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 | ||
) |
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static |
Definition at line 73 of file PrecursorMassFilter.hpp.