpwiz::frequency::ParametrizedFunction< value_type >
oCpwiz::frequency::ParametrizedFunction< double >
oCpwiz::frequency::ParametrizedFunction< std::complex< double > >
oCpwiz::msdata::mz5::ParamGroupMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#referenceableParamGroup
oCpwiz::msdata::mz5::ParamListMZ5Data
oCpwiz::msdata::mz5::ParamListsMZ5This class is used as a generalized container for Targets, SelectedIons, Products and ScanWindows
oCpwiz::msaux::Path
oCpwiz::data::peakdata::Peak
oCpwiz::analysis::PeakSome generic metadata about a peak detected in a signal
oCpwiz::data::peakdata::PeakData
oCpwiz::analysis::PeakDetector
oCpwiz::frequency::PeakDetectorInterface for finding peaks in frequency data
oCpwiz::data::peakdata::PeakelStruct for an eluted peak (PEAK ELution)
oCpwiz::analysis::PeakelGrowerInterface for growing Peakels
oCpwiz::analysis::PeakelPickerInterface for picking Peakels and arranging into Features; note: Peakels are actually removed from the PeakelField
oCpwiz::analysis::PeakExtractorClass 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"
oCpwiz::data::peakdata::PeakFamily
oCpwiz::analysis::PeakFamilyDetectorInterface for peak family (isotope envelope) detection
oCpwiz::analysis::PeakFinderInterface for finding peaks in an array of ordered pairs
oCpwiz::analysis::PeakFitterInterface for fitting peaks in an array of ordered pairs
oCpwiz::identdata::Pep2MzIdentTranslates data from a MinimumPepXML object into a IdentData object tree when a translation is known
oCpwiz::proteome::PeptidePeptide or polypeptide (a sequence of amino acids)
oCpwiz::proteome::PeptideDatabase
oCpwiz::proteome::PeptideDatabaseFormula
oCpwiz::proteome::PeptideDatabaseRecord
oCpwiz::eharmony::PeptideEntry
oCpwiz::identdata::PeptideHypothesisImplementation of PeptideHypothesisType from the mzIdentML schema
oCpwiz::peptideid::PeptideIDThis is an interface for classes that allow access to data sources of identified peptides
oCpwiz::eharmony::PeptideID_dataFetcher
oCpwiz::eharmony::PeptideMatcher
oCpwiz::data::pepxml::PeptideProphetResult
oCpwiz::data::pepxml::PeptideProphetSummary
oCpwiz::analysis::PepxmlRecordReader
oCpwiz::identdata::PepXMLSpecificity
oCpwiz::identdata::person_p
oCpwiz::util::Image::PointStruct for holding pixel coordinates
oCPointsToSame
oCpwiz::msdata::SpectrumInfo::PrecursorInfoStructure for Precursor info
oCpwiz::analysis::PrecursorRecalculator::PrecursorInfo
oCpwiz::analysis::SpectrumList_PrecursorRefine::PrecursorInfo
oCpwiz::msdata::mz5::PrecursorListMZ5Variable length precursor list
oCpwiz::msdata::mz5::PrecursorMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#precursor
oCpwiz::analysis::PrecursorRecalculator
oCpwiz::analysis::ProteinList_DecoyGenerator::PredicateClient-implemented generator predicate – called during construction of ProteinList_DecoyGenerator to create a decoy protein from a target protein
oCpwiz::analysis::ProteinList_Filter::PredicateClient-implemented filter predicate – called during construction of ProteinList_Filter to create the filtered list of proteins
oCpwiz::analysis::SpectrumList_Filter::PredicateClient-implemented filter predicate – called during construction of SpectrumList_Filter to create the filtered list of spectra
oCpwiz::analysis::SpectrumList_Sorter::PredicateClient-implemented sort predicate – called during construction of SpectrumList_Sorter to sort the underlying spectrum list
oCPrintAttribute
oCpwiz::msdata::mz5::ProcessingMethodListMZ5Variable length processing method list
oCpwiz::msdata::mz5::ProcessingMethodMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#processingMethod
oCpwiz::msdata::ProductProduct ion information
oCpwiz::math::MatchedFilter::ProductSpace< X, Y >
oCpwiz::analysis::MSDataAnalyzerDriver::ProgressCallbackProgress callback interface
oCpwiz::proteome::ProteinList
oCpwiz::analysis::ProteinListFactoryFactory for instantiating and wrapping ProteinLists
oCpwiz::proteome::ProteomeData
oCpwiz_RAMPAdapterSWIG-friendly wrapper to provide RAMP-friendly access to MSData library
oCpwiz::data::pepxml::Q3RatioResult
oCpwiz::msdata::RAMPAdapterAdapter to provide RAMP-friendly access to MSData library
oCRAMPFILE
oCpwiz::math::Random
oCpwiz::util::random_access_compressed_ifstream
oCRawMassDatum
oCpwiz::identdata::ReaderInterface for file readers
oCpwiz::proteome::ReaderInterface for file readers
oCpwiz::tradata::ReaderInterface for file readers
oCpwiz::msdata::ReaderInterface for file readers
oCReader1::ReaderConfig
oCReader2::ReaderConfig
oCpwiz::msdata::ReaderFail
oCpwiz::proteome::ReaderFail
oCpwiz::tradata::ReaderFail
oCpwiz::identdata::ReaderFail
oCpwiz::utility::MSIHandler::Record
oCpwiz::peptideid::PeptideID::Record
oCpwiz::proteome::AminoAcid::Info::RecordStruct for holding data for a single amino acid
oCpwiz::chemistry::Element::Info::Record
oCpwiz::proteome::IPIFASTADatabase::RecordStructure for holding peptide info
oCpwiz::analysis::PepxmlRecordReader::record
oCpwiz::msdata::mz5::ReferenceRead_mz5This class is a helper class to read and convert a mz5 file to a MSData object
oCpwiz::msdata::mz5::ReferenceWrite_mz5This class is a helper class for converting and writing mz5 files in mz5 format
oCpwiz::msdata::mz5::RefListMZ5Data
oCpwiz::msdata::mz5::RefMZ5Data
oCpwiz::identdata::ResidueImplementation of ResidueType from the mzIdentML schema
oCpwiz::calibration::CalibratorTrial::Results
oCpwiz::data::pepxml::RocDataPoint
oCRoot
oCpwiz::analysis::RTMatches_Any< T >Predicate always returns true
oCpwiz::analysis::RTMatches_Contains< T >Predicate returns true iff the object's retention time range contains the specified retention time
oCpwiz::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
oCRunHeaderStruct
oCpwiz::msdata::mz5::RunMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#run but without spectrum and chromatogram elements
oCpwiz::data::diff_impl::Same< object_type, config_type >
oCpwiz::data::diff_impl::SameDeep< object_type, config_type >
oCpwiz::data::SampleDatum< abscissa_type, ordinate_type >
oCpwiz::math::MatchedFilter::SampledData< space_type >
oCpwiz::data::pepxml::SampleEnzyme
oCpwiz::msdata::mz5::SampleMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#sample
oCpwiz::minimxml::SAXParser::saxstring
oCpwiz::data::peakdata::Scan
oCScanCacheStruct
oCScanHeaderStruct
oCpwiz::msdata::mz5::ScanListMZ5Variable length scan list
oCpwiz::msdata::mz5::ScanMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#scan
oCpwiz::msdata::mz5::ScanSettingMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#scanSettings
oCpwiz::msdata::ScanSettingsDescription of the acquisition settings of the instrument prior to the start of the run
oCpwiz::msdata::mz5::ScansMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.htmlscanList
oCpwiz::frequency::PeakDetectorMatchedFilter::ScoreStructure for holding the matched filter calculation results
oCpwiz::data::pepxml::SearchDatabase
oCpwiz::data::pepxml::SearchHit
oCpwiz::eharmony::SearchNeighborhoodCalculator
oCpwiz::data::pepxml::SearchResult
oCpwiz::data::pepxml::SearchSummaryDatabase search settings
oCSecond
oCpwiz::SecondIs< T >
oCpwiz::identdata::seq_p
oCpwiz::identdata::sequence_p
oCpwiz::identdata::SequenceCollectionImplementation of SequenceCollectionType from the mzIdentML schema
oCpwiz::proteome::Serializer_FASTAProteomeData <-> FASTA stream serialization
oCpwiz::msdata::Serializer_MGFMSData <-> MGF stream serialization
oCpwiz::msdata::Serializer_MSnMSData <-> MSn stream serialization
oCpwiz::msdata::Serializer_mz5MSData <-> MZ5 file serialization
oCpwiz::identdata::Serializer_mzIdentMLMZIDData <-> mzIdentML stream serialization
oCpwiz::msdata::Serializer_mzMLMSData <-> mzML stream serialization
oCpwiz::msdata::Serializer_mzXMLMSData <-> mzXML stream serialization
oCpwiz::identdata::Serializer_pepXMLMZIDData <-> pepXML stream serialization
oCpwiz::identdata::Serializer_protXMLMZIDData <-> pepXML stream serialization
oCpwiz::identdata::Serializer_TextSerializer_Text reads in and writes out an id file in tab format
oCpwiz::tradata::Serializer_traMLTraData <-> traML stream serialization
oCSetRetentionTime
oCpwiz::util::SHA1_ostreamOstream filter for calculating a SHA-1 hash of data on the fly
oCSHA1_WORKSPACE_BLOCK
oCpwiz::util::SHA1Calculator
oCpwiz::util::SHA1FilterModel of boost::iostreams::Filter
oCpwiz::util::SHA1SymmetricFilterModel of boost::iostreams::SymmetricFilter
oCpwiz::util::shared_map< keyT, valueT, _Pr, _Alloc >Copy semantics of shared_ptr<map<K,V> > with a std::map interface
oCpwiz::msdata::SpectrumIterator::SieveInterface for filtering based on ScanInfo
oCSimple
oCpwiz::analysis::SmootherInterface for a one-dimensional smoothing algorithm
oCpwiz::data::peakdata::Software
oCpwiz::identdata::software_p
oCpwiz::msdata::mz5::SoftwareMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#software
oCpwiz::msdata::mz5::SourceFileMZ5Http://www.peptideatlas.org/tmp/mzML1.1.0.html#sourceFile
oCpwiz::data::pepxml::Specificity
oCpwiz::analysis::SpectrumDataFilter
oCpwiz::msdata::SpectrumIdentityIdentifying information for a spectrum
oCpwiz::msdata::SpectrumInfoSimple structure for holding Spectrum info
oCpwiz::msdata::SpectrumIteratorSpectrumIterator provides convenient iteration through a set of scans in a SpectrumList
oCpwiz::msdata::SpectrumListInterface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML)
oCpwiz::analysis::SpectrumListFactoryFactory for instantiating and wrapping SpectrumLists
oCpwiz::msdata::mz5::SpectrumMZ5*http://www.peptideatlas.org/tmp/mzML1.1.0.html#spectrum but without binary data elements
oCpwiz::data::pepxml::SpectrumQuery
oCpwiz::analysis::RegionAnalyzer::SpectrumStats
oCpwiz::calibration::CalibratorTrial::State
oCpwiz::analysis::RegionAnalyzer::Stats
oCpwiz::math::Stats
oCpwiz::minimxml::SAXParser::Handler::StatusHandler returns the Status struct as a means of changing the parser's behavior
oCpwiz::identdata::SubstitutionModificationImplementation of SubstitutionModificationType from the mzIdentML schema
oCpwiz::utility::TabHandler
oCpwiz::utility::TabReader
oCpwiz::analysis::TabularConfig
oCpwiz::data::TermSingle controlled vocabulary term
oCTestAminoAcid
oCTestChargeStateCalculator
oCTestData
oCTestDatum
oCTestDeisotoper
oCTestETDMassFilter
oCTestFormula
oCTestFragmentation
oCTestInfo
oCTestMetadataFixer
oCTestModification
oCTestModifiedPeptide
oCTestMS2Denoise
oCTestOperator
oCTestPair
oCTestPathmask
oCpwiz::util::TestPathPredicateTest implementations derive from this to define which paths should be tested
oCTestPeptide
oCTestSpectrumInfo
oCTestThresholder
oCpwiz::identdata::TextWriter
oCpwiz::msdata::TextWriter
oCpwiz::tradata::TextWriter
oCpwiz::proteome::TextWriter
oCThreadStatus
oCpwiz::msdata::TimeIntensityPairThe data point type of a chromatogram
oCpwiz::util::Timer
oCpwiz::tradata::TraData
oCpwiz::msdata::mz5::Translator_mz5Helper class to translate mz values
oCpwiz::frequency::TruncatedLorentzianEstimator
oCpwiz::frequency::TruncatedLorentzianParametersStruct for holding parameters for a Truncated Lorentzian function
oCpwiz::util::IterationListener::UpdateMessage
oCpwiz::util::usage_exception
oCpwiz::util::user_error
oCpwiz::data::UserParamUncontrolled 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
oCpwiz::msdata::mz5::UserParamMZ5Data
oCpwiz::frequency::DerivativeTest::VectorFunction< value_type >
oCpwiz::frequency::DerivativeTest::VectorFunction< double >
oCpwiz::Version
oCpwiz::msdata::Version
oCpwiz::tradata::Version
oCpwiz::proteome::Version
oCpwiz::identdata::Version
oCpwiz::analysis::Version
oCpwiz::util::virtual_map< keyT, valueT, _Pr, _Alloc >Wrapper for std::map that will behave properly with polymorphism
oCpwiz::util::virtual_map< int, ModificationList >
oCpwiz::eharmony::WarpFunction
oCpwiz::msdata::MSDataFile::WriteConfigConfiguration for write()
oCpwiz::proteome::ProteomeDataFile::WriteConfigConfiguration for write()
oCpwiz::tradata::TraDataFile::WriteConfigConfiguration for write()
oCpwiz::identdata::IdentDataFile::WriteConfigConfiguration for write()
oCWriteCVParam
oCpwiz::minimxml::XMLWriterSimple, tag-level XML syntax writing
\Cpwiz::analysis::ZeroSampleFillerFills in missing zero samples around signal profiles