| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Member Functions | List of all members
FeatureGroupingAlgorithm Class Referenceabstract

Base class for all feature grouping algorithms. More...

`#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithm.h>`

Inheritance diagram for FeatureGroupingAlgorithm:

## Public Member Functions

| FeatureGroupingAlgorithm ()
| Default constructor. More...
| ~FeatureGroupingAlgorithm () override
| Destructor. More...
virtual void | group (const std::vector< FeatureMap > &maps, ConsensusMap &out)=0
| Applies the algorithm. The features in the input `maps` are grouped and the output is written to the consensus map `out`. 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 DefaultParamHandler & | operator= (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 Param & | getParameters () const
| Non-mutable access to the parameters. More...
const Param & | getDefaults () const
| Non-mutable access to the default parameters. More...
const String & | getName () 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 void | registerChildren ()
| Register all derived classes in this method. More...

## Protected Member Functions

template<class MapType >
void | postprocess_ (const std::vector< MapType > &maps, ConsensusMap &out)
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

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

## Additional Inherited Members

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< String > | subsections_
| 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

Base class for all feature grouping algorithms.

These algorithms group corresponding features in one map or across maps.

## Constructor & Destructor Documentation

## ◆ FeatureGroupingAlgorithm() [1/2]

FeatureGroupingAlgorithm | ( |  | ) |

Default constructor.

## ◆ ~FeatureGroupingAlgorithm()

~FeatureGroupingAlgorithm | ( |  | ) |

override

Destructor.

## ◆ FeatureGroupingAlgorithm() [2/2]

FeatureGroupingAlgorithm | ( | const FeatureGroupingAlgorithm & |  | ) |

private

Copy constructor is not implemented -> private.

## Member Function Documentation

## ◆ group() [1/2]

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

pure virtual

Applies the algorithm. The features in the input `maps` are grouped and the output is written to the consensus map `out`.

Implemented in FeatureGroupingAlgorithmKD, FeatureGroupingAlgorithmUnlabeled, FeatureGroupingAlgorithmLabeled, and FeatureGroupingAlgorithmQT.

## ◆ group() [2/2]

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

virtual

Applies the algorithm. The consensus features in the input `maps` are grouped and the output is written to the consensus map `out` Algorithms not supporting ConsensusMap input should simply not override this method, as the base implementation will forward the data to the FeatureMap version of group()

Reimplemented in FeatureGroupingAlgorithmKD, and FeatureGroupingAlgorithmQT.

## ◆ operator=()

FeatureGroupingAlgorithm& operator= | ( | const FeatureGroupingAlgorithm & |  | ) |

private

Assignment operator is not implemented -> private.

## ◆ postprocess_()

void postprocess_ | ( | const std::vector< MapType > & | maps,
|  | ConsensusMap & | out
| ) |  |

inline protected

after grouping by the subclasses, postprocess unassigned IDs, protein IDs and sort results in a consistent way

References ConsensusMap::getProteinIdentifications(), ConsensusMap::getUnassignedPeptideIdentifications(), ConsensusMap::sortByMaps(), ConsensusMap::sortByQuality(), and ConsensusMap::sortBySize().

## ◆ registerChildren()

static void registerChildren | ( |  | ) |

static

Register all derived classes in this method.

## ◆ transferSubelements()

void transferSubelements | ( | const std::vector< ConsensusMap > & | maps,
|  | ConsensusMap & | out
| ) |  | const

Transfers subelements (grouped features) from input consensus maps to the result consensus map.