OpenMS
FeatureGroupingAlgorithmLabeled Class Reference

A map feature grouping algorithm for labeling techniques with two labels. More...

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

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

 FeatureGroupingAlgorithmLabeled ()
 Default constructor. More...
 
 ~FeatureGroupingAlgorithmLabeled () override
 Destructor. More...
 
void group (const std::vector< FeatureMap > &maps, ConsensusMap &out) override
 Applies the algorithm. More...
 
- Public Member Functions inherited from FeatureGroupingAlgorithm
 FeatureGroupingAlgorithm ()
 Default constructor. More...
 
 ~FeatureGroupingAlgorithm () override
 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...
 
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...
 
- 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...
 

Private Member Functions

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

Additional Inherited Members

- Protected Member Functions inherited from FeatureGroupingAlgorithm
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...
 
- 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 labeling techniques with two labels.

It takes one maps and searches for corresponding features with a defined distance in RT and m/z.

Parameters of this class are:

NameTypeDefaultRestrictionsDescription
rt_estimate stringtrue true, falseIf 'true' the optimal RT pair distance and deviation are estimated by fitting a gaussian distribution to the histogram of pair distance. Note that this works only datasets with a significant amount of pairs! If 'false' the parameters 'rt_pair_dist', 'rt_dev_low' and 'rt_dev_high' define the optimal distance.
rt_pair_dist float-20.0  optimal pair distance in RT [sec] from light to heavy feature
rt_dev_low float15.0 min: 0.0maximum allowed deviation below optimal retention time distance
rt_dev_high float15.0 min: 0.0maximum allowed deviation above optimal retention time distance
mz_pair_dists float list[4.0]  optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge)
mz_dev float0.05 min: 0.0maximum allowed deviation from optimal m/z distance
mrm stringfalse true, falsethis option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account)

Note:
  • If a section name is documented, the documentation is displayed as tooltip.
  • Advanced parameter names are italic.

Constructor & Destructor Documentation

◆ FeatureGroupingAlgorithmLabeled() [1/2]

Default constructor.

◆ ~FeatureGroupingAlgorithmLabeled()

Destructor.

◆ FeatureGroupingAlgorithmLabeled() [2/2]

Copy constructor is not implemented -> private.

Member Function Documentation

◆ create()

static FeatureGroupingAlgorithm* create ( )
inlinestatic

Creates a new instance of this class (for Factory)

◆ getProductName()

static String getProductName ( )
inlinestatic

Returns the product name (for the Factory)

◆ group()

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

Applies the algorithm.

Note
Exactly one input map has to be provided.
The output map has to have two file descriptions, containing the same file name. The file descriptions have to be labeled 'heavy' and 'light'.
Exceptions
Exception::IllegalArgumentis thrown if the input data is not valid.

Implements FeatureGroupingAlgorithm.

◆ operator=()

Assignment operator is not implemented -> private.