Simple feature extension algorithm. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/SimpleExtender.h>

Inheritance diagram for SimpleExtender< PeakType, FeatureType >:

Classes
struct	IndexWithPriority
	A helper structure to sort indizes by their priority. More...
Public Types
typedef FeaFiModule< PeakType, FeatureType >	Base
typedef Base::IntensityType	IntensityType
	Intensity of a data point.
typedef Base::CoordinateType	CoordinateType
	Coordinates of a point (m/z and rt).
typedef DoubleReal	ProbabilityType
	Priority of a point (see below).
Public Member Functions
	SimpleExtender (const MSExperiment< PeakType > map, FeatureMap< FeatureType > features, FeatureFinder *ff)
	Constructor.
virtual	~SimpleExtender ()
	destructor
void	extend (const ChargedIndexSet &seed_region, ChargedIndexSet &result_region)
	return next seed
Protected Member Functions
virtual void	updateMembers_ ()
void	writeDebugFile_ (const std::vector< IndexPair > &peaks, UInt nr_feat)
	write DTA2D debug file for the feature with index `nr_feat`
bool	isTooFarFromCentroid_ (const IndexPair &index)
	Checks if the current peak is too far from the centroid.
void	moveMzUp_ (const IndexPair &index)
	Extends the seed into positive m/z direction.
void	moveMzDown_ (const IndexPair &index)
	Extends the seed into negative m/z direction.
void	moveRtUp_ (const IndexPair &index)
	Extension into positive rt dimension.
void	moveRtDown_ (const IndexPair &index)
	Extends the seed into negative retention time direction.
ProbabilityType	computePeakPriority_ (const IndexPair &index)
	Computes the priority of a peak as function of intensity and distance from seed.
void	checkNeighbour_ (const IndexPair &index)
	Checks the neighbours of the current for insertion into the boundary.
Protected Attributes
Math::AveragePosition< 2 >	running_avg_
	keeps an running average of the peak coordinates weighted by the intensities
std::map< IndexPair, ProbabilityType >	priorities_
	Keeps track of peaks already included in the boundary (value is priority of peak).
DPosition< 2 >	last_pos_extracted_
	Position of last peak extracted from the boundary (used to compute the priority of neighbouring peaks).
std::priority_queue < IndexWithPriority, std::vector< IndexWithPriority > , typename IndexWithPriority::PriorityLess >	boundary_
	Represents the boundary of a feature.
IntensityType	intensity_threshold_
	Mininum intensity of a boundary point. Calculated from 'intensity_factor' and the seed intensity.
CoordinateType	dist_mz_up_
	Maximum distance to seed in positive m/z.
CoordinateType	dist_mz_down_
	Maximum distance to seed in negative m/z.
CoordinateType	dist_rt_up_
	Maximum distance to seed in positive retention time.
CoordinateType	dist_rt_down_
	Maximum distance to seed in negative retention time.
ProbabilityType	priority_threshold_
	Minium priority for points in the feature region (priority is function of intensity and distance to seed).
ChargedIndexSet	region_
	charged index set
Private Member Functions
	SimpleExtender ()
	Not implemented.
SimpleExtender &	operator= (const SimpleExtender &)
	Not implemented.
	SimpleExtender (const SimpleExtender &)
	Not implemented.

Detailed Description

template<class PeakType, class FeatureType>
class OpenMS::SimpleExtender< PeakType, FeatureType >

Simple feature extension algorithm.

This algorithm implements the extension phase of the FeatureFinder as described by Groepl et al. (2005)

We want to determine a region around a seed that is provided by the seeder. Initially, this region is empty. The boundary of this region is implemented using a MutablePriorityQueue which contains only the seed at the beginning.

At each step, we choose a data point from the boundary, move it into the region and explore the neigbourhood of this point in a cross-wise manner (m/z up, m/z down, rt up and rt down). During this exploration we compute the priority of all encountered points as a function of the distance from the extracted point. If this priority exceeds a threshold, we insert the corresponding point into the boundary and proceed.

We stop the extension phase if all peaks contained in the boundary have an intensity lower than a threshold or are too distant from the centroid of the feature.

Parameters of this class are:

Name	Type	Default	Restrictions	Description
dist_mz_up	float	6	min: 0	Maximum high m/z distance of peak in the region/boundary from the seed.
dist_mz_down	float	2	min: 0	Maximum low m/z distance of peak in the region/boundary from the seed.
dist_rt_up	float	5	min: 0	Maximum high RT distance of peak in the region/boundary from the seed.
dist_rt_down	float	5	min: 0	Maximum low RT distance of peak in the region/boundary from the seed.
priority_thr	float	-0.1		Minimum priority for data points to be included into the boundary of the feature (default 0.0). The priority of a data point is a function of its intensity and its distance to the last point included into the feature region. Setting this threshold to zero or a very small value is usually a good idea.
intensity_factor	float	0.03	min: 0 max: 1	Influences for intensity (ion count) threshold in the feature extension. We include only raw data points into this region if their intensity is larger than [intensity_factor * (intensity of the seed)].

Note:

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

Member Typedef Documentation

typedef FeaFiModule<PeakType, FeatureType> Base

typedef Base::CoordinateType CoordinateType

Coordinates of a point (m/z and rt).

typedef Base::IntensityType IntensityType

Intensity of a data point.

typedef DoubleReal ProbabilityType

Priority of a point (see below).

Constructor & Destructor Documentation

SimpleExtender	(	const MSExperiment< PeakType > *	map,
		FeatureMap< FeatureType > *	features,
		FeatureFinder *	ff
	)			`[inline]`

Constructor.

References StringList::create(), DefaultParamHandler::defaults_, DefaultParamHandler::defaultsToParam_(), Param::setMaxFloat(), Param::setMinFloat(), DefaultParamHandler::setName(), and Param::setValue().

virtual ~SimpleExtender ( ) [inline, virtual]

destructor

SimpleExtender ( ) [private]

Not implemented.

SimpleExtender ( const SimpleExtender< PeakType, FeatureType > & ) [private]

Not implemented.

Member Function Documentation

void checkNeighbour_ ( const IndexPair & index ) [inline, protected]

Checks the neighbours of the current for insertion into the boundary.

References SimpleExtender< PeakType, FeatureType >::boundary_, SimpleExtender< PeakType, FeatureType >::computePeakPriority_(), FeaFiModule< PeakType, FeatureType >::ff_, FeatureFinder::getPeakFlag(), FeaFiModule< PeakType, FeatureType >::getPeakIntensity(), SimpleExtender< PeakType, FeatureType >::intensity_threshold_, OPENMS_PRECONDITION, SimpleExtender< PeakType, FeatureType >::priorities_, and SimpleExtender< PeakType, FeatureType >::priority_threshold_.

Referenced by SimpleExtender< PeakType, FeatureType >::moveMzDown_(), SimpleExtender< PeakType, FeatureType >::moveMzUp_(), SimpleExtender< PeakType, FeatureType >::moveRtDown_(), and SimpleExtender< PeakType, FeatureType >::moveRtUp_().

ProbabilityType computePeakPriority_ ( const IndexPair & index ) [inline, protected]

Computes the priority of a peak as function of intensity and distance from seed.

References FeaFiModule< PeakType, FeatureType >::map_.

Referenced by SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), and SimpleExtender< PeakType, FeatureType >::extend().

void extend	(	const ChargedIndexSet &	seed_region,
		ChargedIndexSet &	result_region
	)			`[inline]`

return next seed

Referenced by FeatureFinderAlgorithmSimplest< PeakType, FeatureType >::run(), and FeatureFinderAlgorithmSimple< PeakType, FeatureType >::run().

bool isTooFarFromCentroid_ ( const IndexPair & index ) [inline, protected]

Checks if the current peak is too far from the centroid.

References SimpleExtender< PeakType, FeatureType >::dist_mz_down_, SimpleExtender< PeakType, FeatureType >::dist_mz_up_, SimpleExtender< PeakType, FeatureType >::dist_rt_down_, SimpleExtender< PeakType, FeatureType >::dist_rt_up_, FeaFiModule< PeakType, FeatureType >::getPeakMz(), FeaFiModule< PeakType, FeatureType >::getPeakRt(), AveragePosition< D >::getPosition(), Peak2D::MZ, OPENMS_PRECONDITION, Peak2D::RT, and SimpleExtender< PeakType, FeatureType >::running_avg_.

Referenced by SimpleExtender< PeakType, FeatureType >::moveMzDown_(), SimpleExtender< PeakType, FeatureType >::moveMzUp_(), SimpleExtender< PeakType, FeatureType >::moveRtDown_(), and SimpleExtender< PeakType, FeatureType >::moveRtUp_().

void moveMzDown_ ( const IndexPair & index ) [inline, protected]

Extends the seed into negative m/z direction.

References SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), FeaFiModule< PeakType, FeatureType >::getPrevMz(), and SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_().

Referenced by SimpleExtender< PeakType, FeatureType >::extend().

void moveMzUp_ ( const IndexPair & index ) [inline, protected]

Extends the seed into positive m/z direction.

References SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), FeaFiModule< PeakType, FeatureType >::getNextMz(), and SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_().

Referenced by SimpleExtender< PeakType, FeatureType >::extend().

void moveRtDown_ ( const IndexPair & index ) [inline, protected]

Extends the seed into negative retention time direction.

References SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), FeaFiModule< PeakType, FeatureType >::getPrevRt(), and SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_().

Referenced by SimpleExtender< PeakType, FeatureType >::extend().

void moveRtUp_ ( const IndexPair & index ) [inline, protected]

Extension into positive rt dimension.

References SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), FeaFiModule< PeakType, FeatureType >::getNextRt(), and SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_().

Referenced by SimpleExtender< PeakType, FeatureType >::extend().

SimpleExtender& operator= ( const SimpleExtender< PeakType, FeatureType > & ) [private]

Not implemented.

virtual void updateMembers_ ( ) [inline, protected, virtual]

References SimpleExtender< PeakType, FeatureType >::dist_mz_down_, SimpleExtender< PeakType, FeatureType >::dist_mz_up_, SimpleExtender< PeakType, FeatureType >::dist_rt_down_, SimpleExtender< PeakType, FeatureType >::dist_rt_up_, Param::getValue(), DefaultParamHandler::param_, and SimpleExtender< PeakType, FeatureType >::priority_threshold_.

void writeDebugFile_	(	const std::vector< IndexPair > &	peaks,
		UInt	nr_feat
	)			`[inline, protected]`

write DTA2D debug file for the feature with index nr_feat

References FeaFiModule< PeakType, FeatureType >::getPeakMz(), and FeaFiModule< PeakType, FeatureType >::getPeakRt().

Referenced by SimpleExtender< PeakType, FeatureType >::extend().

Member Data Documentation

std::priority_queue<IndexWithPriority, std::vector<IndexWithPriority>, typename IndexWithPriority::PriorityLess> boundary_ [protected]

Represents the boundary of a feature.

Referenced by SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), and SimpleExtender< PeakType, FeatureType >::extend().

CoordinateType dist_mz_down_ [protected]

Maximum distance to seed in negative m/z.

Referenced by SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_(), and SimpleExtender< PeakType, FeatureType >::updateMembers_().

CoordinateType dist_mz_up_ [protected]

Maximum distance to seed in positive m/z.

Referenced by SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_(), and SimpleExtender< PeakType, FeatureType >::updateMembers_().

CoordinateType dist_rt_down_ [protected]

Maximum distance to seed in negative retention time.

Referenced by SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_(), and SimpleExtender< PeakType, FeatureType >::updateMembers_().

CoordinateType dist_rt_up_ [protected]

Maximum distance to seed in positive retention time.

Referenced by SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_(), and SimpleExtender< PeakType, FeatureType >::updateMembers_().

IntensityType intensity_threshold_ [protected]

Mininum intensity of a boundary point. Calculated from 'intensity_factor' and the seed intensity.

Referenced by SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), and SimpleExtender< PeakType, FeatureType >::extend().

DPosition<2> last_pos_extracted_ [protected]

Position of last peak extracted from the boundary (used to compute the priority of neighbouring peaks).

Referenced by SimpleExtender< PeakType, FeatureType >::extend().

std::map<IndexPair, ProbabilityType> priorities_ [protected]

Keeps track of peaks already included in the boundary (value is priority of peak).

Referenced by SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), and SimpleExtender< PeakType, FeatureType >::extend().

ProbabilityType priority_threshold_ [protected]

Minium priority for points in the feature region (priority is function of intensity and distance to seed).

Referenced by SimpleExtender< PeakType, FeatureType >::checkNeighbour_(), and SimpleExtender< PeakType, FeatureType >::updateMembers_().

ChargedIndexSet region_ [protected]

charged index set

Math::AveragePosition<2> running_avg_ [protected]

keeps an running average of the peak coordinates weighted by the intensities

Referenced by SimpleExtender< PeakType, FeatureType >::extend(), and SimpleExtender< PeakType, FeatureType >::isTooFarFromCentroid_().

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:57 using doxygen 1.7.1

SimpleExtender< PeakType, FeatureType > Class Template Reference [FeatureFinder]

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

template<class PeakType, class FeatureType> class OpenMS::SimpleExtender< PeakType, FeatureType >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

SimpleExtender< PeakType, FeatureType > Class Template Reference
[FeatureFinder]

template<class PeakType, class FeatureType>
class OpenMS::SimpleExtender< PeakType, FeatureType >