OpenMS
2.4.0
|
A map feature grouping algorithm for labeling techniques with two labels. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmLabeled.h>
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... | |
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 FeatureGroupingAlgorithm * | create () |
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 | |
FeatureGroupingAlgorithmLabeled (const FeatureGroupingAlgorithmLabeled &) | |
Copy constructor is not implemented -> private. More... | |
FeatureGroupingAlgorithmLabeled & | operator= (const FeatureGroupingAlgorithmLabeled &) |
Assignment operator is 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< 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... | |
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:Name | Type | Default | Restrictions | Description |
---|---|---|---|---|
rt_estimate | string | true | true, false | If '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 | optimal pair distance in RT [sec] from light to heavy feature | |
rt_dev_low | float | 15 | min: 0 | maximum allowed deviation below optimal retention time distance |
rt_dev_high | float | 15 | min: 0 | maximum allowed deviation above optimal retention time distance |
mz_pair_dists | float list | [4] | optimal pair distances in m/z [Th] for features with charge +1 (adapted to +2, +3, .. by division through charge) | |
mz_dev | float | 0.05 | min: 0 | maximum allowed deviation from optimal m/z distance |
mrm | string | false | true, false | this option should be used if the features correspond mrm chromatograms (additionally the precursor is taken into account) |
Default constructor.
|
override |
Destructor.
|
private |
Copy constructor is not implemented -> private.
|
inlinestatic |
Creates a new instance of this class (for Factory)
|
overridevirtual |
Applies the algorithm.
Exception::IllegalArgument | is thrown if the input data is not valid. |
Implements FeatureGroupingAlgorithm.
|
private |
Assignment operator is not implemented -> private.