A map feature grouping algorithm for identified features. More...
#include <OpenMS/ANALYSIS/MAPMATCHING/FeatureGroupingAlgorithmIdentification.h>
Public Member Functions | |
FeatureGroupingAlgorithmIdentification () | |
Default constructor. More... | |
virtual | ~FeatureGroupingAlgorithmIdentification () |
Destructor. More... | |
virtual void | group (const std::vector< FeatureMap > &maps, ConsensusMap &out) |
Applies the algorithm. More... | |
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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... | |
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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... | |
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static void | registerChildren () |
Register all derived classes in this method. More... | |
Private Member Functions | |
FeatureGroupingAlgorithmIdentification (const FeatureGroupingAlgorithmIdentification &) | |
Copy constructor intentionally not implemented -> private. More... | |
FeatureGroupingAlgorithmIdentification & | operator= (const FeatureGroupingAlgorithmIdentification &) |
Assignment operator intentionally not implemented -> private. More... | |
Additional Inherited Members | |
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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... | |
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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 identified features.
It takes many maps and searches for corresponding features. The corresponding features must be aligned, but may have small position deviations.
Parameters of this class are:Name | Type | Default | Restrictions | Description |
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xcorr_threshold | float | 1.2 | Peptide identifications having a SEQUEST XCorr score smaller than this are discarded. | |
rt_stdev_threshold | float | 100 | Maximum allowed standard deviation of retention times within a group | |
mz_stdev_threshold | float | 1 | Maximum allowed standard deviation of mass-to-charge within a group |
Default constructor.
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virtual |
Destructor.
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private |
Copy constructor intentionally not implemented -> private.
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inlinestatic |
Creates a new instance of this class (for Factory)
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virtual |
Applies the algorithm.
IllegalArgument | is thrown if less than two input maps are given. |
Implements FeatureGroupingAlgorithm.
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private |
Assignment operator intentionally not implemented -> private.
OpenMS / TOPP release 2.0.0 | Documentation generated on Tue Aug 25 2015 05:54:00 using doxygen 1.8.9.1 |