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MapAlignmentAlgorithmPoseClustering Class Reference

A map alignment algorithm based on pose clustering. More...

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

Inheritance diagram for MapAlignmentAlgorithmPoseClustering:
MapAlignmentAlgorithm DefaultParamHandler ProgressLogger

Public Member Functions

 MapAlignmentAlgorithmPoseClustering ()
 Default constructor. More...
 
virtual ~MapAlignmentAlgorithmPoseClustering ()
 Destructor. More...
 
void align (const FeatureMap &map, TransformationDescription &trafo)
 
void align (const MSExperiment<> &map, TransformationDescription &trafo)
 
void align (const ConsensusMap &map, TransformationDescription &trafo)
 
template<typename MapType >
void setReference (const MapType &map)
 
- Public Member Functions inherited from MapAlignmentAlgorithm
 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 MapAlignmentAlgorithmcreate ()
 Creates a new instance of this class (for Factory) More...
 
static String getProductName ()
 Returns the product name (for the Factory) More...
 
- Static Public Member Functions inherited from MapAlignmentAlgorithm
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...
 

Protected Member Functions

virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

PoseClusteringAffineSuperimposer superimposer_
 
StablePairFinder pairfinder_
 
ConsensusMap reference_
 
Int max_num_peaks_considered_
 
- 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_
 

Private Member Functions

 MapAlignmentAlgorithmPoseClustering (const MapAlignmentAlgorithmPoseClustering &)
 Copy constructor intentionally not implemented -> private. More...
 
MapAlignmentAlgorithmPoseClusteringoperator= (const MapAlignmentAlgorithmPoseClustering &)
 Assignment operator intentionally not implemented -> private. More...
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. 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...
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

A map alignment algorithm based on pose clustering.

Pose clustering analyzes pair distances to find the most probable transformation of retention times. The algorithm chooses the x most intensity peaks/features per map. This is modeled via the parameter 'max_num_peaks_considered', which in turn influences the runtime and stability of the results. Bigger values prolong computation, smaller values might lead to no or unstable trafos. Set to -1 to use all features (might take very long for large maps).

For further details see:
Eva Lange et al.
A Geometric Approach for the Alignment of Liquid Chromatography-Mass Spectrometry Data
ISMB/ECCB 2007

Constructor & Destructor Documentation

Default constructor.

Destructor.

Copy constructor intentionally not implemented -> private.

Member Function Documentation

void align ( const FeatureMap map,
TransformationDescription trafo 
)
void align ( const MSExperiment<> &  map,
TransformationDescription trafo 
)
void align ( const ConsensusMap map,
TransformationDescription trafo 
)
static MapAlignmentAlgorithm* create ( )
inlinestatic

Creates a new instance of this class (for Factory)

static String getProductName ( )
inlinestatic

Returns the product name (for the Factory)

Assignment operator intentionally not implemented -> private.

void setReference ( const MapType map)
inline
virtual void updateMembers_ ( )
protectedvirtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

Member Data Documentation

Int max_num_peaks_considered_
protected
StablePairFinder pairfinder_
protected
ConsensusMap reference_
protected
PoseClusteringAffineSuperimposer superimposer_
protected

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