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ProteoWizard
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Classes | |
| class | ChromatogramList_SavitzkyGolaySmoother |
| ChromatogramList implementation to return native centroided chromatogram data. More... | |
| class | ChromatogramListWrapper |
| Inheritable pass-through implementation for wrapping a ChromatogramList. More... | |
| struct | SavitzkyGolaySmoother |
| struct | SpectrumDataFilter |
| struct | ChromatogramDataFilter |
| 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... | |
| struct | LocalMaximumPeakDetector |
| struct | Peak |
| represents some generic metadata about a peak detected in a signal More... | |
| struct | PeakDetector |
| struct | Smoother |
| interface for a one-dimensional smoothing algorithm More... | |
| struct | WhittakerSmoother |
| struct | ZeroSampleFiller |
| fills in missing zero samples around signal profiles More... | |
| class | MetadataReporter |
| writes file-level metadata to a file More... | |
| struct | analyzer_strings< MetadataReporter > |
| class | MSDataAnalyzer |
| Interface for MSData analyzers. More... | |
| 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... | |
| class | MSDataAnalyzerContainer |
| container of MSDataAnalyzer (composite pattern) More... | |
| class | MSDataAnalyzerDriver |
| event generator for MSDataAnalyzer More... | |
| class | MSDataCache |
| simple memory cache for common MSData info More... | |
| class | PepxmlRecordReader |
| class | Pseudo2DGel |
| Creates pseudo-2D-gel images from survey scan data. More... | |
| struct | analyzer_strings< Pseudo2DGel > |
| class | RegionAnalyzer |
| analyzes a rectangular region of m/z-time space More... | |
| class | RegionSIC |
| writes data samples from a single rectangular region More... | |
| struct | analyzer_strings< RegionSIC > |
| class | RegionSlice |
| writes data samples from a single rectangular region More... | |
| struct | analyzer_strings< RegionSlice > |
| class | RegionTIC |
| writes data samples from a single rectangular region More... | |
| struct | analyzer_strings< RegionTIC > |
| class | RunSummary |
| writes table of spectrum metadata to a file More... | |
| struct | analyzer_strings< RunSummary > |
| class | SpectrumBinaryData |
| writes table of spectrum metadata to a file More... | |
| struct | analyzer_strings< SpectrumBinaryData > |
| class | SpectrumTable |
| writes table of spectrum metadata to a file More... | |
| struct | analyzer_strings< SpectrumTable > |
| struct | TabularConfig |
| class | FeatureDetector |
| class | FeatureDetectorPeakel |
| FeatureDetectorPeakel implements a 'template method', delegating to 'strategies' encapsulated by the following interfaces: PeakExtractor PeakelGrower PeakelPicker. More... | |
| class | FeatureDetectorSimple |
| FeatureDetectorSimple detects 'rectangular' features, ie number of peaks in isotope envelope is the same for each scan included in the feature. More... | |
| class | FeatureModeler |
| interface for fitting and scoring Feature data to a model More... | |
| class | FeatureModeler_Gaussian |
| Gaussian implementation. More... | |
| struct | MZRTField |
| MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT. More... | |
| struct | RTMatches_Any |
| predicate always returns true More... | |
| struct | RTMatches_Contains |
| predicate returns true iff the object's retention time range contains the specified retention time More... | |
| 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... | |
| struct | Noise |
| class | NoiseCalculator |
| class | NoiseCalculator_2Pass |
| class | PeakelGrower |
| interface for growing Peakels More... | |
| class | PeakelGrower_Proximity |
| simple PeakelGrower implementation, based on proximity of Peaks More... | |
| class | PeakelPicker |
| interface for picking Peakels and arranging into Features; note: Peakels are actually removed from the PeakelField More... | |
| class | PeakelPicker_Basic |
| basic implementation More... | |
| 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... | |
| class | PeakFamilyDetector |
| interface for peak family (isotope envelope) detection More... | |
| class | PeakFamilyDetectorFT |
| FT-specific implementation of PeakFamilyDetector. More... | |
| class | PeakFinder |
| interface for finding peaks in an array of ordered pairs More... | |
| class | PeakFinder_SNR |
| PeakFinder implementation based on signal-to-noise ratio. More... | |
| class | PeakFitter |
| interface for fitting peaks in an array of ordered pairs More... | |
| class | PeakFitter_Parabola |
| PeakFitter implementation based on fitting a parabola. More... | |
| class | ProteinList_DecoyGenerator |
| ProteinList decoy generator for creating decoy proteins on the fly. More... | |
| class | ProteinList_DecoyGeneratorPredicate_Reversed |
| creates a reversed copy of every target protein with the specified decoy string prefixed to the id More... | |
| class | ProteinList_DecoyGeneratorPredicate_Shuffled |
| creates a randomly shuffled copy of every target protein with the specified decoy string prefixed to the id More... | |
| class | ProteinList_Filter |
| ProteinList filter, for creating Protein sub-lists. More... | |
| class | ProteinList_FilterPredicate_IndexSet |
| class | ProteinList_FilterPredicate_IdSet |
| class | ProteinListFactory |
| Factory for instantiating and wrapping ProteinLists. More... | |
| struct | MS2Deisotoper |
| struct | MS2NoiseFilter |
| struct | PrecursorMassFilter |
| class | PrecursorRecalculator |
| class | PrecursorRecalculatorDefault |
| class | SpectrumList_ChargeStateCalculator |
| SpectrumList implementation that assigns (probable) charge states to tandem mass spectra. More... | |
| class | SpectrumList_Filter |
| SpectrumList filter, for creating Spectrum sub-lists. More... | |
| class | SpectrumList_FilterPredicate_IndexSet |
| class | SpectrumList_FilterPredicate_ScanNumberSet |
| class | SpectrumList_FilterPredicate_ScanEventSet |
| class | SpectrumList_FilterPredicate_ScanTimeRange |
| class | SpectrumList_FilterPredicate_MSLevelSet |
| class | SpectrumList_FilterPredicate_PrecursorMzSet |
| class | SpectrumList_FilterPredicate_DefaultArrayLengthSet |
| class | SpectrumList_FilterPredicate_ActivationType |
| class | SpectrumList_FilterPredicate_AnalyzerType |
| class | SpectrumList_FilterPredicate_Polarity |
| 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... | |
| class | SpectrumList_MZWindow |
| SpectrumList filter, for creating Spectrum sub-lists. More... | |
| class | SpectrumList_PeakFilter |
| SpectrumList implementation that returns spectra with the specified SpectrumDataFilter operation applied. More... | |
| class | SpectrumList_PeakPicker |
| SpectrumList implementation to replace peak profiles with picked peaks. More... | |
| class | SpectrumList_PrecursorRecalculator |
| SpectrumList wrapper that recalculates precursor info on spectrum() requests. More... | |
| class | SpectrumList_PrecursorRefine |
| SpectrumList wrapper that recalculates precursor info on spectrum() requests. More... | |
| class | SpectrumList_Smoother |
| SpectrumList implementation to return smoothed spectral data. More... | |
| class | SpectrumList_Sorter |
| Provides a custom-sorted spectrum list. More... | |
| class | SpectrumList_SorterPredicate_ScanStartTime |
| class | SpectrumList_TitleMaker |
| SpectrumList implementation to add (or replace) a spectrum title to each spectrum according to a user-specified format. More... | |
| class | SpectrumList_ZeroSamplesFilter |
| SpectrumList implementation to return spectra with or without extra zero samples. More... | |
| class | SpectrumListFactory |
| Factory for instantiating and wrapping SpectrumLists. More... | |
| struct | ThresholdFilter |
| struct | Version |
Typedefs | |
| typedef boost::shared_ptr < SpectrumDataFilter > | SpectrumDataFilterPtr |
| typedef boost::shared_ptr < ChromatogramDataFilter > | ChromatogramDataFilterPtr |
| typedef boost::shared_ptr < PeakDetector > | PeakDetectorPtr |
| typedef boost::shared_ptr < Smoother > | SmootherPtr |
| typedef boost::shared_ptr < MSDataAnalyzer > | MSDataAnalyzerPtr |
| typedef MZRTField < pwiz::data::peakdata::Peakel > | PeakelField |
| typedef MZRTField < pwiz::data::peakdata::Feature > | FeatureField |
Functions | |
| PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, PepxmlRecordReader &prr) |
| PWIZ_API_DECL std::ostream & | operator<< (std::ostream &os, const PeakelField &peakelField) |
Variables | |
| static const char * | defaultNeutralLossFormulae [] |
| typedef boost::shared_ptr<SpectrumDataFilter> pwiz::analysis::SpectrumDataFilterPtr |
Definition at line 42 of file DataFilter.hpp.
| typedef boost::shared_ptr<ChromatogramDataFilter> pwiz::analysis::ChromatogramDataFilterPtr |
Definition at line 52 of file DataFilter.hpp.
| typedef boost::shared_ptr<PeakDetector> pwiz::analysis::PeakDetectorPtr |
Definition at line 57 of file PeakDetector.hpp.
| typedef boost::shared_ptr<Smoother> pwiz::analysis::SmootherPtr |
Definition at line 53 of file Smoother.hpp.
| typedef boost::shared_ptr<MSDataAnalyzer> pwiz::analysis::MSDataAnalyzerPtr |
Definition at line 107 of file MSDataAnalyzer.hpp.
Definition at line 111 of file MZRTField.hpp.
Definition at line 112 of file MZRTField.hpp.
| PWIZ_API_DECL std::ostream& pwiz::analysis::operator<< | ( | std::ostream & | os, |
| PepxmlRecordReader & | prr | ||
| ) |
| PWIZ_API_DECL std::ostream & pwiz::analysis::operator<< | ( | std::ostream & | os, |
| const PeakelField & | peakelField | ||
| ) |
|
static |
Definition at line 73 of file PrecursorMassFilter.hpp.
1.8.1.1