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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...
 

Enumerations

enum  MT_QUANTMETHOD { MT_QUANT_AREA = 0, MT_QUANT_MEDIAN, SIZE_OF_MT_QUANTMETHOD }
 

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.

Coordinate type.

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.

enum MT_QUANTMETHOD
Enumerator
MT_QUANT_AREA 
MT_QUANT_MEDIAN 
SIZE_OF_MT_QUANTMETHOD 

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

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:57 using doxygen 1.8.9.1