OpenMS  2.8.0
Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | List of all members
BaseGroupFinder Class Referenceabstract

The base class of all element group finding algorithms. More...

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

Inheritance diagram for BaseGroupFinder:
[legend]
Collaboration diagram for BaseGroupFinder:
[legend]

Public Member Functions

 BaseGroupFinder ()
 Default constructor. More...
 
 ~BaseGroupFinder () override
 Destructor. More...
 
virtual void run (const std::vector< ConsensusMap > &input, ConsensusMap &result)=0
 Run the algorithm. 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...
 
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 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...
 
void nextProgress () const
 increment progress by 1 (according to range begin-end) More...
 

Static Public Member Functions

static void registerChildren ()
 Register all derived classes here. 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

void checkIds_ (const std::vector< ConsensusMap > &maps) const
 Checks if all file descriptions have disjoint map identifiers. 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...
 

Private Member Functions

 BaseGroupFinder (const BaseGroupFinder &)
 Copy constructor intentionally not implemented. More...
 
BaseGroupFinderoperator= (const BaseGroupFinder &)
 Assignment operator intentionally not implemented. 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...
 
- 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 element group finding algorithms.

This class defines the basic interface for all element group finding algorithms.

All derived algorithms take one or several consensus maps and find corresponding features across the maps (or within one map). They return one consensus map containing the found consensus features.

The element indices of the result consensus features are the container access indices of the input maps. The map indices of the result consensus features are are the indices in the input map vector.

Constructor & Destructor Documentation

◆ BaseGroupFinder() [1/2]

Default constructor.

◆ ~BaseGroupFinder()

~BaseGroupFinder ( )
override

Destructor.

◆ BaseGroupFinder() [2/2]

BaseGroupFinder ( const BaseGroupFinder )
private

Copy constructor intentionally not implemented.

Member Function Documentation

◆ checkIds_()

void checkIds_ ( const std::vector< ConsensusMap > &  maps) const
protected

Checks if all file descriptions have disjoint map identifiers.

Exceptions
Exception::IllegalArgumentIs thrown if a file id is found twice

◆ operator=()

BaseGroupFinder& operator= ( const BaseGroupFinder )
private

Assignment operator intentionally not implemented.

◆ registerChildren()

static void registerChildren ( )
static

Register all derived classes here.

◆ run()

virtual void run ( const std::vector< ConsensusMap > &  input,
ConsensusMap result 
)
pure virtual

Run the algorithm.

Exceptions
Exception::IllegalArgumentis thrown if the input data is not valid.

Implemented in StablePairFinder, SimplePairFinder, QTClusterFinder, and LabeledPairFinder.