Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages

FeatureDecharger Class Reference
[Analsysis]

#include <OpenMS/ANALYSIS/DECHARGING/FeatureDecharger.h>

Inheritance diagram for FeatureDecharger:

DefaultParamHandler

List of all members.


Detailed Description

An algorithm to decharge features (i.e. as found by FeatureFinder).

The Decharger uses an hierarchical clustering (complete linkage) to group charge variants of the same peptide, which usually occur in ESI ionization mode. The resulting zero-charge peptides, which are defined by RT and mass are written in a featureXML file. Intensities of charge variants are summed up. The position of the zero charge variant is the average of all clustered peptides in each dimension. If several peptides with the same charge variant are grouped (which is clearly not allowed), a heuristic is used:

FeatureDecharger Parameters are explained on a separate page.

Public Types

typedef FeatureMap FeatureMapType
typedef Feature FeatureType
typedef DPosition< 2 > ClusterPointType

Public Member Functions

void compute (FeatureMapType &map)
 compute a zero-charge feature map from a set of charged features (map)
Constructors and Destructors
 FeatureDecharger ()
 default constructor
 FeatureDecharger (const FeatureDecharger &source)
 Copy constructor.
FeatureDechargeroperator= (const FeatureDecharger &source)
 Assignment operator.
virtual ~FeatureDecharger ()
 destructor
Acessors
const FeatureMapTypegetFeatureMap () const
 retrieve computed zero-charge feature map

Protected Attributes

FeatureMapType featuremap_dc_
 result feature map (zero-charge)


Member Typedef Documentation

typedef FeatureMap FeatureMapType

typedef Feature FeatureType

typedef DPosition<2> ClusterPointType


Constructor & Destructor Documentation

FeatureDecharger (  )  [inline]

default constructor

FeatureDecharger ( const FeatureDecharger source  )  [inline]

Copy constructor.

virtual ~FeatureDecharger (  )  [inline, virtual]

destructor


Member Function Documentation

FeatureDecharger& operator= ( const FeatureDecharger source  )  [inline]

Assignment operator.

const FeatureMapType& getFeatureMap (  )  const [inline]

retrieve computed zero-charge feature map

void compute ( FeatureMapType map  )  [inline]

compute a zero-charge feature map from a set of charged features (map)


Member Data Documentation

FeatureMapType featuremap_dc_ [protected]

result feature map (zero-charge)


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:41 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1