Here are the classes, structs, unions and interfaces with brief descriptions:
[detail level 123456]
  @44 | |
| @464 | |
 boost | |
  date_time | |
| assign | |
| lambda | |
| logic | |
| ublas | |
| eharmony | |
| pwiz | AMTContainer.hpp |
| calibration | |
 Calibrator | Calibrates using EM algorithm using peptide mass database |
| Measurement | Structure for holding frequency-charge pairs |
| CalibratorLog | |
| CalibratorTrial | |
| Configuration | |
| Results | |
| State | |
| ErrorEstimator | |
| LeastSquaresCalibrator | |
| MassDatabase | |
| Entry | |
 MassSpread | |
 Pair | |
| msaux | |
| Path | |
| proteome | |
| AminoAcid | Scope for types related to amino acids |
| Info | Class for accessing information about the amino acids |
| Record | Struct for holding data for a single amino acid |
| examples | |
| PeptideDatabaseFormula | |
| PeptideDatabaseRecord | |
| PeptideDatabase | |
| DefaultReaderList | Default Reader list |
| DiffConfig | Configuration struct for diffs |
| DigestedPeptide | Peptide subclass that contains extra metadata provided by digestion |
| Digestion | Enumerates the peptides from proteolytic digestion of a polypeptide or protein; |
| Config | Sets constraints for valid peptides produced by iterating the digestion |
| const_iterator | Forward-only, read-only iteration to enumerate peptides |
| Modification | Post-translational modification (PTM) modification formula or masses must be provided at instantiation |
| ModificationList | List of modifications on a single amino acid |
| ModificationMap | Maps peptide/protein sequence indexes (0-based) to a modification list |
| Peptide | Peptide or polypeptide (a sequence of amino acids) |
| Fragmentation | Fragment ion masses for a peptide |
| ProteinListCache | Adds a level of flexible MRU caching to a ProteinList processor chain |
| ProteinListWrapper | Inheritable pass-through implementation for wrapping a ProteinList |
| Protein | |
| IndexList | |
| ProteinList | |
| ProteinListSimple | |
| ProteomeData | |
| ProteomeDataFile | ProteomeData object plus file I/O |
| WriteConfig | Configuration for write() |
| Reader | Interface for file readers |
| ReaderFail | |
| ReaderList | Reader container (composite pattern) |
| Reader_FASTA | FASTA -> ProteomeData stream serialization |
| Config | Reader_FASTA configuration |
| Serializer_FASTA | ProteomeData <-> FASTA stream serialization |
| Config | Serializer_FASTA configuration |
| TextWriter | |
| Version | |
| IPIFASTADatabase | Class for accessing data in ipi.*.fasta files |
| Record | Structure for holding peptide info |
| math | |
| MatchedFilter | |
| @406 | |
| details | |
| ProductSpace | |
| SampledData | |
| KernelTraitsBase | |
| KernelTraitsBase< Y(*)(X)> | |
| Correlation | |
| KernelTraits | |
| types | |
| Random | |
| LinearLeastSquares< LinearLeastSquaresType_LU > | |
| LinearLeastSquares< LinearLeastSquaresType_QR > | |
| LinearSolver< LinearSolverType_LU > | |
| LinearSolver< LinearSolverType_QR > | |
| OrderedPair | |
| OrderedPairContainerRef | Wrapper class for accessing contiguous data as a container of OrderedPairs; note that it does not own the underlying data |
| Parabola | |
| Stats | |
| analysis | |
| @117 | |
| ChromatogramList_SavitzkyGolaySmoother | ChromatogramList implementation to return native centroided chromatogram data |
| ChromatogramListWrapper | Inheritable pass-through implementation for wrapping a ChromatogramList |
| SavitzkyGolaySmoother | |
| SpectrumDataFilter | |
| ChromatogramDataFilter | |
| 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 |
| LocalMaximumPeakDetector | |
| Peak | Some generic metadata about a peak detected in a signal |
| PeakDetector | |
| Smoother | Interface for a one-dimensional smoothing algorithm |
| WhittakerSmoother | |
| ZeroSampleFiller | Fills in missing zero samples around signal profiles |
| MetadataReporter | Writes file-level metadata to a file |
| analyzer_strings< MetadataReporter > | |
| MSDataAnalyzer | Interface for MSData analyzers |
| DataInfo | Information about the data to be analyzed |
| analyzer_strings | This auxilliary class should be specialized for MSDataAnalyzers whose instantiation is controlled by user-supplied strings (via command line, config file, etc.) |
| MSDataAnalyzerContainer | Container of MSDataAnalyzer (composite pattern) |
| MSDataAnalyzerDriver | Event generator for MSDataAnalyzer |
| ProgressCallback | Progress callback interface |
| MSDataCache | Simple memory cache for common MSData info |
| Config | MSDataCache configuration |
| PepxmlRecordReader | |
| Config | |
| record | |
| Pseudo2DGel | Creates pseudo-2D-gel images from survey scan data |
| Config | Holds the configuration for an instance of Pseudo2DGel |
| analyzer_strings< Pseudo2DGel > | |
| RegionAnalyzer | Analyzes a rectangular region of m/z-time space |
| Config | |
| SpectrumStats | |
| Stats | |
| RegionSIC | Writes data samples from a single rectangular region |
| Config | |
| analyzer_strings< RegionSIC > | |
| RegionSlice | Writes data samples from a single rectangular region |
| Config | |
| analyzer_strings< RegionSlice > | |
| RegionTIC | Writes data samples from a single rectangular region |
| Config | |
| analyzer_strings< RegionTIC > | |
| RunSummary | Writes table of spectrum metadata to a file |
| Config | |
| analyzer_strings< RunSummary > | |
| SpectrumBinaryData | Writes table of spectrum metadata to a file |
| Config | |
| analyzer_strings< SpectrumBinaryData > | |
| SpectrumTable | Writes table of spectrum metadata to a file |
| Config | |
| analyzer_strings< SpectrumTable > | |
| TabularConfig | |
| FeatureDetector | |
| FeatureDetectorPeakel | FeatureDetectorPeakel implements a 'template method', delegating to 'strategies' encapsulated by the following interfaces: PeakExtractor PeakelGrower PeakelPicker |
| Config | Convenience construction |
| FeatureDetectorSimple | FeatureDetectorSimple detects 'rectangular' features, ie number of peaks in isotope envelope is the same for each scan included in the feature |
| FeatureModeler | Interface for fitting and scoring Feature data to a model |
| FeatureModeler_Gaussian | Gaussian implementation |
| MZRTField | MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT |
| RTMatches_Any | Predicate always returns true |
| RTMatches_Contains | Predicate returns true iff the object's retention time range contains the specified retention time |
| RTMatches_IsContainedIn | 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 |
| Noise | |
| NoiseCalculator | |
| NoiseCalculator_2Pass | |
| Config | |
| PeakelGrower | Interface for growing Peakels |
| PeakelGrower_Proximity | Simple PeakelGrower implementation, based on proximity of Peaks |
| Config | |
| PeakelPicker | Interface for picking Peakels and arranging into Features; note: Peakels are actually removed from the PeakelField |
| PeakelPicker_Basic | Basic implementation |
| Config | |
| 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" |
| PeakFamilyDetector | Interface for peak family (isotope envelope) detection |
| PeakFamilyDetectorFT | FT-specific implementation of PeakFamilyDetector |
| Config | |
| NoDataException | FT-specific exception |
| PeakFinder | Interface for finding peaks in an array of ordered pairs |
| PeakFinder_SNR | PeakFinder implementation based on signal-to-noise ratio |
| Config | |
| PeakFitter | Interface for fitting peaks in an array of ordered pairs |
| PeakFitter_Parabola | PeakFitter implementation based on fitting a parabola |
| Config | |
| ProteinList_DecoyGenerator | ProteinList decoy generator for creating decoy proteins on the fly |
| Predicate | Client-implemented generator predicate – called during construction of ProteinList_DecoyGenerator to create a decoy protein from a target protein |
| ProteinList_DecoyGeneratorPredicate_Reversed | Creates a reversed copy of every target protein with the specified decoy string prefixed to the id |
| ProteinList_DecoyGeneratorPredicate_Shuffled | Creates a randomly shuffled copy of every target protein with the specified decoy string prefixed to the id |
| ProteinList_Filter | ProteinList filter, for creating Protein sub-lists |
| Predicate | Client-implemented filter predicate – called during construction of ProteinList_Filter to create the filtered list of proteins |
| ProteinList_FilterPredicate_IndexSet | |
| ProteinList_FilterPredicate_IdSet | |
| ProteinListFactory | Factory for instantiating and wrapping ProteinLists |
| MS2Deisotoper | |
| Config | PrecursorMassFilter's parameters |
| MS2NoiseFilter | |
| Config | MS2NoiseFilter's parameters |
| PrecursorMassFilter | |
| Config | PrecursorMassFilter's parameters |
| PrecursorRecalculator | |
| PrecursorInfo | |
| PrecursorRecalculatorDefault | |
| Config | |
| SpectrumList_ChargeStateCalculator | SpectrumList implementation that assigns (probable) charge states to tandem mass spectra |
| SpectrumList_Filter | SpectrumList filter, for creating Spectrum sub-lists |
| Predicate | Client-implemented filter predicate – called during construction of SpectrumList_Filter to create the filtered list of spectra |
| SpectrumList_FilterPredicate_IndexSet | |
| SpectrumList_FilterPredicate_ScanNumberSet | |
| SpectrumList_FilterPredicate_ScanEventSet | |
| SpectrumList_FilterPredicate_ScanTimeRange | |
| SpectrumList_FilterPredicate_MSLevelSet | |
| SpectrumList_FilterPredicate_PrecursorMzSet | |
| SpectrumList_FilterPredicate_DefaultArrayLengthSet | |
| SpectrumList_FilterPredicate_ActivationType | |
| SpectrumList_FilterPredicate_AnalyzerType | |
| SpectrumList_FilterPredicate_Polarity | |
| SpectrumList_MetadataFixer | SpectrumList implementation to add (or replace) base peak and total ion metadata with new values calculated from the current binary data |
| SpectrumList_MZWindow | SpectrumList filter, for creating Spectrum sub-lists |
| SpectrumList_PeakFilter | SpectrumList implementation that returns spectra with the specified SpectrumDataFilter operation applied |
| SpectrumList_PeakPicker | SpectrumList implementation to replace peak profiles with picked peaks |
| SpectrumList_PrecursorRecalculator | SpectrumList wrapper that recalculates precursor info on spectrum() requests |
| SpectrumList_PrecursorRefine | SpectrumList wrapper that recalculates precursor info on spectrum() requests |
| PrecursorInfo | |
| SpectrumList_Smoother | SpectrumList implementation to return smoothed spectral data |
| SpectrumList_Sorter | Provides a custom-sorted spectrum list |
| Predicate | Client-implemented sort predicate – called during construction of SpectrumList_Sorter to sort the underlying spectrum list |
| SpectrumList_SorterPredicate_ScanStartTime | |
| SpectrumList_TitleMaker | SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user-specified format |
| SpectrumList_ZeroSamplesFilter | SpectrumList implementation to return spectra with or without extra zero samples |
| SpectrumListFactory | Factory for instantiating and wrapping SpectrumLists |
| ThresholdFilter | |
| Version | |
| eharmony | |
| AMTContainer | |
| AMTDatabase | |
| IslandizedDatabase | |
| Gaussian | |
| Island | |
| DatabaseQuery | |
| DataFetcherContainer | |
| DistanceAttribute | |
| NumberOfMS2IDs | |
| RandomDistance | |
| RTDiffDistribution | |
| HammingDistance | |
| WeightedHammingDistance | |
| EditDistance | |
| Exporter | |
| Feature2PeptideMatcher | |
| Feature_dataFetcher | |
| FeatureSequenced | |
| Matcher | |
| KeyLessThan | |
| Matrix | |
| Observation | |
| ModificationStateEntry | |
| PeptideEntry | |
| MSIAMTData | |
| NeighborJoiner | |
| PeptideID_dataFetcher | |
| PeptideMatcher | |
| SearchNeighborhoodCalculator | |
| NormalDistributionSearch | |
| WarpFunction | |
| LinearWarpFunction | |
| PiecewiseLinearWarpFunction | |
| SplineWarpFunction | |
| frequency | |
| DerivativeTest | |
| VectorFunction | |
| ParametrizedFunctionSlice | |
| ParametrizedDerivativeSlice | |
| AdaptedErrorFunction | |
| AdaptedErrorDerivative | |
| FrequencyEstimator | Interface for frequency estimator modules |
| FrequencyEstimatorPhysicalModel | Physical model implementation of the FrequencyEstimator interface |
| Config | |
| FrequencyEstimatorSimple | Simple implementation of the FrequencyEstimator interface |
| MagnitudeLorentzian | |
| ParameterEstimator | |
| ParametrizedFunction | |
| ErrorFunction | |
| PeakDetector | Interface for finding peaks in frequency data |
| PeakDetectorMatchedFilter | MatchedFilter implementation of the PeakDetector interface |
| Config | Structure for holding configuration |
| Score | Structure for holding the matched filter calculation results |
| PeakDetectorNaive | Naive implementation of the PeakDetector interface |
| TruncatedLorentzian | |
| TruncatedLorentzianEstimator | |
| TruncatedLorentzianParameters | Struct for holding parameters for a Truncated Lorentzian function |
| peptideid | |
| PeptideID | This is an interface for classes that allow access to data sources of identified peptides |
| Iterator | Iterator for |
| IteratorInternal | Interface for |
| Location | |
| Record | |
| nativeID_less | |
| location_less | |
| FlatRecordBuilder | |
| MSInspectRecordBuilder | |
| PeptideID_flat | This class allows access to peptides listed in a flat tab delimited text file |
| PeptideID_pepXml | This class allows access to identified proteins in PeptideProphet files |
| PeptideIDMap | |
| data | |
| diff_impl | |
| HasID | |
| Same | |
| SameDeep | |
| unimod | |
| pepxml | |
| Specificity | |
| SampleEnzyme | |
| SearchDatabase | |
| Q3RatioResult | |
| RocDataPoint | |
| ErrorPoint | |
| DistributionPoint | |
| MixtureModel | |
| PeptideProphetSummary | |
| PeptideProphetResult | |
| AnalysisResult | |
| AlternativeProtein | |
| ModAminoAcidMass | |
| ModificationInfo | |
| Parameter | |
| SearchScore | |
| SearchHit | |
| SearchResult | |
| EnzymaticSearchConstraint | |
| AminoAcidModification | |
| SearchSummary | Database search settings |
| AnalysisTimestamp | Reference for analysis applied to current run (time corresponds with analysis_summary/, id corresponds with analysis_result/) |
| SpectrumQuery | |
| MSMSRunSummary | |
| AnalysisSummary | |
| DataFilter | |
| DatasetDerivation | Source and filtering criteria used to generate dataset |
| MSMSPipelineAnalysis | |
| Match | |
| MatchData | |
| peakdata | |
| Peak | |
| HandlerPeak | |
| PeakFamily | |
| Scan | |
| Software | |
| Parameter | |
| PeakData | |
| Peakel | Struct for an eluted peak (PEAK ELution) |
| HandlerPeakel | |
| Feature | |
| HandlerFeature | |
| FeatureFile | |
| SampleDatumConstant | |
| 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 |
| CVTranslator | Translates text to CV terms |
| BaseDiffConfig | |
| Diff | Calculate diffs of objects in a ProteoWizard data model hierarchy |
| Index | Generic interface for creating and using an index on a stream of serialized objects |
| Entry | Generic type identifying an indexed item by string id, ordinal index, and stream offset |
| 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) |
| Term | Single controlled vocabulary term |
| OBO | Represents a selectively parsed OBO file |
| CVParam | Tag-value pair, where the tag comes from the controlled vocabulary |
| CVParamIs | Functor for finding CVParam with specified exact CVID in a collection of CVParams: |
| CVParamIsChildOf | Functor for finding children of a specified CVID in a collection of CVParams: |
| 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 |
| ParamContainer | The base class for elements that may contain cvParams, userParams, or paramGroup references |
| 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 |
| CalibrationParameters | |
| FrequencyData | Class for binary storage of complex frequency data |
| SampleDatum | |
| cv | |
| CV | Information about an ontology or CV source and a short 'lookup' tag to refer to |
| CVTermInfo | Structure for holding CV term info |
| identdata | |
| examples | |
| IO | |
| References | Functions for resolving references from objects into the internal MSData lists |
| DefaultReaderList | Default Reader list |
| DelimReader | |
| DelimWriter | |
| DiffConfig | |
| Identifiable | Parent class representing extensions of the IdentifiableType from the mzIdentML schema |
| IdentifiableParamContainer | Parent class of all Identifiable objects that have ParamGroups |
| BibliographicReference | Implementation for the BibliographicReferenceType tag in the mzIdentML schema |
| Contact | Implementation of ContactType from mzIdentML |
| Organization | Implementation of AbstractOrganizationType from the mzIdentML schema |
| Person | Implementation of PersonType from the mzIdentML schema |
| ContactRole | Implementation of ContactRoleType from the mzIdentML schema |
| Sample | Implementation of the SampleType from the mzIdentML schema |
| AnalysisSoftware | Implementation of AnalysisSoftwareType from the mzIdentML schema |
| Provider | Implementation of ProviderType from the mzIdentML schema |
| AnalysisSampleCollection | Implementation of AnalysisSampleCollectionType from mzIdentML schema |
| SearchDatabase | Implementation of SearchDatabaseType from the mzIdentML schema |
| DBSequence | Implementation of DBSequenceType from the mzIdentML schema |
| Modification | Implementation of ModificationType from the mzIdentML schema |
| SubstitutionModification | Implementation of SubstitutionModificationType from the mzIdentML schema |
| Peptide | Implementation of PeptideType from the mzIdentML schema |
| SearchModification | Implementation of SearchModificationType from the mzIdentML schema |
| Enzyme | Implementation of EnzymeType from the mzIdentML schema |
| Enzymes | Implementation of EnzymesType from the mzIdentML schema |
| Residue | Implementation of ResidueType from the mzIdentML schema |
| AmbiguousResidue | Implementation of AmbiguousResidueType from the mzIdentML schema |
| MassTable | Implementation of MassTableType from the mzIdentML schema |
| Filter | Implementation of FilterType from the mzIdentML schema |
| TranslationTable | Implementation of TranslationTableType from the mzIdentML schema |
| DatabaseTranslation | Implementation of DatabaseTranslationType from the mzIdentML schema |
| SpectrumIdentificationProtocol | Implementation of SpectrumIdentificationProtocolType from the mzIdentML schema |
| Measure | Implementation of MeasureType from the mzIdentML schema |
| FragmentArray | Implementation of FragmentArrayType from the mzIdentML schema |
| IonType | Implementation of IonTypeType from the mzIdentML schema |
| PeptideEvidence | Implementation of PeptideEvidenceType from the mzIdentML schema |
| SequenceCollection | Implementation of SequenceCollectionType from the mzIdentML schema |
| SpectrumIdentificationItem | Implementation of SpectrumIdentificationItemType from the mzIdentML schema |
| SpectraData | Implementation of SpectraDataType from the mzIdentML schema |
| SpectrumIdentificationResult | Implementation of SpectrumIdentificationResultType from the mzIdentML schema |
| SpectrumIdentificationList | Implementation of SpectrumIdentificationListType from the mzIdentML schema |
| SpectrumIdentification | Implementation of SpectrumIdentificationType from the mzIdentML schema |
| ProteinDetectionProtocol | Implementation of ProteinDetectionProtocolType from the mzIdentML schema |
| PeptideHypothesis | Implementation of PeptideHypothesisType from the mzIdentML schema |
| ProteinDetectionHypothesis | Implementation of ProteinDetectionHypothesisType from the mzIdentML schema |
| ProteinAmbiguityGroup | Implementation of ProteinAmbiguityGroupType from the mzIdentML schema |
| ProteinDetectionList | Implementation of ProteinDetectionListType from the mzIdentML schema |
| ProteinDetection | Implementation of ProteinDetectionType from the mzIdentML schema |
| AnalysisCollection | Implementation of AnalysisCollectionType from the mzIdentML schema |
| AnalysisProtocolCollection | Implementation of AnalysisProtocolCollectionType from the mzIdentML schema |
| SourceFile | Implementation of SourceFileType from the mzIdentML schema |
| Inputs | Implementation of the InputsType from the mzIdentML schema |
| AnalysisData | Implementation of AnalysisDataType from the mzIdentML schema |
| DataCollection | Implementation of DataCollectionType from the mzIdentML schema |
| IdentData | Implementation of the MzIdentMLType from the mzIdentML schema |
| IdentDataFile | IdentData object plus file I/O |
| WriteConfig | Configuration for write() |
| CVMap | |
| RegexCVMap | |
| StringMatchCVMap | |
| CVIDMatchCVMap | |
| MascotReader | |
| id_p | |
| software_p | |
| sequence_p | |
| seq_p | |
| dbsequence_p | |
| organization_p | |
| person_p | |
| Pep2MzIdent | Translates data from a MinimumPepXML object into a IdentData object tree when a translation is known |
| Reader | Interface for file readers |
| Config | HACK: provide an option to read only file-level metadata; once we have an enumerable ResultList implementation this will be deprecated |
| ReaderFail | |
| ReaderList | Reader container (composite pattern) |
| Serializer_mzIdentML | MZIDData <-> mzIdentML stream serialization |
| Config | Serializer_mzIdentML configuration |
| Serializer_pepXML | MZIDData <-> pepXML stream serialization |
| Config | Serializer_pepXML configuration |
| PepXMLSpecificity | |
| Serializer_protXML | MZIDData <-> pepXML stream serialization |
| Config | Serializer_protXML configuration |
| Serializer_Text | Serializer_Text reads in and writes out an id file in tab format |
| Config | < Controls the format of the text file |
| TextWriter | |
| Version | |
| msdata | |
| examples | |
| IO | |
| id | |
| mz5 | |
| Configuration_mz5 | Configuration class for mz5 im- and export |
| Connection_mz5 | This class is used for reading and writing information to a mz5 file |
| FileInformationMZ5Data | General mz5 file information |
| FileInformationMZ5 | |
| ContVocabMZ5Data | |
| ContVocabMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#cv |
| CVRefMZ5Data | |
| CVRefMZ5 | This class will be referenced from CVParamMZ5 and UserParamMZ5 to reduce storage size |
| UserParamMZ5Data | |
| UserParamMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#userParam |
| CVParamMZ5Data | |
| CVParamMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#cvParam |
| RefMZ5Data | |
| RefMZ5 | Is used as a general reference for different tags |
| RefListMZ5Data | |
| RefListMZ5 | Variable length list of references |
| ParamListMZ5Data | |
| ParamListMZ5 | This class represents a pwiz::msdata::ParamContainer but only stores start and end indices for CVParams, UserParams and ParamGroups |
| ParamGroupMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#referenceableParamGroup |
| SourceFileMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#sourceFile |
| SampleMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#sample |
| SoftwareMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#software |
| ParamListsMZ5 | This class is used as a generalized container for Targets, SelectedIons, Products and ScanWindows |
| ScanSettingMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#scanSettings |
| 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 |
| ComponentListMZ5 | List of components |
| ComponentsMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#componentList |
| InstrumentConfigurationMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#instrumentConfiguration |
| ProcessingMethodMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#processingMethod |
| ProcessingMethodListMZ5 | Variable length processing method list |
| DataProcessingMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#dataProcessing |
| PrecursorMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#precursor |
| PrecursorListMZ5 | Variable length precursor list |
| ChromatogramMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#chromatogram but without binary data element |
| ScanMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#scan |
| ScanListMZ5 | Variable length scan list |
| ScansMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.htmlscanList |
| SpectrumMZ5 | *http://www.peptideatlas.org/tmp/mzML1.1.0.html#spectrum but without binary data elements |
| RunMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#run but without spectrum and chromatogram elements |
| BinaryDataMZ5 | Http://www.peptideatlas.org/tmp/mzML1.1.0.html#binaryDataArray but without raw data |
| ReferenceRead_mz5 | This class is a helper class to read and convert a mz5 file to a MSData object |
| ReferenceWrite_mz5 | This class is a helper class for converting and writing mz5 files in mz5 format |
| Translator_mz5 | Helper class to translate mz values |
| References | Functions for resolving references from objects into the internal MSData lists |
| detail | |
| ChromatogramList_ABI | |
| SpectrumList_ABI | |
| SpectrumList_ABI_T2D | |
| ChromatogramList_Agilent | |
| SpectrumList_Agilent | |
| ChromatogramList_Bruker | |
| SpectrumList_Bruker | |
| ChromatogramList_Thermo | |
| SpectrumList_Thermo | |
| ChromatogramList_Waters | |
| SpectrumList_Waters | |
| BinaryDataEncoder | Binary-to-text encoding |
| Config | Encoding/decoding configuration |
| ChromatogramList_mz5 | Implementation of ChromatogramList, backed by an mz5 file |
| ChromatogramList_mzML | Implementation of ChromatogramList, backed by an mzML file |
| ChromatogramListBase | Common functionality for base ChromatogramList implementations |
| Reader_mzML | |
| Reader_mzXML | |
| Reader_MGF | |
| Reader_MSn | |
| Reader_BTDX | |
| Reader_mz5 | |
| DefaultReaderList | Default Reader list |
| DiffConfig | Configuration struct for diffing MSData types |
| Index_mzML | |
| SpectrumIdentityFromXML | Identifying information for a spectrum subclassed to add private information for faster file IO in mzML and mzXML |
| SpectrumIdentityFromMzXML | Identifying information for a spectrum as read from mzML or mzXML subclassed to add private information for faster file IO in mzXML |
| LegacyAdapter_Instrument | Interface for legacy access to Instrument |
| LegacyAdapter_Software | Interface for legacy access to Software |
| MemoryMRUCache | MRU cache for SpectrumPtrs or ChromatogramPtrs |
| 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 |
| SourceFile | Description of the source file, including location and type |
| 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) |
| FileDescription | Information pertaining to the entire mzML file (i.e. not specific to any part of the data set) is stored here |
| Sample | Expansible description of the sample used to generate the dataset, named in sampleName |
| 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) |
| 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 |
| Software | A piece of software |
| Target | TODO |
| ScanSettings | Description of the acquisition settings of the instrument prior to the start of the run |
| 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 |
| 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 |
| DataProcessing | Description of the way in which a particular software was used |
| IsolationWindow | This element captures the isolation (or 'selection') window configured to isolate one or more precursors |
| SelectedIon | TODO |
| Activation | The type and energy level used for activation |
| Precursor | The method of precursor ion selection and activation |
| Product | Product ion information |
| ScanWindow | TODO |
| Scan | Scan or acquisition from original raw file used to create this peak list, as specified in sourceFile |
| ScanList | List and descriptions of scans |
| 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 |
| MZIntensityPair | The data point type of a mass spectrum |
| TimeIntensityPair | The data point type of a chromatogram |
| SpectrumIdentity | Identifying information for a spectrum |
| ChromatogramIdentity | Identifying information for a chromatogram |
| Spectrum | The structure that captures the generation of a peak list (including the underlying acquisitions) |
| Chromatogram | A single chromatogram |
| IndexList | |
| SpectrumList | Interface for accessing spectra, which may be stored in memory or backed by a data file (RAW, mzXML, mzML) |
| SpectrumListSimple | Simple writeable in-memory implementation of SpectrumList |
| ChromatogramList | Interface for accessing chromatograms, which may be stored in memory or backed by a data file (RAW, mzXML, mzML) |
| ChromatogramListSimple | Simple writeable in-memory implementation of ChromatogramList |
| Run | A run in mzML should correspond to a single, consecutive and coherent set of scans on an instrument |
| 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) |
| MSDataFile | MSData object plus file I/O |
| WriteConfig | Configuration for write() |
| MSDataMerger | |
| RAMPAdapter | Adapter to provide RAMP-friendly access to MSData library |
| Reader | Interface for file readers |
| Config | Reader configuration |
| ReaderFail | |
| ReaderList | Reader container (composite pattern) |
| Serializer_MGF | MSData <-> MGF stream serialization |
| Serializer_MSn | MSData <-> MSn stream serialization |
| Serializer_mz5 | MSData <-> MZ5 file serialization |
| Serializer_mzML | MSData <-> mzML stream serialization |
| Config | Serializer_mzML configuration |
| Serializer_mzXML | MSData <-> mzXML stream serialization |
| Config | Serializer_mzXML configuration |
| SHA1OutputObserver | |
| SpectrumInfo | Simple structure for holding Spectrum info |
| PrecursorInfo | Structure for Precursor info |
| SpectrumIterator | SpectrumIterator provides convenient iteration through a set of scans in a SpectrumList |
| Config | SpectrumIterator configuration – note that constructors allow automatic conversion from IntegerSet or Sieve to Config |
| Sieve | Interface for filtering based on ScanInfo |
| SpectrumList_BTDX | SpectrumList backed by a Bruker BioTools DataExchange XML file |
| SpectrumList_MGF | Implementation of SpectrumList, backed by an MGF file |
| MSnHeader | |
| SpectrumList_MSn | Implementation of SpectrumList, backed by an MGF file |
| SpectrumList_mz5 | Implementation of SpectrumList, backed by an mz5 file |
| SpectrumList_mzML | Implementation of SpectrumList, backed by an mzML file |
| SpectrumList_mzXML | Implementation of SpectrumList, backed by an mzXML file |
| index_not_found | Exception thrown if create(*,*,true) is called and the mzXML index cannot be found |
| SpectrumListBase | Common functionality for base SpectrumList implementations |
| SpectrumListCache | Adds a level of flexible MRU caching to a SpectrumList processor chain |
| SpectrumListWrapper | Inheritable pass-through implementation for wrapping a SpectrumList |
| TextWriter | |
| Version | |
| Reader_ABI | |
| Reader_ABI_T2D | |
| Reader_Agilent | |
| Reader_Bruker | |
| ExtendedReaderList | Default ReaderList, extended to include vendor readers |
| Reader_Thermo | |
| Reader_Waters | |
| tradata | |
| examples | |
| IO | |
| References | Functions for resolving references from objects into the internal MSData lists |
| DefaultReaderList | Default Reader list |
| DiffConfig | Configuration struct for diffs |
| Reader | Interface for file readers |
| ReaderFail | |
| ReaderList | Reader container (composite pattern) |
| Serializer_traML | TraData <-> traML stream serialization |
| TextWriter | |
| Contact | |
| Publication | |
| Software | |
| RetentionTime | |
| Prediction | Information about a prediction for a suitable transition using some software |
| Evidence | Information about empirical mass spectrometer observations of the peptide |
| Validation | Information about the state of validation of a transition on a given instrument model |
| Instrument | Instrument on which transitions are validated |
| Configuration | Instrument configuration used in the validation or optimization of the transitions |
| Interpretation | A possible interpration of the product ion for a transition |
| Protein | |
| Modification | A molecule modification specification |
| Peptide | Peptide for which one or more transitions are intended to identify |
| Compound | Chemical compound other than a peptide for which one or more transitions |
| Precursor | Precursor (Q1) of the transition |
| Product | Product (Q3) of the transition |
| Transition | |
| Target | A peptide or compound that is to be included or excluded from a target list of precursor m/z values |
| TargetList | List of precursor m/z targets to include or exclude |
| TraData | |
| TraDataFile | TraData object plus file I/O |
| WriteConfig | Configuration for write() |
| Version | |
| chemistry | |
| Element | Scope for declarations related to elements |
| Info | Class for obtaining information about elements |
| Record | |
| detail | |
| Isotope | |
| Element | |
| Ion | |
| MassAbundance | Struct for holding isotope information |
| Formula | Class to represent a chemical formula |
| IsotopeCalculator | |
| IsotopeEnvelopeEstimator | Class used for calculating a theoretical isotope envelope for a given mass, based on an estimate of the elemental composition for that mass |
| Config | |
| 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 |
| MZTolerance | Struct for expressing m/z tolerance in either amu or ppm |
| minimxml | |
| SAXParser | An extended SAX interface for custom XML stream parsing |
| saxstring | |
| Handler | SAX event handler interface |
| Attributes | |
| attribute | |
| Status | Handler returns the Status struct as a means of changing the parser's behavior |
| XMLWriter | Simple, tag-level XML syntax writing |
| Attributes | Vector of name/value pairs to be written as XML attributes |
| Config | Initial configuration of the XMLWriter |
| OutputObserver | Interface to allow outside observation of data sent to output stream |
| basic_charcounter | |
| category | |
| util | |
| Base64 | Base-64 binary->text encoding (maps 3 bytes <-> 4 chars) |
| env | |
| CharIndexedVectorIterator | Iterator for CharIndexedVector |
| CharIndexedVectorConstIterator | Const_iterator for CharIndexedVector |
| CharIndexedVector | Wrapper for boost::array that is indexable by character; supports indexes 0-127 |
| ClickwrapPrompter | Barrier to force end users to agree/disagree to a prompt before continuing |
| COMInitializer | Singleton used to initialize and uninitialize COM once per thread |
| usage_exception | |
| user_error | |
| Image | Wrapper class for using 'gd' graphics library |
| Color | Struct for holding rgb values (in [0,255]) |
| Point | Struct for holding pixel coordinates |
| IntegerSet | Virtual container of integers, accessible via an iterator interface, stored as union of intervals |
| Interval | Single closed interval of integers |
| Iterator | Forward iterator providing readonly access to the virtual container |
| IterationListener | Interface to be implemented by clients who want progress callbacks |
| UpdateMessage | |
| IterationListenerRegistry | Handles registration of IterationListeners and broadcast of update messages |
| mru_list | |
| once_flag_proxy | |
| random_access_compressed_ifstream | |
| SHA1SymmetricFilter | Model of boost::iostreams::SymmetricFilter |
| SHA1Filter | Model of boost::iostreams::Filter |
| SHA1_ostream | Ostream filter for calculating a SHA-1 hash of data on the fly |
| SHA1Calculator | |
| shared_map | Copy semantics of shared_ptr<map<K,V> > with a std::map interface |
| Timer | |
| TestPathPredicate | Test implementations derive from this to define which paths should be tested |
| virtual_map | Wrapper for std::map that will behave properly with polymorphism |
| utility | |
| MSIHandler | |
| Record | |
| TabHandler | |
| DefaultTabHandler | |
| VectorTabHandler | |
| TabReader | |
| Bin | |
| SecondIs | |
| IsObject | |
| Version | |
| Agilent | |
| Thermo | |
| std | STL namespace |
| AnotherRootHandler | |
| auto_vector | |
| auto_lvalue | |
| BadListener | |
| CancelListener | |
| CancelProgressCallback | |
| CSHA1 | |
| CustomPair | |
| Datum | |
| DefaultArrayLengthSorter | |
| DeletePtr | |
| DigestedPeptideLessThan | |
| EnzymePtr_missedCleavages | |
| EnzymePtr_specificity | |
| EvenMS2Predicate | |
| EvenPredicate | |
| EvenRequester | |
| Fifth | |
| FifthHandler | |
| FilterWrapper | |
| First | |
| FirstHandler | |
| FTSieve | |
| glob_t | |
| Goober | |
| HasBinaryDataPredicate | |
| InstrumentStruct | |
| Is_T2D_Directory | |
| IsDirectory | |
| IsFS | |
| IsInt | |
| IsRawData | |
| IsRawFile | |
| IsSQ | |
| IsWiffFile | |
| LU | |
| MSDataWithSettableVersion | |
| MSLevelSorter | |
| MyBase | |
| MyPred | |
| MyWrapper | |
| mzrtEqual | |
| NestedHandler | |
| OneMinusAbs | |
| ParametrizedCosine | |
| PointsToSame | |
| PrintAttribute | |
| PrintEventHandler | |
| pwiz_RAMPAdapter | SWIG-friendly wrapper to provide RAMP-friendly access to MSData library |
| RAMPFILE | |
| RawMassDatum | |
| Reader1 | |
| Config | |
| ReaderConfig | |
| Reader2 | |
| Config | |
| ReaderConfig | |
| Root | |
| RootHandler | |
| RunHeaderStruct | |
| ScanCacheStruct | |
| ScanHeaderStruct | |
| Second | |
| SecondHandler | |
| SelectedIndexPredicate | |
| SetRetentionTime | |
| SHA1_WORKSPACE_BLOCK | |
| Simple | |
| SimpleAnalyzer | |
| SimpleProgressCallback | |
| TestAminoAcid | |
| TestChargeStateCalculator | |
| TestData | |
| TestDatum | |
| TestDeisotoper | |
| TestETDMassFilter | |
| TestFormula | |
| TestFragmentation | |
| TestInfo | |
| TestIterationListener | |
| TestIterationListener_WithCancel | |
| TestListener | |
| TestMetadataFixer | |
| TestModification | |
| TestModifiedPeptide | |
| TestMS2Denoise | |
| TestOperator | |
| TestOutputObserver | |
| TestPair | |
| TestPathmask | |
| TestPeptide | |
| TestReader | |
| TestSpectrumInfo | |
| TestThresholder | |
| ThreadStatus | |
| WriteCVParam |
