Class for binary storage of complex frequency data. More...

#include <FrequencyData.hpp>

Public Types
types
typedef std::vector < FrequencyDatum >	container
typedef container::iterator	iterator
typedef container::const_iterator	const_iterator

Public Member Functions
instantiation
	FrequencyData ()
	FrequencyData (const std::string &filename, IOMode mode=Automatic)
	FrequencyData (const FrequencyData &that, const_iterator begin, const_iterator end)
	FrequencyData (const FrequencyData &that, const_iterator center, int radius)
	~FrequencyData ()
I/O
void	read (const std::string &filename, IOMode mode=Automatic)
void	read (std::istream &is, IOMode mode=Binary)
void	write (const std::string &filename, IOMode mode=Binary) const
void	write (std::ostream &os, IOMode mode=Binary) const
data access
const container &	data () const
	const access to underlying data
container &	data ()
	non-const access to underlying data – must call analyze() to recache after any changes
metadata
int	scanNumber () const
void	scanNumber (int value)
double	retentionTime () const
void	retentionTime (double value)
const CalibrationParameters &	calibrationParameters () const
void	calibrationParameters (const CalibrationParameters &cp)
double	observationDuration () const
void	observationDuration (double value)
double	noiseFloor () const
void	noiseFloor (double value)
data transformation
void	transform (double shift, std::complex< double > scale)
	transform all underlying data: (x,y) -> (x+shift,y*scale)
double	shift () const
	return current shift of data (compared to original)
std::complex< double >	scale () const
	return current scale of data (compared to original)
void	normalize ()
	normalize by transform( -max.x, 1/abs(max.y) )
void	operator+= (const FrequencyData &that)
	addition
analysis
void	analyze ()
	recache statistics calculations after any direct data changes via non-const data()
const_iterator	max () const
	returns an iterator to FrequencyDatum with highest magnitude
double	mean () const
double	meanSquare () const
double	sumSquares () const
double	variance () const
double	cutoffNoiseFloor () const
	special calculation of noise floor for data with zero holes, e.g.
double	observationDurationEstimatedFromData () const
	calculation of the observation duration from the data
auxilliary
const_iterator	findNearest (double frequency) const
	Finds the FrequencyDatum nearest the desired frequency.

Static Public Member Functions
auxilliary functions
static std::pair< double, double >	magnitudeSample (const FrequencyDatum &datum)
	Returns a <frequency,magnitude> pair.

Private Member Functions
	FrequencyData (FrequencyData &that)
	Hidden to prevent unintended copying of large amounts of data.
FrequencyData &	operator= (FrequencyData &that)
	Hidden to prevent unintended copying of large amounts of data.

Private Attributes
std::auto_ptr< Impl >	impl_

Detailed Description

Class for binary storage of complex frequency data.

Stores raw frequency-domain data, as well as meta-data. Also includes basic access and analysis functions.

Definition at line 48 of file FrequencyData.hpp.

Member Typedef Documentation

typedef std::vector<FrequencyDatum> pwiz::data::FrequencyData::container

Definition at line 55 of file FrequencyData.hpp.

typedef container::iterator pwiz::data::FrequencyData::iterator

Definition at line 56 of file FrequencyData.hpp.

typedef container::const_iterator pwiz::data::FrequencyData::const_iterator

Definition at line 57 of file FrequencyData.hpp.

Constructor & Destructor Documentation

pwiz::data::FrequencyData::FrequencyData ( )

pwiz::data::FrequencyData::FrequencyData	(	const std::string &	filename,
		IOMode	mode = `Automatic`
	)

pwiz::data::FrequencyData::FrequencyData	(	const FrequencyData &	that,
		const_iterator	begin,
		const_iterator	end
	)

pwiz::data::FrequencyData::FrequencyData	(	const FrequencyData &	that,
		const_iterator	center,
		int	radius
	)

pwiz::data::FrequencyData::~FrequencyData ( )

pwiz::data::FrequencyData::FrequencyData ( FrequencyData & that )

private

Hidden to prevent unintended copying of large amounts of data.

Member Function Documentation

void pwiz::data::FrequencyData::read	(	const std::string &	filename,
		IOMode	mode = `Automatic`
	)

void pwiz::data::FrequencyData::read	(	std::istream &	is,
		IOMode	mode = `Binary`
	)

void pwiz::data::FrequencyData::write	(	const std::string &	filename,
		IOMode	mode = `Binary`
	)		const

Referenced by test().

void pwiz::data::FrequencyData::write	(	std::ostream &	os,
		IOMode	mode = `Binary`
	)		const

const container& pwiz::data::FrequencyData::data ( ) const

const access to underlying data

Referenced by initializeWithTestData(), test(), testAddition(), testData(), testData2_LocalMax(), testData2_Parabola(), testFind(), and testNoiseFloorVarianceCalculation().

container& pwiz::data::FrequencyData::data ( )

non-const access to underlying data – must call analyze() to recache after any changes

int pwiz::data::FrequencyData::scanNumber ( ) const

Referenced by test().

void pwiz::data::FrequencyData::scanNumber ( int value )

double pwiz::data::FrequencyData::retentionTime ( ) const

Referenced by test().

void pwiz::data::FrequencyData::retentionTime ( double value )

const CalibrationParameters& pwiz::data::FrequencyData::calibrationParameters ( ) const

Referenced by initializeWithTestData(), and test().

void pwiz::data::FrequencyData::calibrationParameters ( const CalibrationParameters & cp )

double pwiz::data::FrequencyData::observationDuration ( ) const

Referenced by initializeWithTestData(), and test().

void pwiz::data::FrequencyData::observationDuration ( double value )

double pwiz::data::FrequencyData::noiseFloor ( ) const

Referenced by test(), and testNoiseFloor().

void pwiz::data::FrequencyData::noiseFloor ( double value )

void pwiz::data::FrequencyData::transform	(	double	shift,
		std::complex< double >	scale
	)

transform all underlying data: (x,y) -> (x+shift,y*scale)

Referenced by test(), and testAddition().

double pwiz::data::FrequencyData::shift ( ) const

return current shift of data (compared to original)

Referenced by test().

std::complex<double> pwiz::data::FrequencyData::scale ( ) const

return current scale of data (compared to original)

Referenced by test(), and testData().

void pwiz::data::FrequencyData::normalize ( )

normalize by transform( -max.x, 1/abs(max.y) )

Referenced by test(), and testData().

void pwiz::data::FrequencyData::operator+= ( const FrequencyData & that )

addition

void pwiz::data::FrequencyData::analyze ( )

recache statistics calculations after any direct data changes via non-const data()

Referenced by initializeWithTestData(), test(), testFind(), and testNoiseFloorVarianceCalculation().

const_iterator pwiz::data::FrequencyData::max ( ) const

returns an iterator to FrequencyDatum with highest magnitude

Referenced by test(), and testData().

double pwiz::data::FrequencyData::mean ( ) const

Referenced by test().

double pwiz::data::FrequencyData::meanSquare ( ) const

Referenced by test().

double pwiz::data::FrequencyData::sumSquares ( ) const

Referenced by test().

double pwiz::data::FrequencyData::variance ( ) const

Referenced by test(), and testNoiseFloor().

double pwiz::data::FrequencyData::cutoffNoiseFloor ( ) const

special calculation of noise floor for data with zero holes, e.g.

data obtained from RAW file m/z-intensity pairs

Referenced by testNoiseFloorVarianceCalculation().

double pwiz::data::FrequencyData::observationDurationEstimatedFromData ( ) const

calculation of the observation duration from the data

Referenced by test().

const_iterator pwiz::data::FrequencyData::findNearest ( double frequency ) const

Finds the FrequencyDatum nearest the desired frequency.

Referenced by testFind().

static std::pair<double,double> pwiz::data::FrequencyData::magnitudeSample ( const FrequencyDatum & datum )

static

Returns a <frequency,magnitude> pair.

FrequencyData& pwiz::data::FrequencyData::operator= ( FrequencyData & that )

private

Hidden to prevent unintended copying of large amounts of data.

Member Data Documentation

std::auto_ptr<Impl> pwiz::data::FrequencyData::impl_

private

Definition at line 156 of file FrequencyData.hpp.

The documentation for this class was generated from the following file:

/Users/parag/_Research/pwiz/svn/trunk/pwiz/pwiz/data/misc/FrequencyData.hpp

Public Types

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation