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MapAlignmentAlgorithm Class Reference

Base class for all map-alignment algorithms. More...

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

Inheritance diagram for MapAlignmentAlgorithm:
DefaultParamHandler ProgressLogger MapAlignmentAlgorithmIdentification MapAlignmentAlgorithmPoseClustering MapAlignmentAlgorithmSpectrumAlignment

List of all members.

Public Member Functions

 MapAlignmentAlgorithm ()
 Default constructor.
virtual ~MapAlignmentAlgorithm ()
 Destructor.
virtual void alignPeakMaps (std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &)
 Aligns peak maps.
virtual void alignCompactFeatureMaps (std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &)
 Aligns vectors of 2D peaks (memory efficient version of FeatureMap).
virtual void alignFeatureMaps (std::vector< FeatureMap<> > &, std::vector< TransformationDescription > &)
 Aligns feature maps.
virtual void alignConsensusMaps (std::vector< ConsensusMap > &, std::vector< TransformationDescription > &)
 Aligns consensus maps.
virtual void alignPeptideIdentifications (std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &)
 Aligns peptide identifications.
virtual void setReference (Size reference_index=0, const String &reference_file="")
 Defines a reference for the alignment.

Static Public Member Functions

static void fitModel (const String &model_type, const Param &params, std::vector< TransformationDescription > &trafos)
 Fits a model with given parameters to the transformations.
static void registerChildren ()
 Register all derived classes in this method.

Private Member Functions

 MapAlignmentAlgorithm (const MapAlignmentAlgorithm &)
 Copy constructor is not implemented -> private.
MapAlignmentAlgorithm & operator= (const MapAlignmentAlgorithm &)
 Assignment operator is not implemented -> private.

Detailed Description

Base class for all map-alignment algorithms.

It takes two or more maps and corrects for retention time distortions.

The input maps are transformed and the transformation description is returned.

Improvement:
The maps should not be all loaded before the algorithm - in order to save memory e.g. in the star-wise approach (Clemens)

Constructor & Destructor Documentation

MapAlignmentAlgorithm (  ) 

Default constructor.

virtual ~MapAlignmentAlgorithm (  )  [virtual]

Destructor.

MapAlignmentAlgorithm ( const MapAlignmentAlgorithm &   )  [private]

Copy constructor is not implemented -> private.

Member Function Documentation

virtual void alignCompactFeatureMaps ( std::vector< std::vector< Peak2D > > &  ,
std::vector< TransformationDescription > &   
) [virtual]

Aligns vectors of 2D peaks (memory efficient version of FeatureMap).

Exceptions:
Exception::NotImplemented is thrown if an algorithm cannot align feature maps
virtual void alignConsensusMaps ( std::vector< ConsensusMap > &  ,
std::vector< TransformationDescription > &   
) [virtual]

Aligns consensus maps.

Exceptions:
Exception::NotImplemented is thrown if an algorithm cannot align consensus maps

Reimplemented in MapAlignmentAlgorithmIdentification.

virtual void alignFeatureMaps ( std::vector< FeatureMap<> > &  ,
std::vector< TransformationDescription > &   
) [virtual]

Aligns feature maps.

Exceptions:
Exception::NotImplemented is thrown if an algorithm cannot align feature maps

Reimplemented in MapAlignmentAlgorithmIdentification.

virtual void alignPeakMaps ( std::vector< MSExperiment<> > &  ,
std::vector< TransformationDescription > &   
) [virtual]

Aligns peak maps.

Exceptions:
Exception::NotImplemented is thrown if an algorithm cannot align peak maps

Reimplemented in MapAlignmentAlgorithmIdentification, and MapAlignmentAlgorithmSpectrumAlignment.

virtual void alignPeptideIdentifications ( std::vector< std::vector< PeptideIdentification > > &  ,
std::vector< TransformationDescription > &   
) [virtual]

Aligns peptide identifications.

Exceptions:
Exception::NotImplemented is thrown if an algorithm cannot align peptide identifications

Reimplemented in MapAlignmentAlgorithmIdentification.

static void fitModel ( const String &  model_type,
const Param &  params,
std::vector< TransformationDescription > &  trafos 
) [static]

Fits a model with given parameters to the transformations.

This will not alter transformations of reference files (transformation type "identity").

MapAlignmentAlgorithm& operator= ( const MapAlignmentAlgorithm &   )  [private]

Assignment operator is not implemented -> private.

static void registerChildren (  )  [static]

Register all derived classes in this method.

virtual void setReference ( Size  reference_index = 0,
const String &  reference_file = "" 
) [virtual]

Defines a reference for the alignment.

Parameters:
reference_index Index of input file to use as reference (1-based!)
reference_file Path to external reference file
Exceptions:
Exception::InvalidParameter is thrown if the algorithm does not support references

Reimplemented in MapAlignmentAlgorithmIdentification.

OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:49 using doxygen 1.7.1