OpenMS
2.5.0
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Base class for all feature grouping algorithms. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithm.h>
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 ¶m) |
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... | |
Base class for all feature grouping algorithms.
These algorithms group corresponding features in one map or across maps.
Default constructor.
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override |
Destructor.
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private |
Copy constructor is not implemented -> private.
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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.
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pure virtual |
Applies the algorithm. The features in the input maps
are grouped and the output is written to the consensus map out
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Implemented in FeatureGroupingAlgorithmKD, FeatureGroupingAlgorithmUnlabeled, FeatureGroupingAlgorithmLabeled, and FeatureGroupingAlgorithmQT.
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private |
Assignment operator is not implemented -> private.
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inlineprotected |
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().
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static |
Register all derived classes in this method.
void transferSubelements | ( | const std::vector< ConsensusMap > & | maps, |
ConsensusMap & | out | ||
) | const |
Transfers subelements (grouped features) from input consensus maps to the result consensus map.