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::msdata::SpectrumListCache::CacheEntryCache mapping spectrum indices to SpectrumPtrs
 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::analysis::PrecursorMassFilter::ConfigPrecursorMassFilter's parameters
 Cpwiz::msdata::Reader::ConfigReader configuration
 Cpwiz::analysis::PrecursorRecalculatorDefault::Config
 Cpwiz::msdata::Serializer_mzML::ConfigSerializer_mzML configuration
 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::analysis::FeatureDetectorPeakel::ConfigConvenience construction
 Cpwiz::identdata::Reader::ConfigHACK: provide an option to read only file-level metadata; once we have an enumerable ResultList implementation this will be deprecated
 CReader1::Config
 CReader2::Config
 Cpwiz::identdata::Serializer_mzIdentML::ConfigSerializer_mzIdentML configuration
 Cpwiz::identdata::Serializer_pepXML::ConfigSerializer_pepXML configuration
 Cpwiz::identdata::Serializer_Text::Config< Controls the format of the text file
 Cpwiz::identdata::Serializer_protXML::ConfigSerializer_protXML configuration
 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::analysis::PeakFitter_Parabola::Config
 Cpwiz::msdata::BinaryDataEncoder::ConfigEncoding/decoding configuration
 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< CacheEntry, BOOST_MULTI_INDEX_MEMBER(CacheEntry, size_t, index) >
 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::analysis::PepxmlRecordReader::record
 Cpwiz::chemistry::Element::Info::Record
 Cpwiz::util::MSIHandler::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::math::Stats
 Cpwiz::analysis::RegionAnalyzer::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::util::TabHandler
 Cpwiz::util::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::tradata::TextWriter
 Cpwiz::proteome::TextWriter
 Cpwiz::msdata::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
 CUserParamNameIs
 Cstd::vector< T >STL class
 Cpwiz::frequency::DerivativeTest::VectorFunction< value_type >
 Cpwiz::frequency::DerivativeTest::VectorFunction< double >
 Cpwiz::msdata::Version
 Cpwiz::analysis::Version
 Cpwiz::identdata::Version
 Cpwiz::Version
 Cpwiz::tradata::Version
 Cpwiz::proteome::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::tradata::TraDataFile::WriteConfigConfiguration for write()
 Cpwiz::identdata::IdentDataFile::WriteConfigConfiguration for write()
 Cpwiz::proteome::ProteomeDataFile::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