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PairMatcher Class Reference

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

Inheritance diagram for PairMatcher:

FactoryProduct DefaultParamHandler

List of all members.


Detailed Description

The PairMatcher allows the matching of labeled features (features with a fixed distance).

Finds feature pairs that have a defined distance in RT and m/z in the same map.

PairMatcher Parameters are explained on a separate page.

Public Types

Type definitions
typedef Feature FeatureType
typedef FeatureMap FeatureMapType
typedef ElementPair PairType
typedef std::vector< PairTypePairVectorType

Public Member Functions

 PairMatcher (FeatureMapType &features)
 Constructor.
 PairMatcher (const PairMatcher &source)
 Copy constructor.
virtual PairMatcheroperator= (const PairMatcher &source)
 Assignment operator.
virtual ~PairMatcher ()
 Destructor.
const PairVectorTyperun ()
 Pairing step of the PairMatcher.
const PairVectorTypegetBestPairs ()
 Matching step of the PairMatcher.

Static Public Member Functions

static void printInfo (std::ostream &out, const PairVectorType &pairs)
 Print informations about the pair vector pairs to stream out.
static const String getProductName ()

Protected Member Functions

double PValue_ (double x, double m, double sig1, double sig2)

Protected Attributes

FeatureMapTypefeatures_
 features to be paired
PairVectorType pairs_
 all possible pairs (after Pairing)
PairVectorType best_pairs_
 only the best pairs, no ambiguities (after Matching)

Static Protected Attributes

static const double sqrt2_
 Square root of two.

Classes

struct  Comparator
 Compare to pairs by comparing their qualities. More...


Member Typedef Documentation

typedef Feature FeatureType

typedef FeatureMap FeatureMapType

typedef ElementPair PairType

typedef std::vector< PairType > PairVectorType


Constructor & Destructor Documentation

PairMatcher ( FeatureMapType features  ) 

Constructor.

PairMatcher ( const PairMatcher source  ) 

Copy constructor.

virtual ~PairMatcher (  )  [virtual]

Destructor.


Member Function Documentation

virtual PairMatcher& operator= ( const PairMatcher source  )  [virtual]

Assignment operator.

const PairVectorType& run (  ) 

Pairing step of the PairMatcher.

Return pairs of features that have the same charge and a distance lying within a user-defined range.

const PairVectorType& getBestPairs (  ) 

Matching step of the PairMatcher.

Greedy 2-approximation to extract a set of pairs so that each feature is contained in at most one pair.

static void printInfo ( std::ostream &  out,
const PairVectorType pairs 
) [static]

Print informations about the pair vector pairs to stream out.

Print informations (quality, ratio, charge, feature positions, ...) about the pair vector pairs to stream out

static const String getProductName (  )  [inline, static]

double PValue_ ( double  x,
double  m,
double  sig1,
double  sig2 
) [inline, protected]

return the p-value at position x for the bi-Gaussian distribution with mean m and standard deviation sig1 (left) and sig2 (right)


Member Data Documentation

const double sqrt2_ [static, protected]

Square root of two.

FeatureMapType& features_ [protected]

features to be paired

PairVectorType pairs_ [protected]

all possible pairs (after Pairing)

PairVectorType best_pairs_ [protected]

only the best pairs, no ambiguities (after Matching)


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:42 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1