A 2-dimensional raw data point or peak. More...

#include <OpenMS/KERNEL/Peak2D.h>

Inheritance diagram for Peak2D:

Classes
struct	IntensityLess
struct	MZLess
	Comparator by m/z position. More...
struct	PositionLess
	Comparator by position. Lexicographical comparison (first RT then m/z) is done. More...
struct	RTLess
	Comparator by RT position. More...
Public Types
Type definitions

typedef Real	IntensityType
	Intensity type.
typedef DoubleReal	CoordinateType
	Coordinate type (of the position).
typedef DPosition< 2 >	PositionType
	Position type.
Public Member Functions
Peak2D &	operator= (const Peak2D &rhs)
	Assignment operator.
bool	operator== (const Peak2D &rhs) const
	Equality operator.
bool	operator!= (const Peak2D &rhs) const
	Equality operator.
Constructors and Destructor
Default constructor
	Peak2D ()
	Peak2D (const Peak2D &p)
	Copy constructor.
	~Peak2D ()
	Destructor.
Accessors
Non-mutable access to the data point intensity (height)
IntensityType	getIntensity () const
void	setIntensity (IntensityType intensity)
	Non-mutable access to the data point intensity (height).
PositionType const &	getPosition () const
	Non-mutable access to the position.
PositionType &	getPosition ()
	Mutable access to the position.
void	setPosition (const PositionType &position)
	Mutable access to the position.
CoordinateType	getMZ () const
	Returns the m/z coordinate (index 1).
void	setMZ (CoordinateType coordinate)
	Mutable access to the m/z coordinate (index 1).
CoordinateType	getRT () const
	Returns the RT coordinate (index 0).
void	setRT (CoordinateType coordinate)
	Mutable access to the RT coordinate (index 0).
Protected Attributes
PositionType	position_
	The data point position.
IntensityType	intensity_
	The data point intensity.
Friends
std::ostream &	operator<< (std::ostream &os, const Peak2D &point)
	Print the contents to a stream.
Dimension descriptions

enum	DimensionDescription { RT = 0, MZ = 1, DIMENSION = 2 }
	This enum maps the symbolic names of the dimensions to numbers. More...
static char const *const	dimension_name_short_ [DIMENSION]
	Short name of the dimension (abbreviated form).
static char const *const	dimension_name_full_ [DIMENSION]
	Full name of the dimension (self-explanatory form).
static char const *const	dimension_unit_short_ [DIMENSION]
	Unit of measurement (abbreviated form).
static char const *const	dimension_unit_full_ [DIMENSION]
	Unit of measurement (self-explanatory form).
static char const *	shortDimensionName (UInt const dim)
	Short name of the dimension (abbreviated form).
static char const *	shortDimensionNameRT ()
	Short name of the dimension (abbreviated form).
static char const *	shortDimensionNameMZ ()
	Short name of the dimension (abbreviated form).
static char const *	fullDimensionName (UInt const dim)
	Full name of the dimension (self-explanatory form).
static char const *	fullDimensionNameRT ()
	Full name of the dimension (self-explanatory form).
static char const *	fullDimensionNameMZ ()
	Full name of the dimension (self-explanatory form).
static char const *	shortDimensionUnit (UInt const dim)
	Unit of measurement (abbreviated form).
static char const *	shortDimensionUnitRT ()
	Unit of measurement (abbreviated form).
static char const *	shortDimensionUnitMZ ()
	Unit of measurement (abbreviated form).
static char const *	fullDimensionUnit (UInt const dim)
	Unit of measurement (self-explanatory form).
static char const *	fullDimensionUnitRT ()
	Unit of measurement (self-explanatory form).
static char const *	fullDimensionUnitMZ ()
	Unit of measurement (self-explanatory form).

Detailed Description

A 2-dimensional raw data point or peak.

This datastructure is intended for continuous data or peak data. If wou want to annotated single peaks with meta data, use RichPeak2D instead.

Member Typedef Documentation

typedef DoubleReal CoordinateType

Coordinate type (of the position).

typedef Real IntensityType

Intensity type.

typedef DPosition<2> PositionType

Position type.

Member Enumeration Documentation

enum DimensionDescription

This enum maps the symbolic names of the dimensions to numbers.

Enumerator:

RT	Retention time dimension id (0 if used as a const int).
MZ	Mass-to-charge dimension id (1 if used as a const int).
DIMENSION	Number of dimensions.

Constructor & Destructor Documentation

Peak2D ( ) [inline]

Peak2D ( const Peak2D & p ) [inline]

Copy constructor.

~Peak2D ( ) [inline]

Destructor.

Note:: The destructor is non-virtual although many classes are derived from Peak2D. This is intentional, since otherwise we would "waste" space for a vtable pointer in each instance. Normally you should not derive other classes from Peak2D (unless you know what you are doing, of course).

Member Function Documentation

static char const* fullDimensionName ( UInt const dim ) [static]

Full name of the dimension (self-explanatory form).

static char const* fullDimensionNameMZ ( ) [static]

Full name of the dimension (self-explanatory form).

static char const* fullDimensionNameRT ( ) [static]

Full name of the dimension (self-explanatory form).

static char const* fullDimensionUnit ( UInt const dim ) [static]

Unit of measurement (self-explanatory form).

static char const* fullDimensionUnitMZ ( ) [static]

Unit of measurement (self-explanatory form).

static char const* fullDimensionUnitRT ( ) [static]

Unit of measurement (self-explanatory form).

IntensityType getIntensity ( ) const [inline]

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), OpenMS::intensityAscendingComparator(), OpenMS::intensityComparator(), OpenMS::intensityPointerComparator(), InIntensityRange< PeakType >::operator()(), Peak2D::IntensityLess::operator()(), MRMTransitionGroupPicker::pickTransitionGroup(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and EGHTraceFitter< PeakType >::setInitialParameters_().

CoordinateType getMZ ( ) const [inline]

Returns the m/z coordinate (index 1).

Referenced by FeatureFinderAlgorithmPicked< PeakType, FeatureType >::extendMassTraces_(), ModelFitter< PeakType, FeatureType >::fit(), KroenikFile::load(), SpectraMerger::SpectraDistance_::operator()(), Peak2D::MZLess::operator()(), OpenMS::positionComparator(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::writeFeatureDebugInfo_().

PositionType& getPosition ( ) [inline]

Mutable access to the position.

PositionType const& getPosition ( ) const [inline]

Non-mutable access to the position.

Referenced by InMzRange< PeakType >::operator()(), and Peak2D::PositionLess::operator()().

CoordinateType getRT ( ) const [inline]

Returns the RT coordinate (index 0).

Referenced by IDMapper::annotate(), MRMFeatureFinderScoring::calculateSwathScores_(), ModelFitter< PeakType, FeatureType >::fit(), SpectraMerger::SpectraDistance_::operator()(), PrecursorIonSelection::SeqTotalScoreMore::operator()(), Peak2D::RTLess::operator()(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

bool operator!= ( const Peak2D & rhs ) const [inline]

Equality operator.

Peak2D& operator= ( const Peak2D & rhs ) [inline]

Assignment operator.

References Peak2D::intensity_, and Peak2D::position_.

Referenced by RichPeak2D::operator=(), and FeatureHandle::operator=().

bool operator== ( const Peak2D & rhs ) const [inline]

Equality operator.

References Peak2D::intensity_, and Peak2D::position_.

Referenced by RichPeak2D::operator==().

void setIntensity ( IntensityType intensity ) [inline]

Non-mutable access to the data point intensity (height).

Referenced by FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::createHRData(), MRMTransitionGroupPicker::createMRMFeature(), ThresholdMower::filterSpectrum(), ModelFitter< PeakType, FeatureType >::fit(), XMassFile::load(), SpecArrayFile::load(), MsInspectFile::load(), KroenikFile::load(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), PeakPickerHiRes::pick(), MRMTransitionGroupPicker::remove_overlapping_features(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

void setMZ ( CoordinateType coordinate ) [inline]

Mutable access to the m/z coordinate (index 1).

Referenced by ChromatogramTools::convertChromatogramsToSpectra(), FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::createHRData(), MRMTransitionGroupPicker::createMRMFeature(), ModelFitter< PeakType, FeatureType >::fit(), SpecArrayFile::load(), MsInspectFile::load(), KroenikFile::load(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), SpectraMerger::mergeSpectraPrecursors(), PeakPickerHiRes::pick(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

void setPosition ( const PositionType & position ) [inline]

Mutable access to the position.

Referenced by XMassFile::load(), MascotInfile::load(), MascotGenericFile::load(), DBAdapter::loadSpectrum(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

void setRT ( CoordinateType coordinate ) [inline]

Mutable access to the RT coordinate (index 0).

Referenced by ChromatogramTools::convertSpectraToChromatograms(), MRMTransitionGroupPicker::createMRMFeature(), ModelFitter< PeakType, FeatureType >::fit(), SpecArrayFile::load(), MsInspectFile::load(), KroenikFile::load(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), SpectraMerger::mergeSpectraPrecursors(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmMRM< PeakType, FeatureType >::run().

static char const* shortDimensionName ( UInt const dim ) [static]

Short name of the dimension (abbreviated form).

Referenced by ProductModel< 2 >::ProductModel(), ProductModel< 2 >::setModel(), and ProductModel< 2 >::updateMembers_().

static char const* shortDimensionNameMZ ( ) [static]

Short name of the dimension (abbreviated form).

static char const* shortDimensionNameRT ( ) [static]

Short name of the dimension (abbreviated form).

static char const* shortDimensionUnit ( UInt const dim ) [static]

Unit of measurement (abbreviated form).

static char const* shortDimensionUnitMZ ( ) [static]

Unit of measurement (abbreviated form).

static char const* shortDimensionUnitRT ( ) [static]

Unit of measurement (abbreviated form).

Friends And Related Function Documentation

std::ostream& operator<<	(	std::ostream &	os,
		const Peak2D &	point
	)			`[friend]`

Print the contents to a stream.

Member Data Documentation

char const* const dimension_name_full_[DIMENSION] [static, protected]

Full name of the dimension (self-explanatory form).

char const* const dimension_name_short_[DIMENSION] [static, protected]

Short name of the dimension (abbreviated form).

char const* const dimension_unit_full_[DIMENSION] [static, protected]

Unit of measurement (self-explanatory form).

char const* const dimension_unit_short_[DIMENSION] [static, protected]

Unit of measurement (abbreviated form).

IntensityType intensity_ [protected]

The data point intensity.

Referenced by Peak2D::operator=(), and Peak2D::operator==().

PositionType position_ [protected]

The data point position.

Referenced by Peak2D::operator=(), and Peak2D::operator==().

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:55 using doxygen 1.7.1

Peak2D Class Reference [Kernel]

Classes

Public Types

Public Member Functions

Protected Attributes

Friends

Dimension descriptions

Detailed Description

Member Typedef Documentation

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation

Peak2D Class Reference
[Kernel]