MapAlignmentAlgorithmPoseClustering Class Reference

A map alignment algorithm based on pose clustering. More...

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

Inheritance diagram for MapAlignmentAlgorithmPoseClustering:

Public Member Functions
	MapAlignmentAlgorithmPoseClustering ()
	Default constructor. More...
virtual	~MapAlignmentAlgorithmPoseClustering ()
	Destructor. More...
void	align (const FeatureMap &map, TransformationDescription &trafo)
void	align (const MSExperiment<> &map, TransformationDescription &trafo)
void	align (const ConsensusMap &map, TransformationDescription &trafo)
template<typename MapType >
void	setReference (const MapType &map)
Public Member Functions inherited from MapAlignmentAlgorithm
	MapAlignmentAlgorithm ()
	Default constructor. More...
virtual	~MapAlignmentAlgorithm ()
	Destructor. More...
virtual void	alignPeakMaps (std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &)
	Aligns peak maps. More...
virtual void	alignCompactFeatureMaps (std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &)
	Aligns vectors of 2D peaks (memory efficient version of FeatureMap) More...
virtual void	alignFeatureMaps (std::vector< FeatureMap > &, std::vector< TransformationDescription > &)
	Aligns feature maps. More...
virtual void	alignConsensusMaps (std::vector< ConsensusMap > &, std::vector< TransformationDescription > &)
	Aligns consensus maps. More...
virtual void	alignPeptideIdentifications (std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &)
	Aligns peptide identifications. More...
virtual void	setReference (Size reference_index=0, const String &reference_file="")
	Defines a reference for the alignment. 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 DefaultParamHandler &	operator= (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 Param &	getParameters () const
	Non-mutable access to the parameters. More...
const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...
const String &	getName () 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...
Public Member Functions inherited from ProgressLogger
	ProgressLogger ()
	Constructor. More...
	~ProgressLogger ()
	Destructor. More...
	ProgressLogger (const ProgressLogger &other)
	Copy constructor. More...
ProgressLogger &	operator= (const ProgressLogger &other)
	Assignment Operator. More...
void	setLogType (LogType type) const
	Sets the progress log that should be used. The default type is NONE! More...
LogType	getLogType () const
	Returns the type of progress log being used. More...
void	startProgress (SignedSize begin, SignedSize end, const String &label) const
	Initializes the progress display. More...
void	setProgress (SignedSize value) const
	Sets the current progress. More...
void	endProgress () const
	Ends the progress display. More...

Static Public Member Functions
static MapAlignmentAlgorithm *	create ()
	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 MapAlignmentAlgorithm
static void	fitModel (const String &model_type, const Param &params, std::vector< TransformationDescription > &trafos)
	Fits a model with given parameters to the transformations. More...
static void	registerChildren ()
	Register all derived classes in this method. More...

Protected Member Functions
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...
Protected Member Functions inherited from DefaultParamHandler
void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes
PoseClusteringAffineSuperimposer	superimposer_
StablePairFinder	pairfinder_
ConsensusMap	reference_
Int	max_num_peaks_considered_
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< String >	subsections_
	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...
Protected Attributes inherited from ProgressLogger
LogType	type_
time_t	last_invoke_
ProgressLoggerImpl *	current_logger_

Private Member Functions
	MapAlignmentAlgorithmPoseClustering (const MapAlignmentAlgorithmPoseClustering &)
	Copy constructor intentionally not implemented -> private. More...
MapAlignmentAlgorithmPoseClustering &	operator= (const MapAlignmentAlgorithmPoseClustering &)
	Assignment operator intentionally not implemented -> private. More...

Additional Inherited Members
Public Types inherited from ProgressLogger
enum	LogType { CMD, GUI, NONE }
	Possible log types. More...
Static Protected Member Functions inherited from ProgressLogger
static String	logTypeToFactoryName_ (LogType type)
	Return the name of the factory product used for this log type. More...
Static Protected Attributes inherited from ProgressLogger
static int	recursion_depth_

Detailed Description

A map alignment algorithm based on pose clustering.

Pose clustering analyzes pair distances to find the most probable transformation of retention times. The algorithm chooses the x most intensity peaks/features per map. This is modeled via the parameter 'max_num_peaks_considered', which in turn influences the runtime and stability of the results. Bigger values prolong computation, smaller values might lead to no or unstable trafos. Set to -1 to use all features (might take very long for large maps).

For further details see:
Eva Lange et al.
A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data
ISMB/ECCB 2007

Constructor & Destructor Documentation

MapAlignmentAlgorithmPoseClustering

(

)

Default constructor.

virtual ~MapAlignmentAlgorithmPoseClustering ( )

virtual

Destructor.

MapAlignmentAlgorithmPoseClustering ( const MapAlignmentAlgorithmPoseClustering &  )

private

Copy constructor intentionally not implemented -> private.

Member Function Documentation

void align	(	const FeatureMap &	map,
		TransformationDescription &	trafo
	)

void align	(	const MSExperiment<> &	map,
		TransformationDescription &	trafo
	)

void align	(	const ConsensusMap &	map,
		TransformationDescription &	trafo
	)

static MapAlignmentAlgorithm* create ( )

inlinestatic

Creates a new instance of this class (for Factory)

static String getProductName ( )

inlinestatic

Returns the product name (for the Factory)

MapAlignmentAlgorithmPoseClustering& operator= ( const MapAlignmentAlgorithmPoseClustering &  )

private

Assignment operator intentionally not implemented -> private.

void setReference ( const MapType &  map )

inline

References MapConversion::convert().

virtual void updateMembers_ ( )

protectedvirtual

This method is used to update extra member variables at the end of the setParameters() 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

Int max_num_peaks_considered_

protected

StablePairFinder pairfinder_

protected

ConsensusMap reference_

protected

PoseClusteringAffineSuperimposer superimposer_

protected