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

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

Inheritance diagram for MapAlignmentAlgorithmPoseClustering:

Collaboration diagram for MapAlignmentAlgorithmPoseClustering:

Public Member Functions
	MapAlignmentAlgorithmPoseClustering ()
	Default constructor. More...

	~MapAlignmentAlgorithmPoseClustering () override
	Destructor. More...

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

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

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

template<typename MapType >
void	setReference (const MapType &map)
	Sets the 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...

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...

virtual	~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	setLogger (ProgressLoggerImpl *logger)
	Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const

void	nextProgress () const
	increment progress by 1 (according to range begin-end) More...

Protected Member Functions
void	updateMembers_ () override
	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 Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
	Writes all parameters to meta values. 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

Parameters of this class are:

Name	Type	Default	Restrictions	Description
max_num_peaks_considered	int	1000	min: -1	The maximal number of peaks/features to be considered per map. To use all, set to '-1'.
superimposer:mz_pair_max_distance	float	0.5	min: 0.0	Maximum of m/z deviation of corresponding elements in different maps. This condition applies to the pairs considered in hashing.
superimposer:rt_pair_distance_fraction	float	0.1	min: 0.0 max: 1.0	Within each of the two maps, the pairs considered for pose clustering must be separated by at least this fraction of the total elution time interval (i.e., max - min).
superimposer:num_used_points	int	2000	min: -1	Maximum number of elements considered in each map (selected by intensity). Use this to reduce the running time and to disregard weak signals during alignment. For using all points, set this to -1.
superimposer:scaling_bucket_size	float	5.0e-03	min: 0.0	The scaling of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be a bit smaller than the error you would expect from repeated runs.
superimposer:shift_bucket_size	float	3.0	min: 0.0	The shift at the lower (respectively, higher) end of the retention time interval is being hashed into buckets of this size during pose clustering. A good choice for this would be about the time between consecutive MS scans.
superimposer:max_shift	float	1000.0	min: 0.0	Maximal shift which is considered during histogramming (in seconds). This applies for both directions.
superimposer:max_scaling	float	2.0	min: 1.0	Maximal scaling which is considered during histogramming. The minimal scaling is the reciprocal of this.
superimposer:dump_buckets	string			[DEBUG] If non-empty, base filename where hash table buckets will be dumped to. A serial number for each invocation will be appended automatically.
superimposer:dump_pairs	string			[DEBUG] If non-empty, base filename where the individual hashed pairs will be dumped to (large!). A serial number for each invocation will be appended automatically.
pairfinder:second_nearest_gap	float	2.0	min: 1.0	Only link features whose distance to the second nearest neighbors (for both sides) is larger by 'second_nearest_gap' than the distance between the matched pair itself.
pairfinder:use_identifications	string	false	true, false	Never link features that are annotated with different peptides (features without ID's always match; only the best hit per peptide identification is considered).
pairfinder:ignore_charge	string	false	true, false	false [default]: pairing requires equal charge state (or at least one unknown charge '0'); true: Pairing irrespective of charge state
pairfinder:ignore_adduct	string	true	true, false	true [default]: pairing requires equal adducts (or at least one without adduct annotation); true: Pairing irrespective of adducts
pairfinder:distance_RT:max_difference	float	100.0	min: 0.0	Never pair features with a larger RT distance (in seconds).
pairfinder:distance_RT:exponent	float	1.0	min: 0.0	Normalized RT differences ([0-1], relative to 'max_difference') are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
pairfinder:distance_RT:weight	float	1.0	min: 0.0	Final RT distances are weighted by this factor
pairfinder:distance_MZ:max_difference	float	0.3	min: 0.0	Never pair features with larger m/z distance (unit defined by 'unit')
pairfinder:distance_MZ:unit	string	Da	Da, ppm	Unit of the 'max_difference' parameter
pairfinder:distance_MZ:exponent	float	2.0	min: 0.0	Normalized ([0-1], relative to 'max_difference') m/z differences are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
pairfinder:distance_MZ:weight	float	1.0	min: 0.0	Final m/z distances are weighted by this factor
pairfinder:distance_intensity:exponent	float	1.0	min: 0.0	Differences in relative intensity ([0-1]) are raised to this power (using 1 or 2 will be fast, everything else is REALLY slow)
pairfinder:distance_intensity:weight	float	0.0	min: 0.0	Final intensity distances are weighted by this factor
pairfinder:distance_intensity:log_transform	string	disabled	enabled, disabled	Log-transform intensities? If disabled, d = \|int_f2 - int_f1\| / int_max. If enabled, d = \|log(int_f2 + 1) - log(int_f1 + 1)\| / log(int_max + 1))

Note:

If a section name is documented, the documentation is displayed as tooltip.
Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ MapAlignmentAlgorithmPoseClustering() [1/2]

MapAlignmentAlgorithmPoseClustering ( )

Default constructor.

◆ ~MapAlignmentAlgorithmPoseClustering()

~MapAlignmentAlgorithmPoseClustering ( )

override

Destructor.

◆ MapAlignmentAlgorithmPoseClustering() [2/2]

MapAlignmentAlgorithmPoseClustering ( const MapAlignmentAlgorithmPoseClustering & )

private

Copy constructor intentionally not implemented -> private.

Member Function Documentation

◆ align() [1/3]

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

◆ align() [2/3]

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

◆ align() [3/3]

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

◆ operator=()

MapAlignmentAlgorithmPoseClustering& operator= ( const MapAlignmentAlgorithmPoseClustering & )

private

Assignment operator intentionally not implemented -> private.

◆ setReference()

void setReference ( const MapType & map )

inline

Sets the reference for the alignment.

References MapConversion::convert().

◆ updateMembers_()

void updateMembers_ ( )

overrideprotectedvirtual

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

◆ max_num_peaks_considered_

Int max_num_peaks_considered_

protected

◆ pairfinder_

StablePairFinder pairfinder_

protected

◆ reference_

ConsensusMap reference_

protected

◆ superimposer_

PoseClusteringAffineSuperimposer superimposer_

protected

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ MapAlignmentAlgorithmPoseClustering() [1/2]

◆ ~MapAlignmentAlgorithmPoseClustering()

◆ MapAlignmentAlgorithmPoseClustering() [2/2]

Member Function Documentation

◆ align() [1/3]

◆ align() [2/3]

◆ align() [3/3]

◆ operator=()

◆ setReference()

◆ updateMembers_()

Member Data Documentation

◆ max_num_peaks_considered_

◆ pairfinder_

◆ reference_

◆ superimposer_