#include <OpenMS/ANALYSIS/MAPMATCHING/BaseAlignment.h>
This class is the base class for the alignment 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 in the final consensus map (a stl vector of consensus elements).
Public Types | |
typedef ConsensusElementT | ConsensusElementType |
Consensus element type. | |
typedef ConsensusElementType::ElementType | ElementType |
Element type (the type of the elements that are grouped together). | |
typedef ConsensusElementType::ElementContainerType | ElementContainerType |
Element container type (the type of the element maps, that are aligned). | |
typedef std::vector < ConsensusElementType > | ConsensusVectorType |
Consensus map type. | |
Public Member Functions | |
BaseAlignment () | |
Constructor. | |
virtual | ~BaseAlignment () |
Destructor. | |
void | setElementMapVector (const std::vector< ElementContainerType * > &element_map_vector) |
Mutable access to the vector of maps. | |
std::vector < ElementContainerType * > & | getElementMapVector () |
Mutable access to the vector of maps. | |
const std::vector < ElementContainerType * > & | getElementMapVector () const |
Non-mutable access to the vector of maps. | |
void | setTransformationVector (const std::vector< Grid > &transformations) |
Mutable access to the transformations. | |
const std::vector< Grid > & | getTransformationVector () const |
Non-mutable access to the transformations. | |
void | setFileNames (const std::vector< String > &file_names) |
Mutable access to the vector of file names. | |
const std::vector< String > & | getFileNames () const |
Non-mutable access to the vector of file names. | |
void | setMapType (const String &map_type) |
Mutable access to the map type. | |
const String & | getMapType () const |
Non-mutable access to the map type (map type can be "feature_map", "peak_map" or "consensus_map". | |
const ConsensusMap < ConsensusElementType > & | getFinalConsensusMap () const |
Non-mutable access to the final consensus map. | |
void | setFinalConsensusMap (const ConsensusMap< ConsensusElementType > &final_consensus_map) |
Mutable access to the final consensus map. | |
virtual void | run ()=0 throw (Exception::InvalidValue) |
Start the alignment. | |
virtual String | getAlignmentTree () const =0 |
Return the alignment tree in Newick Tree format. | |
Protected Member Functions | |
void | buildConsensusVectorTypeInsertInGroup_ (UInt map_index, std::vector< ConsensusElementType > &cons_map) |
Build a consensus map of the map with index map_index (the set of grouped elements contains the element itself). | |
void | buildConsensusVectorType_ (UInt map_index, std::vector< ConsensusElementType > &cons_map) |
Build a consensus map of the map with index map_index (the set of grouped elements doesn't contain the element itself). | |
void | updateMembers_ () |
This method is used to update extra member variables at the end of the setParam() method. | |
Protected Attributes | |
ConsensusMap < ConsensusElementType > | final_consensus_map_ |
Final consensus map. | |
std::vector< Grid > | transformations_ |
The transformation vector. | |
String | map_type_ |
The map type. |
typedef ConsensusElementT ConsensusElementType |
Consensus element type.
Reimplemented in StarAlignment, and StarAlignment< AlignmentT::ConsensusElementType >.
typedef ConsensusElementType::ElementType ElementType |
Element type (the type of the elements that are grouped together).
Reimplemented in StarAlignment, and StarAlignment< AlignmentT::ConsensusElementType >.
typedef ConsensusElementType::ElementContainerType ElementContainerType |
Element container type (the type of the element maps, that are aligned).
Reimplemented in StarAlignment, and StarAlignment< AlignmentT::ConsensusElementType >.
typedef std::vector< ConsensusElementType > ConsensusVectorType |
Consensus map type.
Reimplemented in StarAlignment, and StarAlignment< AlignmentT::ConsensusElementType >.
BaseAlignment | ( | ) | [inline] |
Constructor.
virtual ~BaseAlignment | ( | ) | [inline, virtual] |
Destructor.
void setElementMapVector | ( | const std::vector< ElementContainerType * > & | element_map_vector | ) | [inline] |
Mutable access to the vector of maps.
std::vector< ElementContainerType* >& getElementMapVector | ( | ) | [inline] |
Mutable access to the vector of maps.
const std::vector< ElementContainerType* >& getElementMapVector | ( | ) | const [inline] |
Non-mutable access to the vector of maps.
void setTransformationVector | ( | const std::vector< Grid > & | transformations | ) | [inline] |
Mutable access to the transformations.
const std::vector< Grid >& getTransformationVector | ( | ) | const [inline] |
Non-mutable access to the transformations.
void setFileNames | ( | const std::vector< String > & | file_names | ) | [inline] |
Mutable access to the vector of file names.
const std::vector< String >& getFileNames | ( | ) | const [inline] |
Non-mutable access to the vector of file names.
void setMapType | ( | const String & | map_type | ) | [inline] |
Mutable access to the map type.
const String& getMapType | ( | ) | const [inline] |
Non-mutable access to the map type (map type can be "feature_map", "peak_map" or "consensus_map".
const ConsensusMap< ConsensusElementType >& getFinalConsensusMap | ( | ) | const [inline] |
Non-mutable access to the final consensus map.
void setFinalConsensusMap | ( | const ConsensusMap< ConsensusElementType > & | final_consensus_map | ) | [inline] |
Mutable access to the final consensus map.
virtual void run | ( | ) | throw (Exception::InvalidValue) [pure virtual] |
Start the alignment.
Implemented in StarAlignment, and StarAlignment< AlignmentT::ConsensusElementType >.
virtual String getAlignmentTree | ( | ) | const [pure virtual] |
Return the alignment tree in Newick Tree format.
Implemented in StarAlignment, and StarAlignment< AlignmentT::ConsensusElementType >.
void buildConsensusVectorTypeInsertInGroup_ | ( | UInt | map_index, | |
std::vector< ConsensusElementType > & | cons_map | |||
) | [inline, protected] |
Build a consensus map of the map with index map_index (the set of grouped elements contains the element itself).
void buildConsensusVectorType_ | ( | UInt | map_index, | |
std::vector< ConsensusElementType > & | cons_map | |||
) | [inline, protected] |
Build a consensus map of the map with index map_index (the set of grouped elements doesn't contain the element itself).
void updateMembers_ | ( | ) | [inline, protected, virtual] |
This method is used to update extra member variables at the end of the setParam() method.
Also call it at the end of the derived classes' copy constructor and assignment operator.
The default implementation is empty.
Reimplemented from DefaultParamHandler.
ConsensusMap< ConsensusElementType > final_consensus_map_ [protected] |
Final consensus map.
std::vector< Grid > transformations_ [protected] |
The transformation vector.
Generated Tue Apr 1 15:36:41 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |