Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Member Functions | Static Public Member Functions | Private Member Functions | List of all members
FeatureGroupingAlgorithmIdentification Class Reference

A map feature grouping algorithm for identified features. More...

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

Inheritance diagram for FeatureGroupingAlgorithmIdentification:
FeatureGroupingAlgorithm DefaultParamHandler

Public Member Functions

 FeatureGroupingAlgorithmIdentification ()
 Default constructor. More...
 
virtual ~FeatureGroupingAlgorithmIdentification ()
 Destructor. More...
 
virtual void group (const std::vector< FeatureMap<> > &maps, ConsensusMap &out)
 Applies the algorithm. More...
 
- Public Member Functions inherited from FeatureGroupingAlgorithm
 FeatureGroupingAlgorithm ()
 Default constructor. More...
 
virtual ~FeatureGroupingAlgorithm ()
 Destructor. More...
 
virtual void group (const std::vector< ConsensusMap > &maps, ConsensusMap &out)
 
void transferSubelements (const std::vector< ConsensusMap > &maps, ConsensusMap &out) const
 Transfers subelements (grouped features) from input consensus maps to the result consensus map. 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...
 

Static Public Member Functions

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

Private Member Functions

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

Additional Inherited Members

- 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...
 

Detailed Description

A map feature grouping algorithm for identified features.

Deprecated:
Deprecated in OpenMS 1.7.

It takes many maps and searches for corresponding features. The corresponding features must be aligned, but may have small position deviations.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
xcorr_threshold float1.2  Peptide identifications having a SEQUEST XCorr score smaller than this are discarded.
rt_stdev_threshold float100  Maximum allowed standard deviation of retention times within a group
mz_stdev_threshold float1  Maximum allowed standard deviation of mass-to-charge within a group

Note:

Constructor & Destructor Documentation

Default constructor.

Destructor.

Copy constructor intentionally not implemented -> private.

Member Function Documentation

static FeatureGroupingAlgorithm* create ( )
inlinestatic

Creates a new instance of this class (for Factory)

static String getProductName ( )
inlinestatic

Returns the product name (for the Factory)

virtual void group ( const std::vector< FeatureMap<> > &  maps,
ConsensusMap out 
)
virtual

Applies the algorithm.

Exceptions
IllegalArgumentis thrown if less than two input maps are given.

Implements FeatureGroupingAlgorithm.

Assignment operator intentionally not implemented -> private.


OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5