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... | |
| virtual | ~FeatureGroupingAlgorithmLabeled () | 
| 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 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.
| 
 | virtual | 
Destructor.
| 
 | private | 
Copy constructor is not implemented -> private.
| 
 | inlinestatic | 
Creates a new instance of this class (for Factory)
| 
 | virtual | 
Applies the algorithm.
| Exception::IllegalArgument | is thrown if the input data is not valid. | 
Implements FeatureGroupingAlgorithm.
| 
 | private | 
Assignment operator is not implemented -> private.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |