Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages

BaseSuperimposer Class Template Reference

#include <OpenMS/ANALYSIS/MAPMATCHING/BaseSuperimposer.h>

Inheritance diagram for BaseSuperimposer:

FactoryProduct DefaultParamHandler PoseClusteringAffineSuperimposer PoseClusteringShiftSuperimposer

List of all members.


Detailed Description

template<typename MapT = FeatureMap<>>
class OpenMS::BaseSuperimposer< MapT >

The base class of all superimposer algorithms.

This class defines the basic interface for all superimposer algorithms. It works on two element maps (FeatureMap is the default map type, but you can also use a pointer map like DPeakConstReferenceArray) and computes a transformation, that maps the elements of one map (scene map) as near as possible to the elements in the other map (model map). A element can be a DPeak, a DFeature, a ConsensusPeak or ConsensusFeature (wheras DFeature is the default element type).

Policy for copy constructor and assignment: element_map_ is maintained as pointer and taken shallow copy.

Public Types

enum  LCMS { RT = 0, MZ = 1 }
enum  Maps { MODEL = 0, SCENE = 1 }
typedef MapT PointMapType
 Container for input elements.
typedef PointMapType::value_type PointType
 Type of elements considered here.
typedef DoubleReal QualityType
 Quality type.
typedef DPosition< 2 > PositionType
 Position type.
typedef DoubleReal IntensityType
typedef LinearMapping TransformationType
 Type of estimated transformation.

Public Member Functions

 BaseSuperimposer ()
 Constructor.
virtual ~BaseSuperimposer ()
 Destructor.
void setElementMap (UInt const index, const PointMapType &element_map)
 Set element map.
const PointMapTypegetElementMap (UInt index)
 Get element map.
const PointMapTypegetElementMap (UInt index) const
 Get element maps (non-mutable).
void setTransformation (UInt dim, const TransformationType &trafo)
 Set transformation.
const TransformationTypegetTransformation (UInt dim) const
 Get transformation.
virtual void run ()=0
 Estimates the transformation for each grid cell.

Static Public Member Functions

static void registerChildren ()
 Register all derived classes here.

Protected Attributes

PointMapType const * element_map_ [2]
 Two maps of elements to be matched.
TransformationType final_transformation_ [2]
 Final transformation.


Member Typedef Documentation

typedef MapT PointMapType

Container for input elements.

Reimplemented in PoseClusteringAffineSuperimposer, and PoseClusteringShiftSuperimposer.

typedef PointMapType::value_type PointType

Type of elements considered here.

Reimplemented in PoseClusteringAffineSuperimposer, and PoseClusteringShiftSuperimposer.

typedef DoubleReal QualityType

Quality type.

Reimplemented in PoseClusteringAffineSuperimposer, and PoseClusteringShiftSuperimposer.

typedef DPosition< 2 > PositionType

Position type.

Reimplemented in PoseClusteringAffineSuperimposer, and PoseClusteringShiftSuperimposer.

typedef DoubleReal IntensityType

Reimplemented in PoseClusteringAffineSuperimposer, and PoseClusteringShiftSuperimposer.

typedef LinearMapping TransformationType

Type of estimated transformation.


Member Enumeration Documentation

enum LCMS

Symbolic names for indices for the two dimensions of LC-MS

Enumerator:
RT 
MZ 

enum Maps

Symbolic names for indices of element maps etc. This should make things more understandable and maintainable.

Enumerator:
MODEL 
SCENE 

Reimplemented in PoseClusteringAffineSuperimposer, and PoseClusteringShiftSuperimposer.


Constructor & Destructor Documentation

BaseSuperimposer (  )  [inline]

Constructor.

virtual ~BaseSuperimposer (  )  [inline, virtual]

Destructor.


Member Function Documentation

void setElementMap ( UInt const   index,
const PointMapType element_map 
) [inline]

Set element map.

const PointMapType& getElementMap ( UInt  index  )  [inline]

Get element map.

const PointMapType& getElementMap ( UInt  index  )  const [inline]

Get element maps (non-mutable).

void setTransformation ( UInt  dim,
const TransformationType trafo 
) [inline]

Set transformation.

const TransformationType& getTransformation ( UInt  dim  )  const [inline]

Get transformation.

virtual void run (  )  [pure virtual]

Estimates the transformation for each grid cell.

Implemented in PoseClusteringAffineSuperimposer, and PoseClusteringShiftSuperimposer.

void registerChildren (  )  [inline, static]

Register all derived classes here.


Member Data Documentation

PointMapType const* element_map_[2] [protected]

Two maps of elements to be matched.

TransformationType final_transformation_[2] [protected]

Final transformation.


The documentation for this class was generated from the following files:
Generated Tue Apr 1 15:36:41 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1