CalibrationData Class Reference

A helper class, holding all calibration points. More...

#include <OpenMS/DATASTRUCTURES/CalibrationData.h>

Collaboration diagram for CalibrationData:

Public Types
typedef RichPeak2D	CalDataType
typedef std::vector< CalDataType >::const_iterator	const_iterator
typedef std::vector< CalDataType >::value_type	value_type

Public Member Functions
	CalibrationData ()
	Default constructor. More...
CalDataType::CoordinateType	getMZ (Size i) const
	Retrieve the observed m/z of the i'th calibration point. More...
CalDataType::CoordinateType	getRT (Size i) const
	Retrieve the observed RT of the i'th calibration point. More...
CalDataType::CoordinateType	getIntensity (Size i) const
	Retrieve the intensity of the i'th calibration point. More...
const_iterator	begin () const
	Begin iterator for calibration points. More...
const_iterator	end () const
	Past-the-end iterator for calibration points. More...
Size	size () const
	Number of calibration points. More...
bool	empty () const
	Do we have any calibration points. More...
void	clear ()
	Remove all calibration points. More...
void	setUsePPM (bool usePPM)
	When calling getError(), should ppm error or m/z error be returned? More...
bool	usePPM () const
	Current error unit (ppm or Th) More...
void	insertCalibrationPoint (CalDataType::CoordinateType rt, CalDataType::CoordinateType mz_obs, CalDataType::IntensityType intensity, CalDataType::CoordinateType mz_ref, double weight, int group=-1)
	Add a new calibration point. More...
Size	getNrOfGroups () const
	Number of peak groups (can be 0). More...
CalDataType::CoordinateType	getError (Size i) const
	Retrieve the error for i'th calibrant in either ppm or Th (depending on usePPM()) More...
CalDataType::CoordinateType	getRefMZ (Size i) const
	Retrieve the theoretical m/z of the i'th calibration point. More...
CalDataType::CoordinateType	getWeight (Size i) const
	Retrieve the weight of the i'th calibration point. More...
int	getGroup (Size i) const
	Retrieve the group of the i'th calibration point. More...
CalibrationData	median (double rt_left, double rt_right) const
	Compute the median in the given RT range for every peak group. More...
void	sortByRT ()
	Sort calibration points by RT, to allow for valid RT chunking. More...

Static Public Member Functions
static StringList	getMetaValues ()
	List of meta-values which are used internally (for conversion to PeakMap). More...

Private Attributes
std::vector< RichPeak2D >	data_
	calibration points More...
bool	use_ppm_
	return ppm values as y-values for the model instead of absolute delta in [Th] More...
std::set< int >	groups_
	peak groups present in this data More...

Detailed Description

A helper class, holding all calibration points.

Calibration points can be filled from Peptide IDs (using FeatureMaps or vector<PeptideIds>) or from lock masses in Raw data (MSExperiment).

The m/z error can be queried using getError(). The unit of error is either ppm or Th, depending on usePPM().

Each calibration point can be assigned to a peak group. This should be done for calibration points derived from lock masses, to enable querying for a medianized representation of a lock mass trace in a certain RT range (see median()). For calibration points derived from peptide IDs, this does not make sense.

From this data, a calibration function can be computed (see MZTrafoModel class).

Member Typedef Documentation

CalDataType

typedef RichPeak2D CalDataType

const_iterator

typedef std::vector<CalDataType>::const_iterator const_iterator

value_type

typedef std::vector<CalDataType>::value_type value_type

Constructor & Destructor Documentation

CalibrationData()

CalibrationData

(

)

Default constructor.

Member Function Documentation

begin()

const_iterator begin

(

)

const

Begin iterator for calibration points.

clear()

void clear

(

)

Remove all calibration points.

empty()

bool empty

(

)

const

Do we have any calibration points.

end()

const_iterator end

(

)

const

Past-the-end iterator for calibration points.

getError()

CalDataType::CoordinateType getError

(

Size

i

)

const

Retrieve the error for i'th calibrant in either ppm or Th (depending on usePPM())

getGroup()

int getGroup

(

Size

i

)

const

Retrieve the group of the i'th calibration point.

Parameters

i

Index

Returns

Group; returns -1 if peak has no group.

getIntensity()

CalDataType::CoordinateType getIntensity

(

Size

i

)

const

Retrieve the intensity of the i'th calibration point.

getMetaValues()

static StringList getMetaValues ( )

static

List of meta-values which are used internally (for conversion to PeakMap).

getMZ()

CalDataType::CoordinateType getMZ

(

Size

i

)

const

Retrieve the observed m/z of the i'th calibration point.

getNrOfGroups()

Size getNrOfGroups

(

)

const

Number of peak groups (can be 0).

getRefMZ()

CalDataType::CoordinateType getRefMZ

(

Size

i

)

const

Retrieve the theoretical m/z of the i'th calibration point.

getRT()

CalDataType::CoordinateType getRT

(

Size

i

)

const

Retrieve the observed RT of the i'th calibration point.

getWeight()

CalDataType::CoordinateType getWeight

(

Size

i

)

const

Retrieve the weight of the i'th calibration point.

insertCalibrationPoint()

void insertCalibrationPoint	(	CalDataType::CoordinateType	rt,
		CalDataType::CoordinateType	mz_obs,
		CalDataType::IntensityType	intensity,
		CalDataType::CoordinateType	mz_ref,
		double	weight,
		int	group = -1
	)

Add a new calibration point.

Parameters

rt	Retention time
mz_obs	Observed m/z
intensity	Intensity (useful for weighted model fitting)
mz_ref	Theoretical m/z
weight	Weight of calibration point (useful for weighted model fitting)
group	Peak group of this calibration point. Using -1 will not assign any peak group. See also: median()

median()

CalibrationData median	(	double	rt_left,
		double	rt_right
	)		const

Compute the median in the given RT range for every peak group.

This is usually applied on calibration data obtained from lock masses, where each lock mass has its own peak group. Median() then computes an 'medianized' observed(!) lock mass within a certain RT range and returns calibration data with one calibration point per group. Also intensity is 'medianized'. The theoretical m/z is expected to be identical for all calibration points in a peak group.

Groups must be specified during insertCalibrationPoint(). If no groups are present, the result is empty.

The container must be sorted by RT (see sortByRT())!

Parameters

rt_left	Left border of RT range to medianize
rt_right	Right border of RT range to medianize

Returns

New container, containing median representation for each peak group

setUsePPM()

void setUsePPM

(

bool

usePPM

)

When calling getError(), should ppm error or m/z error be returned?

size()

Size size

(

)

const

Number of calibration points.

sortByRT()

void sortByRT

(

)

Sort calibration points by RT, to allow for valid RT chunking.

usePPM()

bool usePPM

(

)

const

Current error unit (ppm or Th)

Member Data Documentation

data_

std::vector<RichPeak2D> data_

private

calibration points

groups_

std::set<int> groups_

private

peak groups present in this data

use_ppm_

bool use_ppm_

private

return ppm values as y-values for the model instead of absolute delta in [Th]