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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

Public Member Functions

 MapAlignmentAlgorithm ()
 Default constructor. More...
 
virtual ~MapAlignmentAlgorithm ()
 Destructor. More...
 
virtual void alignPeakMaps (std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &)
 Aligns peak maps. More...
 
virtual void alignCompactFeatureMaps (std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &)
 Aligns vectors of 2D peaks (memory efficient version of FeatureMap) More...
 
virtual void alignFeatureMaps (std::vector< FeatureMap > &, std::vector< TransformationDescription > &)
 Aligns feature maps. More...
 
virtual void alignConsensusMaps (std::vector< ConsensusMap > &, std::vector< TransformationDescription > &)
 Aligns consensus maps. More...
 
virtual void alignPeptideIdentifications (std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &)
 Aligns peptide identifications. More...
 
virtual void setReference (Size reference_index=0, const String &reference_file="")
 Defines a reference for the alignment. More...
 
- Public Member Functions inherited from DefaultParamHandler
 DefaultParamHandler (const String &name)
 Constructor with name that is displayed in error messages. More...
 
 DefaultParamHandler (const DefaultParamHandler &rhs)
 Copy constructor. More...
 
virtual ~DefaultParamHandler ()
 Destructor. More...
 
virtual DefaultParamHandleroperator= (const DefaultParamHandler &rhs)
 Assignment operator. More...
 
virtual bool operator== (const DefaultParamHandler &rhs) const
 Equality operator. More...
 
void setParameters (const Param &param)
 Sets the parameters. More...
 
const ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () const
 Non-mutable access to the name. More...
 
void setName (const String &name)
 Mutable access to the name. More...
 
const std::vector< String > & getSubsections () const
 Non-mutable access to the registered subsections. More...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (const ProgressLogger &other)
 Assignment Operator. More...
 
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
 
LogType getLogType () const
 Returns the type of progress log being used. More...
 
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
 
void setProgress (SignedSize value) const
 Sets the current progress. More...
 
void endProgress () const
 Ends the progress display. More...
 

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. More...
 
static void registerChildren ()
 Register all derived classes in this method. More...
 

Private Member Functions

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

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- Protected Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- Static Protected Member Functions inherited from ProgressLogger
static String logTypeToFactoryName_ (LogType type)
 Return the name of the factory product used for this log type. More...
 
- Protected Attributes inherited from DefaultParamHandler
Param param_
 Container for current parameters. More...
 
Param defaults_
 Container for default parameters. This member should be filled in the constructor of derived classes! More...
 
std::vector< Stringsubsections_
 Container for registered subsections. This member should be filled in the constructor of derived classes! More...
 
String error_name_
 Name that is displayed in error messages during the parameter checking. More...
 
bool check_defaults_
 If this member is set to false no checking if parameters in done;. More...
 
bool warn_empty_defaults_
 If this member is set to false no warning is emitted when defaults are empty;. More...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
time_t last_invoke_
 
ProgressLoggerImplcurrent_logger_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

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

Default constructor.

virtual ~MapAlignmentAlgorithm ( )
virtual

Destructor.

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::NotImplementedis thrown if an algorithm cannot align feature maps
virtual void alignConsensusMaps ( std::vector< ConsensusMap > &  ,
std::vector< TransformationDescription > &   
)
virtual

Aligns consensus maps.

Exceptions
Exception::NotImplementedis 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::NotImplementedis 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::NotImplementedis 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::NotImplementedis 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_indexIndex of input file to use as reference (1-based!)
reference_filePath to external reference file
Exceptions
Exception::InvalidParameteris thrown if the algorithm does not support references

Reimplemented in MapAlignmentAlgorithmIdentification.


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 12:49:28 using doxygen 1.8.11