#include <OpenMS/ANALYSIS/MAPMATCHING/StarAlignment.h>
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.
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< ElementType > | ElementPairVectorType |
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. |
typedef BaseAlignment< ConsensusElementT > Base |
Base class.
typedef Base::ElementType ElementType |
Element type (the type of the elements that are grouped together).
Reimplemented from BaseAlignment.
Element container type (the type of the element maps, that are aligned).
Reimplemented from BaseAlignment.
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.
enum Maps |
StarAlignment | ( | ) | [inline] |
Constructor.
virtual ~StarAlignment | ( | ) | [inline, virtual] |
Destructor.
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] |
virtual String getAlignmentTree | ( | ) | const [inline, virtual] |
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.
UInt reference_map_index_ [protected] |
Int of the reference map.
Generated Tue Apr 1 15:36:42 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |