OpenMS
BaseSuperimposer Class Referenceabstract

The base class of all superimposer algorithms. More...

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

Inheritance diagram for BaseSuperimposer:
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Collaboration diagram for BaseSuperimposer:
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Public Member Functions

 BaseSuperimposer ()
 Constructor. More...
 
 ~BaseSuperimposer () override
 Destructor. More...
 
virtual void run (const ConsensusMap &map_model, const ConsensusMap &map_scene, TransformationDescription &transformation)=0
 Estimates the transformation between input maps and returns the estimated transformations. 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...
 
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...
 
virtual ~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 setLogger (ProgressLoggerImpl *logger)
 Sets the logger to be used for progress logging. 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 (UInt64 bytes_processed=0) const
 
void nextProgress () const
 increment progress by 1 (according to range begin-end) More...
 

Private Member Functions

 BaseSuperimposer (const BaseSuperimposer &)
 Copy constructor intentionally not implemented. More...
 
BaseSuperimposeroperator= (const BaseSuperimposer &)
 Assignment operator intentionally not implemented. More...
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD , GUI , NONE }
 Possible log types. More...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. 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...
 
- 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

The base class of all superimposer algorithms.

This class defines the basic interface for all superimposer algorithms. It works on several element maps and computes transformations that map the elements of the maps as near as possible to each other.

Constructor & Destructor Documentation

◆ BaseSuperimposer() [1/2]

Constructor.

◆ ~BaseSuperimposer()

~BaseSuperimposer ( )
override

Destructor.

◆ BaseSuperimposer() [2/2]

BaseSuperimposer ( const BaseSuperimposer )
private

Copy constructor intentionally not implemented.

Member Function Documentation

◆ operator=()

BaseSuperimposer& operator= ( const BaseSuperimposer )
private

Assignment operator intentionally not implemented.

◆ run()

virtual void run ( const ConsensusMap map_model,
const ConsensusMap map_scene,
TransformationDescription transformation 
)
pure virtual

Estimates the transformation between input maps and returns the estimated transformations.

Exceptions
IllegalArgumentis thrown if the input maps are invalid.

Implemented in PoseClusteringShiftSuperimposer, and PoseClusteringAffineSuperimposer.