QTCluster Class Reference [Datastructures]

A representation of a QT cluster used for feature grouping. More...

#include <OpenMS/DATASTRUCTURES/QTCluster.h>

List of all members.

Public Member Functions
	QTCluster (GridFeature *center_point, Size num_maps, DoubleReal max_distance, bool use_IDs)
	Detailed constructor.
virtual	~QTCluster ()
	Destructor.
DoubleReal	getCenterRT () const
	Returns the RT value of the cluster.
DoubleReal	getCenterMZ () const
	Returns the m/z value of the cluster center.
Size	size () const
	Returns the size of the cluster (number of elements, incl. center).
bool	operator< (QTCluster &cluster)
	Compare by quality.
void	add (GridFeature *element, DoubleReal distance)
	Adds a new element/neighbor to the cluster.
void	getElements (std::map< Size, GridFeature * > &elements)
	Gets the clustered elements.
bool	update (const std::map< Size, GridFeature * > &removed)
	Updates the cluster after data points were removed.
DoubleReal	getQuality ()
	Returns the cluster quality.
const std::set< AASequence > &	getAnnotations ()
	Return the set of peptide sequences annotated to the cluster center.
Private Types
typedef std::map< Size, std::multimap< DoubleReal, GridFeature * > >	NeighborMap
	Mapping: input map -> distance to center -> neighboring point.
Private Member Functions
	QTCluster ()
	Base constructor (not accessible).
void	computeQuality_ ()
	Computes the quality of the cluster.
DoubleReal	optimizeAnnotations_ ()
	Finds the optimal annotation (peptide sequences) for the cluster.
Private Attributes
GridFeature *	center_point_
	Pointer to the cluster center.
NeighborMap	neighbors_
	Neighbors of the cluster center, sorted by distance, for different input maps.
DoubleReal	max_distance_
	Maximum distance of a point that can still belong to the cluster.
Size	num_maps_
	Number of input maps.
DoubleReal	quality_
	Quality of the cluster.
bool	changed_
	Has the cluster changed (if yes, quality needs to be recomputed)?
bool	use_IDs_
	Keep track of peptide IDs and use them for matching?
std::set< AASequence >	annotations_
	Set of annotations of the cluster.

---

Detailed Description

A representation of a QT cluster used for feature grouping.

Ultimately, a cluster represents a group of corresponding features (or consensus features) from different input maps (feature maps or consensus maps).

Clusters are defined by their center points (one feature each). A cluster also stores a number of potential cluster elements (other features) from different input maps, together with their distances to the cluster center. Every feature that satisfies certain constraints with respect to the cluster center is a potential cluster element. However, since a feature group can only contain one feature from each input map, only the "best" (i.e. closest to the cluster center) such feature is considered a true cluster element.

The QT clustering algorithm has the characteristic of initially producing all possible, overlapping clusters. Iteratively, the best cluster is then extracted and the clustering is recomputed for the remaining points.

In our implementation, multiple rounds of clustering are not necessary. Instead, the clustering is updated in each iteration. This is the reason for storing all potential cluster elements: When a certain cluster is finalized, its elements have to be removed from the remaining clusters, and affected clusters change their composition. (Note that clusters can also be invalidated by this, if the cluster center is being removed.)

The quality of a cluster is the normalized average distance to the cluster center for present and missing cluster elements. The distance value for missing elements (if the cluster contains no feature from a certain input map) is the user-defined threshold that marks the maximum allowed radius of a cluster.

See also:

QTClusterFinder

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Member Typedef Documentation

typedef std::map<Size, std::multimap<DoubleReal, GridFeature *> > NeighborMap [private]

Mapping: input map -> distance to center -> neighboring point.

Note:

There should never be an empty sub-map! (When a sub-map becomes empty, it should be removed from the overall map.)

---

Constructor & Destructor Documentation

QTCluster

(

)

[private]

Base constructor (not accessible).

QTCluster	(	GridFeature *	center_point,
		Size	num_maps,
		DoubleReal	max_distance,
		bool	use_IDs
	)

Detailed constructor.

Parameters:

	center_point	Pointer to the center point
	num_maps	Number of input maps
	max_distance	Maximum allowed distance of two points
	use_IDs	Use peptide annotations?

virtual ~QTCluster

(

)

[virtual]

Destructor.

---

Member Function Documentation

void add	(	GridFeature *	element,
		DoubleReal	distance
	)

Adds a new element/neighbor to the cluster.

Note:

There is no check whether the element/neighbor already exists in the cluster!

Parameters:

	element	The element to be added
	distance	Distance of the element to the center point

void computeQuality_

(

)

[private]

Computes the quality of the cluster.

const std::set<AASequence>& getAnnotations

(

)

Return the set of peptide sequences annotated to the cluster center.

DoubleReal getCenterMZ

(

)

const

Returns the m/z value of the cluster center.

DoubleReal getCenterRT

(

)

const

Returns the RT value of the cluster.

void getElements

(

std::map< Size, GridFeature * > &

elements

)

Gets the clustered elements.

DoubleReal getQuality

(

)

Returns the cluster quality.

bool operator<

(

QTCluster &

cluster

)

Compare by quality.

DoubleReal optimizeAnnotations_

(

)

[private]

Finds the optimal annotation (peptide sequences) for the cluster.

The optimal annotation is the one that results in the best quality. It is stored in annotations_;

Returns:

The total distance between cluster elements and the center.

Size size

(

)

const

Returns the size of the cluster (number of elements, incl. center).

bool update

(

const std::map< Size, GridFeature * > &

removed

)

Updates the cluster after data points were removed.

Returns:

Whether the cluster is still valid (it's not if the cluster center is among the removed points).

---

Member Data Documentation

std::set<AASequence> annotations_ [private]

Set of annotations of the cluster.

The set of peptide sequences that is compatible to the cluster center and results in the best cluster quality.

GridFeature* center_point_ [private]

Pointer to the cluster center.

bool changed_ [private]

Has the cluster changed (if yes, quality needs to be recomputed)?

DoubleReal max_distance_ [private]

Maximum distance of a point that can still belong to the cluster.

NeighborMap neighbors_ [private]

Neighbors of the cluster center, sorted by distance, for different input maps.

The first (best) point in each sub-map is considered a cluster element.

Size num_maps_ [private]

Number of input maps.

DoubleReal quality_ [private]

Quality of the cluster.

bool use_IDs_ [private]

Keep track of peptide IDs and use them for matching?