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struct | analyzer_strings |
| This auxilliary class should be specialized for MSDataAnalyzers whose instantiation is controlled by user-supplied strings (via command line, config file, etc.). More...
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struct | analyzer_strings< MetadataReporter > |
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struct | analyzer_strings< RegionSIC > |
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struct | analyzer_strings< RegionSlice > |
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struct | analyzer_strings< RegionTIC > |
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struct | analyzer_strings< RunSummary > |
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struct | analyzer_strings< SpectrumBinaryData > |
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struct | analyzer_strings< SpectrumTable > |
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struct | ChromatogramDataFilter |
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struct | CwtPeakDetector |
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struct | 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 More...
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class | FeatureDetector |
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class | FeatureDetectorPeakel |
| FeatureDetectorPeakel implements a 'template method', delegating to 'strategies' encapsulated by the following interfaces: PeakExtractor PeakelGrower PeakelPicker. More...
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class | FeatureDetectorSimple |
| FeatureDetectorSimple detects 'rectangular' features, ie number of peaks in isotope envelope is the same for each scan included in the feature. More...
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class | FeatureModeler |
| interface for fitting and scoring Feature data to a model More...
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class | FeatureModeler_Gaussian |
| Gaussian implementation. More...
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struct | LocalMaximumPeakDetector |
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class | MetadataReporter |
| writes file-level metadata to a file More...
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struct | MS2Deisotoper |
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struct | MS2NoiseFilter |
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class | MSDataAnalyzer |
| Interface for MSData analyzers. More...
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class | MSDataAnalyzerContainer |
| container of MSDataAnalyzer (composite pattern) More...
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class | MSDataAnalyzerDriver |
| event generator for MSDataAnalyzer More...
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class | MSDataCache |
| simple memory cache for common MSData info More...
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struct | MZRTField |
| MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT. More...
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struct | Noise |
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class | NoiseCalculator |
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class | NoiseCalculator_2Pass |
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class | NoVendorPeakPickingException |
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struct | Peak |
| represents some generic metadata about a peak detected in a signal More...
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struct | PeakDetector |
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class | PeakelGrower |
| interface for growing Peakels More...
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class | PeakelGrower_Proximity |
| simple PeakelGrower implementation, based on proximity of Peaks More...
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class | PeakelPicker |
| interface for picking Peakels and arranging into Features; note: Peakels are actually removed from the PeakelField More...
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class | PeakelPicker_Basic |
| basic implementation More...
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class | 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". More...
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class | PeakFamilyDetector |
| interface for peak family (isotope envelope) detection More...
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class | PeakFamilyDetectorFT |
| FT-specific implementation of PeakFamilyDetector. More...
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class | PeakFinder |
| interface for finding peaks in an array of ordered pairs More...
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class | PeakFinder_SNR |
| PeakFinder implementation based on signal-to-noise ratio. More...
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class | PeakFitter |
| interface for fitting peaks in an array of ordered pairs More...
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class | PeakFitter_Parabola |
| PeakFitter implementation based on fitting a parabola. More...
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class | PepxmlRecordReader |
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struct | PrecursorMassFilter |
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class | PrecursorRecalculator |
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class | PrecursorRecalculatorDefault |
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class | ProteinList_DecoyGenerator |
| ProteinList decoy generator for creating decoy proteins on the fly. More...
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class | ProteinList_DecoyGeneratorPredicate_Reversed |
| creates a reversed copy of every target protein with the specified decoy string prefixed to the id More...
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class | ProteinList_DecoyGeneratorPredicate_Shuffled |
| creates a randomly shuffled copy of every target protein with the specified decoy string prefixed to the id More...
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class | ProteinList_Filter |
| ProteinList filter, for creating Protein sub-lists. More...
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class | ProteinList_FilterPredicate_IdSet |
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class | ProteinList_FilterPredicate_IndexSet |
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class | ProteinListFactory |
| Factory for instantiating and wrapping ProteinLists. More...
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class | RegionAnalyzer |
| analyzes a rectangular region of m/z-time space More...
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class | RegionSIC |
| writes data samples from a single rectangular region More...
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class | RegionSlice |
| writes data samples from a single rectangular region More...
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class | RegionTIC |
| writes data samples from a single rectangular region More...
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struct | RTMatches_Any |
| predicate always returns true More...
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struct | RTMatches_Contains |
| predicate returns true iff the object's retention time range contains the specified retention time More...
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struct | 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 More...
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class | RunSummary |
| writes table of spectrum metadata to a file More...
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struct | SavitzkyGolaySmoother |
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struct | Smoother |
| interface for a one-dimensional smoothing algorithm More...
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class | SpectrumBinaryData |
| writes table of spectrum metadata to a file More...
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struct | SpectrumDataFilter |
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class | SpectrumList_3D |
| SpectrumList implementation that can create 3D spectra of ion mobility drift time and m/z. More...
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class | SpectrumList_ChargeFromIsotope |
| SpectrumList implementation that assigns (probable) charge states to tandem mass spectra. More...
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class | SpectrumList_ChargeStateCalculator |
| SpectrumList implementation that assigns (probable) charge states to tandem mass spectra. More...
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class | SpectrumList_Filter |
| SpectrumList filter, for creating Spectrum sub-lists. More...
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class | SpectrumList_FilterPredicate_ActivationType |
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class | SpectrumList_FilterPredicate_AnalyzerType |
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class | SpectrumList_FilterPredicate_ChargeStateSet |
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class | SpectrumList_FilterPredicate_DefaultArrayLengthSet |
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class | SpectrumList_FilterPredicate_IndexSet |
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class | SpectrumList_FilterPredicate_MSLevelSet |
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class | SpectrumList_FilterPredicate_MzPresent |
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class | SpectrumList_FilterPredicate_Polarity |
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class | SpectrumList_FilterPredicate_PrecursorMzSet |
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class | SpectrumList_FilterPredicate_ScanEventSet |
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class | SpectrumList_FilterPredicate_ScanNumberSet |
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class | SpectrumList_FilterPredicate_ScanTimeRange |
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class | SpectrumList_IonMobility |
| SpectrumList implementation that provides access to vendor-specific ion mobility functions. More...
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class | SpectrumList_LockmassRefiner |
| SpectrumList implementation to replace peak profiles with picked peaks. More...
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class | SpectrumList_MetadataFixer |
| SpectrumList implementation to add (or replace) base peak and total ion metadata with new values calculated from the current binary data. More...
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class | SpectrumList_MZRefiner |
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class | SpectrumList_MZWindow |
| SpectrumList filter, for creating Spectrum sub-lists. More...
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class | SpectrumList_PeakFilter |
| SpectrumList implementation that returns spectra with the specified SpectrumDataFilter operation applied. More...
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class | SpectrumList_PeakPicker |
| SpectrumList implementation to replace peak profiles with picked peaks. More...
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class | SpectrumList_PrecursorRecalculator |
| SpectrumList wrapper that recalculates precursor info on spectrum() requests. More...
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class | SpectrumList_PrecursorRefine |
| SpectrumList wrapper that recalculates precursor info on spectrum() requests. More...
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class | SpectrumList_ScanSummer |
| Provides a custom-sorted spectrum list. More...
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class | SpectrumList_Smoother |
| SpectrumList implementation to return smoothed spectral data. More...
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class | SpectrumList_Sorter |
| Provides a custom-sorted spectrum list. More...
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class | SpectrumList_SorterPredicate_ScanStartTime |
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class | SpectrumList_TitleMaker |
| SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user-specified format. More...
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class | SpectrumList_ZeroSamplesFilter |
| SpectrumList implementation to return spectra with or without extra zero samples. More...
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class | SpectrumListFactory |
| Factory for instantiating and wrapping SpectrumLists. More...
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class | SpectrumTable |
| writes table of spectrum metadata to a file More...
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struct | TabularConfig |
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struct | ThresholdFilter |
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struct | Version |
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struct | WhittakerSmoother |
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struct | ZeroSampleFiller |
| fills in missing zero samples around signal profiles More...
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