pwiz::analysis Namespace Reference

Classes
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...
struct	analyzer_strings< MetadataReporter >
struct	analyzer_strings< RegionSIC >
struct	analyzer_strings< RegionSlice >
struct	analyzer_strings< RegionTIC >
struct	analyzer_strings< RunSummary >
struct	analyzer_strings< SpectrumBinaryData >
struct	analyzer_strings< SpectrumTable >
struct	ChromatogramDataFilter
struct	CwtPeakDetector
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...
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	LocalMaximumPeakDetector
class	MetadataReporter
	writes file-level metadata to a file More...
struct	MS2Deisotoper
struct	MS2NoiseFilter
class	MSDataAnalyzer
	Interface for MSData analyzers. 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...
struct	MZRTField
	MZRTField is a std::set of boost::shared_ptrs, stored as a binary tree ordered by LessThan_MZRT. More...
struct	Noise
class	NoiseCalculator
class	NoiseCalculator_2Pass
class	NoVendorPeakPickingException
struct	Peak
	represents some generic metadata about a peak detected in a signal More...
struct	PeakDetector
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	PepxmlRecordReader
struct	PrecursorMassFilter
class	PrecursorRecalculator
class	PrecursorRecalculatorDefault
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_IdSet
class	ProteinList_FilterPredicate_IndexSet
class	ProteinListFactory
	Factory for instantiating and wrapping ProteinLists. More...
class	RegionAnalyzer
	analyzes a rectangular region of m/z-time space More...
class	RegionSIC
	writes data samples from a single rectangular region More...
class	RegionSlice
	writes data samples from a single rectangular region More...
class	RegionTIC
	writes data samples from a single rectangular region 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...
class	RunSummary
	writes table of spectrum metadata to a file More...
struct	SavitzkyGolaySmoother
struct	Smoother
	interface for a one-dimensional smoothing algorithm More...
class	SpectrumBinaryData
	writes table of spectrum metadata to a file More...
struct	SpectrumDataFilter
class	SpectrumList_3D
	SpectrumList implementation that can create 3D spectra of ion mobility drift time and m/z. More...
class	SpectrumList_ChargeFromIsotope
	SpectrumList implementation that assigns (probable) charge states to tandem mass spectra. More...
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_ActivationType
class	SpectrumList_FilterPredicate_AnalyzerType
class	SpectrumList_FilterPredicate_ChargeStateSet
class	SpectrumList_FilterPredicate_DefaultArrayLengthSet
class	SpectrumList_FilterPredicate_IndexSet
class	SpectrumList_FilterPredicate_MSLevelSet
class	SpectrumList_FilterPredicate_MzPresent
class	SpectrumList_FilterPredicate_Polarity
class	SpectrumList_FilterPredicate_PrecursorMzSet
class	SpectrumList_FilterPredicate_ScanEventSet
class	SpectrumList_FilterPredicate_ScanNumberSet
class	SpectrumList_FilterPredicate_ScanTimeRange
class	SpectrumList_LockmassRefiner
	SpectrumList implementation to replace peak profiles with picked peaks. More...
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_MZRefiner
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_ScanSummer
	Provides a custom-sorted spectrum list. 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...
class	SpectrumTable
	writes table of spectrum metadata to a file More...
struct	TabularConfig
struct	ThresholdFilter
struct	Version
struct	WhittakerSmoother
struct	ZeroSampleFiller
	fills in missing zero samples around signal profiles More...

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
typedef boost::container::flat_map< double, boost::container::flat_map< double, float > >	Spectrum3D
typedef boost::shared_ptr< Spectrum3D >	Spectrum3DPtr

Functions
template<typename value_type >
bool	parseRange (const std::string &desiredArg, const std::string &text, std::pair< value_type, value_type > &result, const std::string &callerName)
template<typename value_type >
bool	parseValue (const std::string &desiredArg, const std::string &text, value_type &result, const std::string &callerName)
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 Documentation

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 108 of file MSDataAnalyzer.hpp.

typedef MZRTField<pwiz::data::peakdata::Peakel> pwiz::analysis::PeakelField

Definition at line 111 of file MZRTField.hpp.

typedef MZRTField<pwiz::data::peakdata::Feature> pwiz::analysis::FeatureField

Definition at line 112 of file MZRTField.hpp.

typedef boost::container::flat_map<double, boost::container::flat_map<double, float> > pwiz::analysis::Spectrum3D

Definition at line 35 of file SpectrumList_3D.hpp.

typedef boost::shared_ptr<Spectrum3D> pwiz::analysis::Spectrum3DPtr

Definition at line 36 of file SpectrumList_3D.hpp.

Function Documentation

template<typename value_type >

bool pwiz::analysis::parseRange	(	const std::string &	desiredArg,
		const std::string &	text,
		std::pair< value_type, value_type > &	result,
		const std::string &	callerName
	)

Definition at line 193 of file MSDataAnalyzer.hpp.

References boost::lexical_cast().

{
    if (!text.compare(0,desiredArg.size()+1,desiredArg+"="))
    {
        std::string val = text.substr(desiredArg.size()+1);
        std::string::size_type indexPairSeperator = val.find(',');
        if (std::string::npos == indexPairSeperator)
        {   // no comma, perhaps a dash instead?
            indexPairSeperator = val.find('-');
            if (0==indexPairSeperator) // assume that's just a negative value
            {
                indexPairSeperator = string::npos;
            }
        }
        int bracket =  (val[0] == '[')?1:0;
        if (val.empty() ||
           ((bracket!=0) && val[val.size()-1] != ']'))
        {
            std::cerr << "[" << callerName << "] Unable to parse range: " << text << endl;
            return false;
        }
    
        try
        {
            if (std::string::npos == indexPairSeperator) 
            {   // form "<start>", read as "<start>-<start>"
                std::string first = val.substr(bracket,val.size()-(2*bracket));
                result.first = result.second = lexical_cast<value_type>(first);
            }
            else
            {   // form "<start>-<end>" or "<start>-" 
                std::string first = val.substr(bracket, indexPairSeperator-bracket);
                std::string second = val.substr(indexPairSeperator+1, val.size()-indexPairSeperator-(1+bracket));
                result.first = lexical_cast<value_type>(first);
                if (second.size()) // form "<start>-<end>"
                    result.second = lexical_cast<value_type>(second);
                else  // form "<start>-", assume that's "<start>-maxval"
                    result.second = numeric_limits<value_type>::max();
            }
            return true;
        }
        catch (boost::bad_lexical_cast&)
        {
            std::cerr << "[" << callerName << "] Unable to parse range: " << text << endl;
        }
    }

    return false;
}

template<typename value_type >

bool pwiz::analysis::parseValue	(	const std::string &	desiredArg,
		const std::string &	text,
		value_type &	result,
		const std::string &	callerName
	)

Definition at line 243 of file MSDataAnalyzer.hpp.

References boost::lexical_cast().

{
    if (!text.compare(0,desiredArg.size()+1,desiredArg+"="))
    {
        std::string val = text.substr(desiredArg.size()+1);
        if (val.empty())
        {
            std::cerr << "[" << callerName << "] Unable to parse value: " << text << endl;
            return false;
        }
    
        try
        {
            result = lexical_cast<value_type>(val);
            return true;
        }
        catch (boost::bad_lexical_cast&)
        {
            std::cerr << "[" << callerName << "] Unable to parse value: " << text << endl;
        }
    }

    return false;
}

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
	)

Variable Documentation

const char* pwiz::analysis::defaultNeutralLossFormulae[]

static

Initial value:

= {
    "H1",          
    "N1H2",        
    "N1H3",
    "H2O1",
    "C1O1",
    "C1H4O1",
    "N2H6",        
    "H5N1O1",      
    "H4O2",        
    "C1H3N2",      
    "C1H4N2",
    "C1H3N1O1",
    "C1H2O2",
    "C2H6O1",
    "C2H5N1O1",
    "C1H5N3",
    "C2H4O2",      
    "C4H11N1",     
    "C3H6S1",      
    "C4H6N2",      
    "C3H8N3",      
    "C4H9N3",      
    "C4H11N3",     
    "C7H8O1",      
    "C9H9N1"       
}

Definition at line 73 of file PrecursorMassFilter.hpp.