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StarAlignment Class Template Reference
[Analsysis]

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

Inheritance diagram for StarAlignment:

BaseAlignment DefaultParamHandler

List of all members.


Detailed Description

template<typename ConsensusElementT = ConsensusFeature< FeatureMap < > >>
class OpenMS::StarAlignment< ConsensusElementT >

A star alignment class.

This class aligns elements of multiple element maps. An element can be a DPeak, a DFeature, a ConsensusPeak or a ConsensusFeature. Corresponding elements are grouped together and stored as a consensus element. This class computes a star-alignment, that means a reference map is chosen and in a first step all maps are mapped onto the reference map using the PoseClusteringPairwiseMapMatcher. In the second the final_consensus_map_ is determined. At the beginning of the alignment the final_consensus_map_ contains all elements of the reference_map as single consensus elements. Each transformed map is successive aligned to the final_consensus_map_ and corresponding elements are grouped together. At the end of the alignment the resulting final_consensus_map_ covers the elements of all maps, whereas corresponding elements are arranged together into ConsensusFeature or ConsensusPeak.

Note:
If you use consensus maps, the consensus elements are used as normal elements and you will loose the former consensus information.

Public Types

enum  Maps { MODEL = 0, SCENE = 1 }
typedef BaseAlignment
< ConsensusElementT > 
Base
 Base class.
typedef Base::ConsensusElementType ConsensusElementType
 Consensus element type.
typedef Base::ElementType ElementType
 Element type (the type of the elements that are grouped together).
typedef Base::ElementContainerType ElementContainerType
 Element container type (the type of the element maps, that are aligned).
typedef Base::ConsensusVectorType ConsensusVectorType
 Consensus map type.
typedef
DPeakConstReferenceArray
< ElementContainerType
PeakConstReferenceMapType
 Pointer vector.
typedef DPosition< 2 > PositionType
 Position.
typedef DoubleReal QualityType
 Quality.
typedef DoubleReal IntensityType
typedef ElementPair
< ConsensusElementType
ElementPairType
 Type of element pairs.
typedef std::vector
< ConsensusElementType
ConsensusElementPairVectorType
 Container for generated consensus element pairs.
typedef std::vector< ElementTypeElementPairVectorType
 Container for generated element pairs.

Public Member Functions

 StarAlignment ()
 Constructor.
virtual ~StarAlignment ()
 Destructor.
void setReferenceMapIndex (UInt index) throw (Exception::InvalidValue)
 Mutable access to the index of the reference map.
UInt getReferenceMapIndex () const
 Non-mutable access to the index of the reference map.
virtual void run () throw (Exception::InvalidValue)
 Estimates the transformation for each grid cell.
virtual String getAlignmentTree () const
 Return the Alignment tree in Newick Tree format.
void merge (ConsensusMap< ConsensusElementType > &new_map)
 Merge the elements of the final consensus map.

Protected Member Functions

void assignReferenceMap_ ()
 Define the map with the most elements as the reference map.
void alignMultipleFeatureMaps_ ()
 Align all feature maps to the reference map.
void alignMultiplePeakMaps_ ()
 Align all peak maps to the reference map.
void alignMultipleConsensusMaps_ ()
 Align all peak maps to the reference map.

Protected Attributes

UInt reference_map_index_
 Int of the reference map.

Member Typedef Documentation

typedef BaseAlignment< ConsensusElementT > Base

Base class.

typedef Base::ConsensusElementType ConsensusElementType

Consensus element type.

Reimplemented from BaseAlignment.

typedef Base::ElementType ElementType

Element type (the type of the elements that are grouped together).

Reimplemented from BaseAlignment.

typedef Base::ElementContainerType ElementContainerType

Element container type (the type of the element maps, that are aligned).

Reimplemented from BaseAlignment.

typedef Base::ConsensusVectorType ConsensusVectorType

Consensus map type.

Reimplemented from BaseAlignment.

typedef DPeakConstReferenceArray< ElementContainerType > PeakConstReferenceMapType

Pointer vector.

typedef DPosition< 2 > PositionType

Position.

typedef DoubleReal QualityType

Quality.

typedef DoubleReal IntensityType

typedef ElementPair< ConsensusElementType > ElementPairType

Type of element pairs.

typedef std::vector< ConsensusElementType > ConsensusElementPairVectorType

Container for generated consensus element pairs.

typedef std::vector< ElementType > ElementPairVectorType

Container for generated element pairs.


Member Enumeration Documentation

enum Maps

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

Enumerator:
MODEL 
SCENE 


Constructor & Destructor Documentation

StarAlignment (  )  [inline]

Constructor.

virtual ~StarAlignment (  )  [inline, virtual]

Destructor.


Member Function Documentation

void setReferenceMapIndex ( UInt  index  )  throw (Exception::InvalidValue) [inline]

Mutable access to the index of the reference map.

UInt getReferenceMapIndex (  )  const [inline]

Non-mutable access to the index of the reference map.

virtual void run (  )  throw (Exception::InvalidValue) [inline, virtual]

Estimates the transformation for each grid cell.

Implements BaseAlignment.

virtual String getAlignmentTree (  )  const [inline, virtual]

Return the Alignment tree in Newick Tree format.

Implements BaseAlignment.

void merge ( ConsensusMap< ConsensusElementType > &  new_map  )  [inline]

Merge the elements of the final consensus map.

void assignReferenceMap_ (  )  [inline, protected]

Define the map with the most elements as the reference map.

void alignMultipleFeatureMaps_ (  )  [inline, protected]

Align all feature maps to the reference map.

Pairwise map matcher

void alignMultiplePeakMaps_ (  )  [inline, protected]

Align all peak maps to the reference map.

void alignMultipleConsensusMaps_ (  )  [inline, protected]

Align all peak maps to the reference map.


Member Data Documentation

UInt reference_map_index_ [protected]

Int of the reference map.


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:42 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1