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BaseAlignment Class Template Reference

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

Inheritance diagram for BaseAlignment:

DefaultParamHandler StarAlignment

List of all members.


Detailed Description

template<typename ConsensusElementT>
class OpenMS::BaseAlignment< ConsensusElementT >

Base alignment class.

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 StringgetMapType () 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< Gridtransformations_
 The transformation vector.
String map_type_
 The map type.


Member Typedef Documentation

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 >.


Constructor & Destructor Documentation

BaseAlignment (  )  [inline]

Constructor.

virtual ~BaseAlignment (  )  [inline, virtual]

Destructor.


Member Function Documentation

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.


Member Data Documentation

ConsensusMap< ConsensusElementType > final_consensus_map_ [protected]

Final consensus map.

std::vector< Grid > transformations_ [protected]

The transformation vector.

String map_type_ [protected]

The map type.


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