Stores a set of features, together with a 2D tree for fast search. More...

#include <OpenMS/ANALYSIS/QUANTITATION/KDTreeFeatureMaps.h>

Inheritance diagram for KDTreeFeatureMaps:

Collaboration diagram for KDTreeFeatureMaps:

Public Types
typedef KDTree::KDTree< 2, KDTreeFeatureNode >	FeatureKDTree
	2D tree on features More...

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

template<typename MapType >
	KDTreeFeatureMaps (const std::vector< MapType > &maps, const Param &param)
	Constructor. More...

	~KDTreeFeatureMaps () override
	Destructor. More...

template<typename MapType >
void	addMaps (const std::vector< MapType > &maps)
	Add `maps` and balance kd-tree. More...

void	addFeature (Size mt_map_index, const BaseFeature *feature)
	Add feature. More...

const BaseFeature *	feature (Size i) const
	Return pointer to feature i. More...

double	rt (Size i) const
	RT. More...

double	mz (Size i) const
	m/z More...

float	intensity (Size i) const
	Intensity. More...

Int	charge (Size i) const
	Charge. More...

Size	mapIndex (Size i) const
	Map index. More...

Size	size () const
	Number of features stored. More...

Size	treeSize () const
	Number of points in the tree. More...

Size	numMaps () const
	Number of maps. More...

void	clear ()
	Clear all data. More...

void	optimizeTree ()
	Optimize the kD tree. More...

void	getNeighborhood (Size index, std::vector< Size > &result_indices, double rt_tol, double mz_tol, bool mz_ppm, bool include_features_from_same_map=false, double max_pairwise_log_fc=-1.0) const
	Fill `result` with indices of all features compatible (wrt. RT, m/z, map index) to the feature with `index`. More...

void	queryRegion (double rt_low, double rt_high, double mz_low, double mz_high, std::vector< Size > &result_indices, Size ignored_map_index=std::numeric_limits< Size >::max()) const
	Fill `result` with indices of all features within the specified boundaries. More...

void	applyTransformations (const std::vector< TransformationModelLowess * > &trafos)
	Apply RT transformations. 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...

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
std::vector< const BaseFeature * >	features_
	Feature data. More...

std::vector< Size >	map_index_
	Map indices. More...

std::vector< double >	rt_
	(Potentially transformed) retention times More...

Size	num_maps_
	Number of maps. More...

FeatureKDTree	kd_tree_
	2D tree on features from all input maps. 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< 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...

Additional Inherited Members
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...

Detailed Description

Stores a set of features, together with a 2D tree for fast search.

Member Typedef Documentation

◆ FeatureKDTree

typedef KDTree::KDTree<2,KDTreeFeatureNode> FeatureKDTree

2D tree on features

Constructor & Destructor Documentation

◆ KDTreeFeatureMaps() [1/2]

KDTreeFeatureMaps ( )

inline

Default constructor.

◆ KDTreeFeatureMaps() [2/2]

KDTreeFeatureMaps	(	const std::vector< MapType > &	maps,
		const Param &	param
	)

inline

Constructor.

◆ ~KDTreeFeatureMaps()

~KDTreeFeatureMaps ( )

inlineoverride

Destructor.

Member Function Documentation

◆ addFeature()

void addFeature	(	Size	mt_map_index,
		const BaseFeature *	feature
	)

Add feature.

◆ addMaps()

void addMaps ( const std::vector< MapType > & maps )

inline

Add maps and balance kd-tree.

References MSExperiment::begin(), and MSExperiment::end().

◆ applyTransformations()

void applyTransformations ( const std::vector< TransformationModelLowess * > & trafos )

Apply RT transformations.

◆ charge()

Int charge ( Size i ) const

Charge.

◆ clear()

void clear ( )

Clear all data.

◆ feature()

const BaseFeature* feature ( Size i ) const

Return pointer to feature i.

◆ getNeighborhood()

void getNeighborhood	(	Size	index,
		std::vector< Size > &	result_indices,
		double	rt_tol,
		double	mz_tol,
		bool	mz_ppm,
		bool	include_features_from_same_map = `false`,
		double	max_pairwise_log_fc = `-1.0`
	)		const

Fill result with indices of all features compatible (wrt. RT, m/z, map index) to the feature with index.

◆ intensity()

float intensity ( Size i ) const

Intensity.

◆ mapIndex()

Size mapIndex ( Size i ) const

Map index.

◆ mz()

double mz ( Size i ) const

m/z

◆ numMaps()

Size numMaps ( ) const

Number of maps.

◆ optimizeTree()

void optimizeTree ( )

Optimize the kD tree.

◆ queryRegion()

void queryRegion	(	double	rt_low,
		double	rt_high,
		double	mz_low,
		double	mz_high,
		std::vector< Size > &	result_indices,
		Size	ignored_map_index = `std::numeric_limits< Size >::max()`
	)		const

Fill result with indices of all features within the specified boundaries.

◆ rt()

double rt ( Size i ) const

RT.

◆ size()

Size size ( ) const

Number of features stored.

◆ treeSize()

Size treeSize ( ) const

Number of points in the tree.

◆ 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

◆ features_

std::vector<const BaseFeature*> features_

protected

Feature data.

◆ kd_tree_

FeatureKDTree kd_tree_

protected

2D tree on features from all input maps.

◆ map_index_

std::vector<Size> map_index_

protected

Map indices.

◆ num_maps_

Size num_maps_

protected

Number of maps.

◆ rt_

std::vector<double> rt_

protected

(Potentially transformed) retention times

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ FeatureKDTree

Constructor & Destructor Documentation

◆ KDTreeFeatureMaps() [1/2]

◆ KDTreeFeatureMaps() [2/2]

◆ ~KDTreeFeatureMaps()

Member Function Documentation

◆ addFeature()

◆ addMaps()

◆ applyTransformations()

◆ charge()

◆ clear()

◆ feature()

◆ getNeighborhood()

◆ intensity()

◆ mapIndex()

◆ mz()

◆ numMaps()

◆ optimizeTree()

◆ queryRegion()

◆ rt()

◆ size()

◆ treeSize()

◆ updateMembers_()

Member Data Documentation

◆ features_

◆ kd_tree_

◆ map_index_

◆ num_maps_

◆ rt_