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FeatureGroupingAlgorithmQT Class Reference

A feature grouping algorithm for unlabeled data. More...

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

Inheritance diagram for FeatureGroupingAlgorithmQT:
FeatureGroupingAlgorithm DefaultParamHandler

Public Member Functions

 FeatureGroupingAlgorithmQT ()
 Default constructor. More...
 
virtual ~FeatureGroupingAlgorithmQT ()
 Destructor. More...
 
virtual void group (const std::vector< FeatureMap > &maps, ConsensusMap &out)
 Applies the algorithm to feature maps. More...
 
virtual void group (const std::vector< ConsensusMap > &maps, ConsensusMap &out)
 Applies the algorithm to consensus maps. More...
 
- Public Member Functions inherited from FeatureGroupingAlgorithm
 FeatureGroupingAlgorithm ()
 Default constructor. More...
 
virtual ~FeatureGroupingAlgorithm ()
 Destructor. More...
 
void transferSubelements (const std::vector< ConsensusMap > &maps, ConsensusMap &out) const
 Transfers subelements (grouped features) from input consensus maps to the result consensus map. More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 

Static Public Member Functions

static FeatureGroupingAlgorithmcreate ()
 Creates a new instance of this class (for Factory) More...
 
static String getProductName ()
 Returns the product name (for the Factory) More...
 
- Static Public Member Functions inherited from FeatureGroupingAlgorithm
static void registerChildren ()
 Register all derived classes in this method. More...
 

Private Member Functions

 FeatureGroupingAlgorithmQT (const FeatureGroupingAlgorithmQT &)
 Copy constructor intentionally not implemented -> private. More...
 
FeatureGroupingAlgorithmQToperator= (const FeatureGroupingAlgorithmQT &)
 Assignment operator intentionally not implemented -> private. More...
 
template<typename MapType >
void group_ (const std::vector< MapType > &maps, ConsensusMap &out)
 Applies the algorithm to feature or consensus maps. More...
 

Additional Inherited Members

- Protected Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 

Detailed Description

A feature grouping algorithm for unlabeled data.

The algorithm takes a number of feature or consensus maps and searches for corresponding (consensus) features across different maps. The maps have to be aligned (i.e. retention time distortions corrected, e.g. using one of the MapAlignmentAlgorithms), but small deviations are tolerated.

This particular algorithm accumulates the features from all input maps, then applies a variant of QT clustering to find groups of corresponding features. For more details, see QTClusterFinder.

Constructor & Destructor Documentation

Default constructor.

virtual ~FeatureGroupingAlgorithmQT ( )
virtual

Destructor.

Copy constructor intentionally not implemented -> private.

Member Function Documentation

static FeatureGroupingAlgorithm* create ( )
inlinestatic

Creates a new instance of this class (for Factory)

static String getProductName ( )
inlinestatic

Returns the product name (for the Factory)

virtual void group ( const std::vector< FeatureMap > &  maps,
ConsensusMap out 
)
virtual

Applies the algorithm to feature maps.

Precondition
The data ranges of the input maps have to be up-to-date (use FeatureMap::updateRanges).
Exceptions
IllegalArgumentis thrown if less than two input maps are given.

Implements FeatureGroupingAlgorithm.

virtual void group ( const std::vector< ConsensusMap > &  maps,
ConsensusMap out 
)
virtual

Applies the algorithm to consensus maps.

Precondition
The data ranges of the input maps have to be up-to-date (use ConsensusMap::updateRanges).
Exceptions
IllegalArgumentis thrown if less than two input maps are given.

Reimplemented from FeatureGroupingAlgorithm.

void group_ ( const std::vector< MapType > &  maps,
ConsensusMap out 
)
private

Applies the algorithm to feature or consensus maps.

Precondition
The data ranges of the input maps have to be up-to-date (use MapType::updateRanges).
Exceptions
IllegalArgumentis thrown if less than two input maps are given.
FeatureGroupingAlgorithmQT& operator= ( const FeatureGroupingAlgorithmQT )
private

Assignment operator intentionally not implemented -> private.


OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11