Kernel

Kernel datastructures. More...

Modules
	ComparatorUtils
	A collection of utilities for comparators.
	RangeUtils
	Predicates for range operations.

Classes
struct	BaseFeature::QualityLess
	Compare by quality. More...
class	BaseFeature
	A basic LC-MS feature. More...
struct	ChromatogramPeak::IntensityLess
	Comparator by intensity. More...
struct	ChromatogramPeak::RTLess
	Comparator by RT position. More...
struct	ChromatogramPeak::PositionLess
	Comparator by position. As this class has dimension 1, this is basically an alias for RTLess. More...
class	ChromatogramPeak
	A 1-dimensional raw data point or peak for chromatograms. More...
class	ChromatogramTools
	Conversion class to convert chromatograms. More...
struct	ConsensusFeature::SizeLess
	Compare by size(), the number of consensus elements. More...
struct	ConsensusFeature::MapsLess
	Compare by the sets of consensus elements (lexicographically) More...
struct	ConsensusFeature::Ratio
	slim struct to feed the need for systematically storing of ratios ( More...
class	ConsensusFeature
	A 2-dimensional consensus feature. More...
struct	ConsensusMap::FileDescription
	Source file description for input files. More...
class	ConsensusMap
	A container for consensus elements. More...
class	Feature
	An LC-MS feature. More...
struct	FeatureHandle::IndexLess
	Comparator by map and unique id. More...
class	FeatureHandle
	Representation of a Peak2D, RichPeak2D or Feature . More...
class	FeatureMap
	A container for features. More...
class	MassTrace
	A container type that gathers peaks similar in m/z and moving along retention time. More...
struct	MSChromatogram< PeakT >::MZLess
	Comparator for the retention time. More...
class	MSChromatogram< PeakT >
	The representation of a chromatogram. More...
struct	MSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, addMassTraces >
	Helper class to add either general data points in set2DData or use mass traces from meta values. More...
struct	MSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, false >
struct	MSExperiment< PeakT, ChromatogramPeakT >::ContainerAdd_< ContainerIterator, true >
class	MSExperiment< PeakT, ChromatogramPeakT >
	In-Memory representation of a mass spectrometry experiment. More...
struct	MSSpectrum< PeakT >::RTLess
	Comparator for the retention time. More...
class	MSSpectrum< PeakT >
	The representation of a 1D spectrum. More...
class	OnDiscMSExperiment< PeakT, ChromatogramPeakT >
	Representation of a mass spectrometry experiment on disk. More...
struct	Peak1D::IntensityLess
struct	Peak1D::MZLess
	Comparator by m/z position. More...
struct	Peak1D::PositionLess
	Comparator by position. As this class has dimension 1, this is basically an alias for MZLess. More...
class	Peak1D
	A 1-dimensional raw data point or peak. More...
struct	Peak2D::IntensityLess
struct	Peak2D::RTLess
	Comparator by RT position. More...
struct	Peak2D::MZLess
	Comparator by m/z position. More...
struct	Peak2D::PositionLess
	Comparator by position. Lexicographical comparison (first RT then m/z) is done. More...
class	Peak2D
	A 2-dimensional raw data point or peak. More...
class	RichPeak1D
	A 1-dimensional raw data point or peak with meta information. More...
class	RichPeak2D
	A 2-dimensional raw data point or peak with meta information. More...

Type definitions
enum	AnnotationState {   FEATURE_ID_NONE, FEATURE_ID_SINGLE, FEATURE_ID_MULTIPLE_SAME, FEATURE_ID_MULTIPLE_DIVERGENT,   SIZE_OF_ANNOTATIONSTATE }
	state of identification, use getIDState() to query it More...
typedef float	QualityType
	Type of quality values. More...
typedef Int	ChargeType
	Type of charge values. More...
typedef float	WidthType
	Type of feature width/FWHM (RT) More...
static const std::string	NamesOfAnnotationState [SIZE_OF_ANNOTATIONSTATE]

Type definitions
enum	{ DIMENSION = 1 }
	Dimension. More...
typedef double	IntensityType
	Intensity type. More...
typedef DPosition< 1 >	PositionType
	Position type. More...
typedef double	CoordinateType
	Coordinate type. More...

Type definitions
Dimension
enum	{ DIMENSION = 1 }
typedef float	IntensityType
	Intensity type. More...
typedef DPosition< 1 >	PositionType
	Position type. More...
typedef double	CoordinateType
	Coordinate type. More...

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) More...
static char const *const	dimension_name_full_ [DIMENSION]
	Full name of the dimension (self-explanatory form) More...
static char const *const	dimension_unit_short_ [DIMENSION]
	Unit of measurement (abbreviated form) More...
static char const *const	dimension_unit_full_ [DIMENSION]
	Unit of measurement (self-explanatory form) More...
static char const *	shortDimensionName (UInt const dim)
	Short name of the dimension (abbreviated form) More...
static char const *	shortDimensionNameRT ()
	Short name of the dimension (abbreviated form) More...
static char const *	shortDimensionNameMZ ()
	Short name of the dimension (abbreviated form) More...
static char const *	fullDimensionName (UInt const dim)
	Full name of the dimension (self-explanatory form) More...
static char const *	fullDimensionNameRT ()
	Full name of the dimension (self-explanatory form) More...
static char const *	fullDimensionNameMZ ()
	Full name of the dimension (self-explanatory form) More...
static char const *	shortDimensionUnit (UInt const dim)
	Unit of measurement (abbreviated form) More...
static char const *	shortDimensionUnitRT ()
	Unit of measurement (abbreviated form) More...
static char const *	shortDimensionUnitMZ ()
	Unit of measurement (abbreviated form) More...
static char const *	fullDimensionUnit (UInt const dim)
	Unit of measurement (self-explanatory form) More...
static char const *	fullDimensionUnitRT ()
	Unit of measurement (self-explanatory form) More...
static char const *	fullDimensionUnitMZ ()
	Unit of measurement (self-explanatory form) More...
typedef MSSpectrum< Peak1D >	PeakSpectrum
	Spectrum consisting of raw data points or peaks. More...
typedef MSExperiment< Peak1D >	PeakMap
	Two-dimensional map of raw data points or peaks. More...
typedef MSSpectrum< RichPeak1D >	RichPeakSpectrum
	Spectrum consisting of raw data points or peaks with meta information. More...
typedef MSExperiment< RichPeak1D >	RichPeakMap
	Two-dimensional map of raw data points or peaks with meta information. More...
typedef MSChromatogram< ChromatogramPeak >	Chromatogram
	Chromatogram consisting of raw data points or peaks. More...

Detailed Description

Kernel datastructures.

Typedef Documentation

typedef Int ChargeType

Type of charge values.

typedef MSChromatogram<ChromatogramPeak> Chromatogram

Chromatogram consisting of raw data points or peaks.

typedef double CoordinateType

Coordinate type.

typedef double CoordinateType

Coordinate type.

typedef float IntensityType

Intensity type.

typedef double IntensityType

Intensity type.

typedef MSExperiment<Peak1D> PeakMap

Two-dimensional map of raw data points or peaks.

typedef MSSpectrum<Peak1D> PeakSpectrum

Spectrum consisting of raw data points or peaks.

Meta information includes retention time and MS-level.

typedef DPosition<1> PositionType

Position type.

typedef DPosition<1> PositionType

Position type.

typedef float QualityType

Type of quality values.

typedef MSExperiment<RichPeak1D> RichPeakMap

Two-dimensional map of raw data points or peaks with meta information.

typedef MSSpectrum<RichPeak1D> RichPeakSpectrum

Spectrum consisting of raw data points or peaks with meta information.

typedef float WidthType

Type of feature width/FWHM (RT)

Enumeration Type Documentation

anonymous enum

Dimension.

Enumerator
DIMENSION

anonymous enum

Enumerator
DIMENSION

enum AnnotationState

state of identification, use getIDState() to query it

Enumerator
FEATURE_ID_NONE
FEATURE_ID_SINGLE
FEATURE_ID_MULTIPLE_SAME
FEATURE_ID_MULTIPLE_DIVERGENT
SIZE_OF_ANNOTATIONSTATE

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.

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)

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)

Variable Documentation

char const* const dimension_name_full_[DIMENSION]

staticprotected

Full name of the dimension (self-explanatory form)

char const* const dimension_name_short_[DIMENSION]

staticprotected

Short name of the dimension (abbreviated form)

char const* const dimension_unit_full_[DIMENSION]

staticprotected

Unit of measurement (self-explanatory form)

char const* const dimension_unit_short_[DIMENSION]

staticprotected

Unit of measurement (abbreviated form)

const std::string NamesOfAnnotationState[SIZE_OF_ANNOTATIONSTATE]

static