ProteoWizard
Class Hierarchy
This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 12345]
 Cpwiz::data::pepxml::AlternativeProtein
 Cpwiz::data::pepxml::AminoAcidModification
 Cpwiz::identdata::AnalysisCollectionImplementation of AnalysisCollectionType from the mzIdentML schema
 Cpwiz::identdata::AnalysisDataImplementation of AnalysisDataType from the mzIdentML schema
 Cpwiz::identdata::AnalysisProtocolCollectionImplementation of AnalysisProtocolCollectionType from the mzIdentML schema
 Cpwiz::data::pepxml::AnalysisResult
 Cpwiz::identdata::AnalysisSampleCollectionImplementation of AnalysisSampleCollectionType from mzIdentML schema
 Cpwiz::data::pepxml::AnalysisSummary
 Cpwiz::data::pepxml::AnalysisTimestampReference for analysis applied to current run (time corresponds with analysis_summary/, id corresponds with analysis_result/)
 Cpwiz::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.)
 Cpwiz::analysis::analyzer_strings< MetadataReporter >
 Cpwiz::analysis::analyzer_strings< RegionSIC >
 Cpwiz::analysis::analyzer_strings< RegionSlice >
 Cpwiz::analysis::analyzer_strings< RegionTIC >
 Cpwiz::analysis::analyzer_strings< RunSummary >
 Cpwiz::analysis::analyzer_strings< SpectrumBinaryData >
 Cpwiz::analysis::analyzer_strings< SpectrumTable >
 Carray
 Cpwiz::minimxml::SAXParser::Handler::Attributes::attribute
 Cpwiz::minimxml::SAXParser::Handler::Attributes
 Cpwiz::data::BaseDiffConfig
 Cpwiz::minimxml::basic_charcounter< Ch >
 Cralab::base::resample::Bin1D
 Cbinary_function
 Cpwiz::msdata::BinaryDataEncoderBinary-to-text encoding
 Cralab::base::resample::Bucket1D
 Cpwiz::data::CalibrationParameters
 Cpwiz::util::CharIndexedVectorConstIterator< T >Const_iterator for CharIndexedVector
 Cpwiz::util::CharIndexedVectorIterator< T >Iterator for CharIndexedVector
 Cpwiz::analysis::ChromatogramDataFilter
 Cpwiz::msdata::ChromatogramIdentityIdentifying information for a chromatogram
 Cpwiz::msdata::ChromatogramListInterface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML)
 Cpwiz::util::ClickwrapPrompterBarrier to force end users to agree/disagree to a prompt before continuing
 Cpwiz::util::Image::ColorStruct for holding rgb values (in [0,255])
 Cpwiz::analysis::MS2Deisotoper::ConfigPrecursorMassFilter's parameters
 Cpwiz::analysis::MS2NoiseFilter::ConfigMS2NoiseFilter's parameters
 Cpwiz::msdata::Reader::ConfigReader configuration
 Cpwiz::analysis::PrecursorMassFilter::ConfigPrecursorMassFilter's parameters
 Cpwiz::msdata::Serializer_mzML::ConfigSerializer_mzML configuration
 Cpwiz::analysis::PrecursorRecalculatorDefault::Config
 Cpwiz::msdata::Serializer_mzXML::ConfigSerializer_mzXML configuration
 Cpwiz::msdata::SpectrumIterator::ConfigSpectrumIterator configuration – note that constructors allow automatic conversion from IntegerSet or Sieve to Config
 Cpwiz::proteome::Digestion::ConfigSets constraints for valid peptides produced by iterating the digestion
 Cpwiz::frequency::FrequencyEstimatorPhysicalModel::Config
 Cpwiz::proteome::Reader_FASTA::ConfigReader_FASTA configuration
 Cpwiz::proteome::Serializer_FASTA::ConfigSerializer_FASTA configuration
 Cpwiz::frequency::PeakDetectorMatchedFilter::ConfigStructure for holding configuration
 Cpwiz::chemistry::IsotopeEnvelopeEstimator::Config
 Cpwiz::analysis::MSDataCache::ConfigMSDataCache configuration
 Cpwiz::analysis::PepxmlRecordReader::Config
 Cpwiz::minimxml::XMLWriter::ConfigInitial configuration of the XMLWriter
 Cpwiz::analysis::SpectrumBinaryData::Config
 Cpwiz::identdata::Reader::ConfigHACK: provide an option to read only file-level metadata; once we have an enumerable ResultList implementation this will be deprecated
 Cpwiz::analysis::FeatureDetectorPeakel::ConfigConvenience construction
 CReader1::Config
 CReader2::Config
 Cpwiz::identdata::Serializer_mzIdentML::ConfigSerializer_mzIdentML configuration
 Cpwiz::identdata::Serializer_pepXML::ConfigSerializer_pepXML configuration
 Cpwiz::identdata::Serializer_protXML::ConfigSerializer_protXML configuration
 Cpwiz::identdata::Serializer_Text::Config< Controls the format of the text file
 Cpwiz::analysis::NoiseCalculator_2Pass::Config
 Cpwiz::analysis::PeakelGrower_Proximity::Config
 Cpwiz::analysis::PeakelPicker_Basic::Config
 Cpwiz::analysis::PeakFamilyDetectorFT::Config
 Cpwiz::analysis::PeakFinder_SNR::Config
 Cpwiz::msdata::BinaryDataEncoder::ConfigEncoding/decoding configuration
 Cpwiz::analysis::PeakFitter_Parabola::Config
 Cpwiz::proteome::Digestion::const_iteratorForward-only, read-only iteration to enumerate peptides
 Cralab::base::resample::Convert2Dense
 Cpwiz::math::MatchedFilter::Correlation< Y >
 Cralab::base::base::utilities::CosineInterpolate< TReal >CosineInterpolate Functor Linear interpolation results in discontinuities at each point
 CCSHA1
 Cralab::base::base::utilities::CubicInterpolate< TReal >CubicInterpolate Functor
 CCustomPair
 Cpwiz::cv::CVInformation about an ontology or CV source and a short 'lookup' tag to refer to
 Cpwiz::identdata::CVMap
 Cpwiz::data::CVParamTag-value pair, where the tag comes from the controlled vocabulary
 Cpwiz::data::CVParamIsFunctor for finding CVParam with specified exact CVID in a collection of CVParams:
 Cpwiz::data::CVParamIsChildOfFunctor for finding children of a specified CVID in a collection of CVParams:
 Cpwiz::cv::CVTermInfoStructure for holding CV term info
 Cpwiz::data::CVTranslatorTranslates text to CV terms
 Cralab::base::resample::DaCompFunctor< TReal >Da Comparator - constant mass error
 Cpwiz::identdata::DatabaseTranslationImplementation of DatabaseTranslationType from the mzIdentML schema
 Cpwiz::identdata::DataCollectionImplementation of DataCollectionType from the mzIdentML schema
 Cpwiz::data::pepxml::DataFilter
 Cpwiz::analysis::MSDataAnalyzer::DataInfoInformation about the data to be analyzed
 Cpwiz::msdata::DataProcessingDescription of the way in which a particular software was used
 Cpwiz::data::pepxml::DatasetDerivationSource and filtering criteria used to generate dataset
 CDatum
 Cpwiz::identdata::dbsequence_p
 Cpwiz::identdata::DelimWriter
 Cpwiz::data::Diff< object_type, config_type, object_result_type >Calculate diffs of objects in a ProteoWizard data model hierarchy
 CDigestedPeptideLessThan
 Cpwiz::proteome::DigestionEnumerates the peptides from proteolytic digestion of a polypeptide or protein;
 Cpwiz::data::pepxml::DistributionPoint
 Cdual_use
 Cpwiz::math::MatchedFilter::KernelTraits< Kernel >::Dummy< T >
 Cpwiz::chemistry::detail::Element
 Cpwiz::data::Index::EntryGeneric type identifying an indexed item by string id, ordinal index, and stream offset
 Cpwiz::data::pepxml::EnzymaticSearchConstraint
 CEnzymePtr_missedCleavages
 CEnzymePtr_specificity
 Cpwiz::identdata::EnzymesImplementation of EnzymesType from the mzIdentML schema
 Cpwiz::frequency::ParametrizedFunction< value_type >::ErrorFunction
 Cpwiz::data::pepxml::ErrorPoint
 Cstd::exceptionSTL class
 Cpwiz::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
 Cpwiz::data::peakdata::Feature
 Cpwiz::analysis::FeatureDetector
 Cpwiz::data::peakdata::FeatureFile
 Cpwiz::analysis::FeatureModelerInterface for fitting and scoring Feature data to a model
 CFifth
 Cpwiz::msdata::FileDescriptionInformation pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here
 Cpwiz::identdata::FilterImplementation of FilterType from the mzIdentML schema
 Cfilter_tag
 Cfiltering_ostream
 CFirst
 Cpwiz::peptideid::FlatRecordBuilder
 Cpwiz::chemistry::FormulaClass to represent a chemical formula
 Cpwiz::identdata::FragmentArrayImplementation of FragmentArrayType from the mzIdentML schema
 Cpwiz::proteome::FragmentationFragment ion masses for a peptide
 Cpwiz::data::FrequencyDataClass for binary storage of complex frequency data
 Cpwiz::frequency::FrequencyEstimatorInterface for frequency estimator modules
 Cralab::base::resample::FTMSCompFunctor< TReal >FTMS Comparator
 CGoober
 Cpwiz::minimxml::SAXParser::HandlerSAX event handler interface
 Cpwiz::data::diff_impl::HasID< object_type >
 Cralab::base::base::utilities::HermiteInterpolate< TReal >HermiteInterpolation
 Cpwiz::identdata::id_p< T >
 Cpwiz::identdata::IdentifiableParent class representing extensions of the IdentifiableType from the mzIdentML schema
 Cpwiz::util::ImageWrapper class for using 'gd' graphics library
 Cpwiz::data::IndexGeneric interface for creating and using an index on a stream of serialized objects
 Cpwiz::msdata::Index_mzML
 Cpwiz::identdata::InputsImplementation of the InputsType from the mzIdentML schema
 Cpwiz::util::IntegerSetVirtual container of integers, accessible via an iterator interface, stored as union of intervals
 Cpwiz::util::IntegerSet::IntervalSingle closed interval of integers
 Cstd::ios_baseSTL class
 Cpwiz::proteome::IPIFASTADatabaseClass for accessing data in ipi.*.fasta files
 CisoChain
 Cpwiz::chemistry::detail::Isotope
 Cpwiz::chemistry::IsotopeCalculator
 CisotopeChain
 Cpwiz::chemistry::IsotopeEnvelopeEstimatorClass used for calculating a theoretical isotope envelope for a given mass, based on an estimate of the elemental composition for that mass
 Cpwiz::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
 Cpwiz::util::IterationListenerInterface to be implemented by clients who want progress callbacks
 Cpwiz::util::IterationListenerRegistryHandles registration of IterationListeners and broadcast of update messages
 Cpwiz::util::IntegerSet::IteratorForward iterator providing readonly access to the virtual container
 Citerator_facade
 Cpwiz::peptideid::PeptideID::IteratorInternalInterface for
 Cpwiz::math::MatchedFilter::KernelTraits< Kernel >
 Cpwiz::math::MatchedFilter::KernelTraitsBase< Kernel >
 Cpwiz::math::MatchedFilter::KernelTraitsBase< Y(*)(X)>
 Cpwiz::msdata::LegacyAdapter_InstrumentInterface for legacy access to Instrument
 Cpwiz::msdata::LegacyAdapter_SoftwareInterface for legacy access to Software
 Cralab::base::base::utilities::LinearInterpolate< TReal >LinearInterpolate Functor
 Cpwiz::math::LinearLeastSquares< lls_type >
 Cpwiz::math::LinearLeastSquares< LinearLeastSquaresType_LU >
 Cpwiz::math::LinearLeastSquares< LinearLeastSquaresType_QR >
 Cpwiz::math::LinearSolver< solver_type >
 Cpwiz::math::LinearSolver< LinearSolverType_LU >
 Cpwiz::math::LinearSolver< LinearSolverType_QR >
 Cralab::base::ms::LocalMinPeakArea< TReal >Extends peak to the left and to the right to the next local minimum or a predefined threshol or a maximum allowed extension
 Cpwiz::peptideid::PeptideID::Location
 Cpwiz::peptideid::location_less
 Cpwiz::frequency::MagnitudeLorentzian
 Cstd::map< K, T >STL class
 Cpwiz::chemistry::MassAbundanceStruct for holding isotope information
 Cpwiz::identdata::MassTableImplementation of MassTableType from the mzIdentML schema
 Cpwiz::data::pepxml::Match
 Cpwiz::data::pepxml::MatchData
 Cpwiz::data::pepxml::MixtureModel
 Cpwiz::data::pepxml::ModAminoAcidMass
 Cpwiz::proteome::ModificationPost-translational modification (PTM) modification formula or masses must be provided at instantiation
 Cpwiz::data::pepxml::ModificationInfo
 Cpwiz::util::mru_list< Item, KeyExtractor >
 Cpwiz::util::mru_list< KeyValuePair, boost::multi_index::member_offset< KeyValuePair, size_t, first_offset > >
 Cpwiz::util::mru_list< PtrType, KeyExtractor >
 Cpwiz::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)
 Cpwiz::analysis::MSDataAnalyzerInterface for MSData analyzers
 Cpwiz::analysis::MSDataAnalyzerDriverEvent generator for MSDataAnalyzer
 Cpwiz::data::pepxml::MSMSPipelineAnalysis
 Cpwiz::data::pepxml::MSMSRunSummary
 Cpwiz::msdata::MSnHeader
 Cmultichar_tag
 CMyPred
 Cpwiz::msdata::MZIntensityPairThe data point type of a mass spectrum
 CmzrtEqual
 Cpwiz::chemistry::MZToleranceStruct for expressing m/z tolerance in either amu or ppm
 Cpwiz::peptideid::nativeID_less
 Cpwiz::analysis::Noise
 Cpwiz::analysis::NoiseCalculator
 Cpwiz::data::OBORepresents a selectively parsed OBO file
 Cpwiz::util::once_flag_proxy
 COneMinusAbs
 Coptimally_buffered_tag
 Cpwiz::math::OrderedPair
 Cpwiz::math::OrderedPairContainerRefWrapper class for accessing contiguous data as a container of OrderedPairs; note that it does not own the underlying data
 Cpwiz::identdata::organization_p
 Cpwiz::minimxml::XMLWriter::OutputObserverInterface to allow outside observation of data sent to output stream
 CpairData
 Cpwiz::math::Parabola
 Cpwiz::data::ParamContainerThe base class for elements that may contain cvParams, userParams, or paramGroup references
 Cpwiz::data::pepxml::Parameter
 Cpwiz::data::peakdata::Software::Parameter
 Cpwiz::frequency::ParameterEstimator
 Cpwiz::frequency::ParametrizedFunction< value_type >
 Cpwiz::frequency::ParametrizedFunction< double >
 Cpwiz::frequency::ParametrizedFunction< std::complex< double > >
 CparentIon
 Cpwiz::analysis::PeakSome generic metadata about a peak detected in a signal
 Cpwiz::data::peakdata::Peak
 Cpwiz::data::peakdata::PeakData
 Cpwiz::analysis::PeakDetector
 Cpwiz::frequency::PeakDetectorInterface for finding peaks in frequency data
 Cpwiz::data::peakdata::PeakelStruct for an eluted peak (PEAK ELution)
 Cpwiz::analysis::PeakelGrowerInterface for growing Peakels
 Cpwiz::analysis::PeakelPickerInterface for picking Peakels and arranging into Features; note: Peakels are actually removed from the PeakelField
 Cpwiz::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"
 Cpwiz::data::peakdata::PeakFamily
 Cpwiz::analysis::PeakFamilyDetectorInterface for peak family (isotope envelope) detection
 Cpwiz::analysis::PeakFinderInterface for finding peaks in an array of ordered pairs
 Cpwiz::analysis::PeakFitterInterface for fitting peaks in an array of ordered pairs
 Cralab::base::ms::PeakPicker< TReal, TIntegrator >Resamples spectrum, apply smoothing, determines zero crossings, integrates peaks
 Cpwiz::identdata::Pep2MzIdentTranslates data from a MinimumPepXML object into a IdentData object tree when a translation is known
 Cpwiz::proteome::PeptidePeptide or polypeptide (a sequence of amino acids)
 Cpwiz::identdata::PeptideHypothesisImplementation of PeptideHypothesisType from the mzIdentML schema
 Cpwiz::peptideid::PeptideIDThis is an interface for classes that allow access to data sources of identified peptides
 Cpwiz::data::pepxml::PeptideProphetResult
 Cpwiz::data::pepxml::PeptideProphetSummary
 Cpwiz::analysis::PepxmlRecordReader
 Cpwiz::identdata::PepXMLSpecificity
 Cpwiz::identdata::person_p
 Cpwiz::util::Image::PointStruct for holding pixel coordinates
 Cralab::base::resample::PPMCompFunctor< TReal >TODO Do checking on TReal thats a real
 CprecursorGroup
 Cpwiz::analysis::PrecursorRecalculator::PrecursorInfo
 Cpwiz::msdata::SpectrumInfo::PrecursorInfoStructure for Precursor info
 Cpwiz::analysis::SpectrumList_PrecursorRefine::PrecursorInfo
 Cpwiz::analysis::PrecursorRecalculator
 Cpwiz::analysis::ProteinList_DecoyGenerator::PredicateClient-implemented generator predicate – called during construction of ProteinList_DecoyGenerator to create a decoy protein from a target protein
 Cpwiz::analysis::ProteinList_Filter::PredicateClient-implemented filter predicate – called during construction of ProteinList_Filter to create the filtered list of proteins
 Cpwiz::analysis::SpectrumList_Filter::PredicateClient-implemented filter predicate – called during construction of SpectrumList_Filter to create the filtered list of spectra
 Cpwiz::analysis::SpectrumList_Sorter::PredicateClient-implemented sort predicate – called during construction of SpectrumList_Sorter to sort the underlying spectrum list
 CPrintAttribute
 Cpwiz::msdata::ProductProduct ion information
 Cpwiz::math::MatchedFilter::ProductSpace< X, Y >
 Cpwiz::analysis::MSDataAnalyzerDriver::ProgressCallbackProgress callback interface
 Cpwiz::proteome::ProteinList
 Cpwiz::analysis::ProteinListFactoryFactory for instantiating and wrapping ProteinLists
 Cpwiz::proteome::ProteomeData
 Cpwiz::data::pepxml::Q3RatioResult
 CRawMassDatum
 Cpwiz::msdata::ReaderInterface for file readers
 Cpwiz::proteome::ReaderInterface for file readers
 Cpwiz::tradata::ReaderInterface for file readers
 Cpwiz::identdata::ReaderInterface for file readers
 CReader1::ReaderConfig
 CReader2::ReaderConfig
 Cpwiz::proteome::AminoAcid::Info::RecordStruct for holding data for a single amino acid
 Cpwiz::chemistry::Element::Info::Record
 Cpwiz::utility::MSIHandler::Record
 Cpwiz::analysis::PepxmlRecordReader::record
 Cpwiz::proteome::IPIFASTADatabase::RecordStructure for holding peptide info
 Cpwiz::peptideid::PeptideID::Record
 Cpwiz::identdata::ResidueImplementation of ResidueType from the mzIdentML schema
 CridgeLine
 Cpwiz::data::pepxml::RocDataPoint
 CRoot
 CrtimeMap
 Cpwiz::analysis::RTMatches_Any< T >Predicate always returns true
 Cpwiz::analysis::RTMatches_Contains< T >Predicate returns true iff the object's retention time range contains the specified retention time
 Cpwiz::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
 Cpwiz::data::diff_impl::Same< object_type, config_type >
 Cpwiz::data::diff_impl::SameDeep< object_type, config_type >
 Cpwiz::data::SampleDatum< abscissa_type, ordinate_type >
 Cpwiz::math::MatchedFilter::SampledData< space_type >
 Cpwiz::data::pepxml::SampleEnzyme
 Cralab::base::resample::SamplingWith
 Cpwiz::minimxml::SAXParser::saxstring
 Cpwiz::data::peakdata::Scan
 Cpwiz::msdata::ScanSettingsDescription of the acquisition settings of the instrument prior to the start of the run
 Cpwiz::frequency::PeakDetectorMatchedFilter::ScoreStructure for holding the matched filter calculation results
 CscoreChain
 Cpwiz::data::pepxml::SearchDatabase
 Cpwiz::data::pepxml::SearchHit
 Cpwiz::data::pepxml::SearchResult
 Cpwiz::data::pepxml::SearchSummaryDatabase search settings
 CSecond
 Cpwiz::identdata::seq_p
 Cralab::base::base::utilities::SeqMinus< TReal >
 Cralab::base::base::utilities::SeqPlus< TReal >
 Cpwiz::identdata::sequence_p
 Cpwiz::identdata::SequenceCollectionImplementation of SequenceCollectionType from the mzIdentML schema
 Cpwiz::proteome::Serializer_FASTAProteomeData <-> FASTA stream serialization
 Cpwiz::msdata::Serializer_MGFMSData <-> MGF stream serialization
 Cpwiz::msdata::Serializer_MSnMSData <-> MSn stream serialization
 Cpwiz::identdata::Serializer_mzIdentMLMZIDData <-> mzIdentML stream serialization
 Cpwiz::msdata::Serializer_mzMLMSData <-> mzML stream serialization
 Cpwiz::msdata::Serializer_mzXMLMSData <-> mzXML stream serialization
 Cpwiz::identdata::Serializer_pepXMLMZIDData <-> pepXML stream serialization
 Cpwiz::identdata::Serializer_protXMLMZIDData <-> pepXML stream serialization
 Cpwiz::identdata::Serializer_TextSerializer_Text reads in and writes out an id file in tab format
 Cpwiz::tradata::Serializer_traMLTraData <-> traML stream serialization
 Cstd::set< K >STL class
 CSetRetentionTime
 CSHA1_WORKSPACE_BLOCK
 Cpwiz::util::SHA1Calculator
 Cpwiz::util::SHA1SymmetricFilterModel of boost::iostreams::SymmetricFilter
 Cpwiz::util::shared_map< keyT, valueT, _Pr, _Alloc >Copy semantics of shared_ptr<map<K,V> > with a std::map interface
 Cpwiz::msdata::SpectrumIterator::SieveInterface for filtering based on ScanInfo
 CSimple
 Cralab::base::ms::SimplePeakArea< TReal >Resamples spectrum, apply smoothing, determines zero crossings, integrates peaks
 Cralab::base::ms::SimplePicker< TReal >
 Cpwiz::analysis::SmootherInterface for a one-dimensional smoothing algorithm
 Cpwiz::data::peakdata::Software
 Cpwiz::identdata::software_p
 Cpwiz::data::pepxml::Specificity
 Cpwiz::analysis::SpectrumDataFilter
 Cpwiz::msdata::SpectrumIdentityIdentifying information for a spectrum
 Cpwiz::msdata::SpectrumInfoSimple structure for holding Spectrum info
 Cpwiz::msdata::SpectrumIteratorSpectrumIterator provides convenient iteration through a set of scans in a SpectrumList
 Cpwiz::msdata::SpectrumListInterface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML)
 Cpwiz::analysis::SpectrumListFactoryFactory for instantiating and wrapping SpectrumLists
 CSpectrumListWrapper
 Cpwiz::data::pepxml::SpectrumQuery
 Cpwiz::analysis::RegionAnalyzer::SpectrumStats
 Cpwiz::msdata::SpectrumWorkerThreads
 Cralab::base::resample::SquareRoot< TReal >
 Cpwiz::analysis::RegionAnalyzer::Stats
 Cpwiz::math::Stats
 Cpwiz::minimxml::SAXParser::Handler::StatusHandler returns the Status struct as a means of changing the parser's behavior
 Cpwiz::identdata::SubstitutionModificationImplementation of SubstitutionModificationType from the mzIdentML schema
 Csymmetric_filter
 Cpwiz::utility::TabHandler
 Cpwiz::utility::TabReader
 Cpwiz::analysis::TabularConfig
 Cpwiz::data::TermSingle controlled vocabulary term
 CTestAminoAcid
 CTestChargeStateCalculator
 CTestData
 CTestDatum
 CTestDeisotopeCalculator
 CTestDeisotoper
 CTestETDMassFilter
 CTestFormula
 CTestFragmentation
 CTestInfo
 CTestMetadataFixer
 CTestModification
 CTestModifiedPeptide
 CTestMS2Denoise
 CTestOperator
 CTestPair
 CTestPathmask
 Cpwiz::util::TestPathPredicateTest implementations derive from this to define which paths should be tested
 CTestPeptide
 CTestScanSummerCalculator
 CTestSpectrumInfo
 CTestThresholder
 Cpwiz::identdata::TextWriter
 Cpwiz::msdata::TextWriter
 Cpwiz::proteome::TextWriter
 Cpwiz::tradata::TextWriter
 CThreadStatus
 Cpwiz::msdata::TimeIntensityPairThe data point type of a chromatogram
 Cpwiz::util::Timer
 Cpwiz::tradata::TraData
 Cpwiz::frequency::TruncatedLorentzianEstimator
 Cpwiz::frequency::TruncatedLorentzianParametersStruct for holding parameters for a Truncated Lorentzian function
 Cunary_function
 Cpwiz::util::IterationListener::UpdateMessage
 Cpwiz::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
 Cstd::vector< T >STL class
 Cpwiz::frequency::DerivativeTest::VectorFunction< value_type >
 Cpwiz::frequency::DerivativeTest::VectorFunction< double >
 Cpwiz::proteome::Version
 Cpwiz::analysis::Version
 Cpwiz::Version
 Cpwiz::msdata::Version
 Cpwiz::identdata::Version
 Cpwiz::tradata::Version
 Cpwiz::util::virtual_map< keyT, valueT, _Pr, _Alloc >Wrapper for std::map that will behave properly with polymorphism
 Cpwiz::util::virtual_map< int, ModificationList >
 Cpwiz::identdata::IdentDataFile::WriteConfigConfiguration for write()
 Cpwiz::proteome::ProteomeDataFile::WriteConfigConfiguration for write()
 Cpwiz::tradata::TraDataFile::WriteConfigConfiguration for write()
 Cpwiz::msdata::MSDataFile::WriteConfigConfiguration for write()
 CWriteCVParam
 Cpwiz::minimxml::XMLWriterSimple, tag-level XML syntax writing
 Cpwiz::analysis::ZeroSampleFillerFills in missing zero samples around signal profiles