The LabeledPairFinder allows the matching of labeled features (features with a fixed distance). More...
#include <OpenMS/ANALYSIS/MAPMATCHING/LabeledPairFinder.h>
Public Member Functions | |
| LabeledPairFinder () | |
| Default constructor. More... | |
| virtual | ~LabeledPairFinder () |
| Destructor. More... | |
| virtual void | run (const std::vector< ConsensusMap > &input_maps, ConsensusMap &result_map) |
| Run the algorithm. More... | |
Public Member Functions inherited from BaseGroupFinder | |
| BaseGroupFinder () | |
| Default constructor. More... | |
| virtual | ~BaseGroupFinder () |
| Destructor. 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... | |
Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor. More... | |
| ~ProgressLogger () | |
| Destructor. More... | |
| void | setLogType (LogType type) const |
| Sets the progress log that should be used. The default type is NONE! More... | |
| LogType | getLogType () const |
| Returns the type of progress log being used. More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const |
| Initializes the progress display. More... | |
| void | setProgress (SignedSize value) const |
| Sets the current progress. More... | |
| void | endProgress () const |
| Ends the progress display. More... | |
Static Public Member Functions | |
| static BaseGroupFinder * | create () |
| Returns an instance of this class. More... | |
| static const String | getProductName () |
| Returns the name of this module. More... | |
Static Public Member Functions inherited from BaseGroupFinder | |
| static void | registerChildren () |
| Register all derived classes here. More... | |
Protected Member Functions | |
| DoubleReal | PValue_ (DoubleReal x, DoubleReal m, DoubleReal sig1, DoubleReal sig2) |
return the p-value at position x for the bi-Gaussian distribution with mean m and standard deviation sig1 (left) and sig2 (right) More... | |
Protected Member Functions inherited from BaseGroupFinder | |
| void | checkIds_ (const std::vector< ConsensusMap > &maps) const |
| Checks if all file descriptions have disjoint map identifiers. More... | |
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 | |
| LabeledPairFinder (const LabeledPairFinder &source) | |
| Copy constructor not implemented => private. More... | |
| LabeledPairFinder & | operator= (const LabeledPairFinder &source) |
| Assignment operator not implemented => private. More... | |
Additional Inherited Members | |
Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } |
| Possible log types. 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... | |
Protected Attributes inherited from ProgressLogger | |
| LogType | type_ |
| SignedSize | begin_ |
| SignedSize | end_ |
| SignedSize | value_ |
| QProgressDialog * | dlg_ |
| StopWatch | stop_watch_ |
| time_t | last_invoke_ |
Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ |
The LabeledPairFinder allows the matching of labeled features (features with a fixed distance).
Finds feature pairs that have a defined distance in RT and m/z in the same map.
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) |
Implement support for labled MRM experiments, Q1 m/z value and charges. (Andreas)
Implement support for more than one mass delta, e.g. from missed cleavages and so on (Andreas)
Default constructor.
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inlinevirtual |
Destructor.
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private |
Copy constructor not implemented => private.
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inlinestatic |
Returns an instance of this class.
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inlinestatic |
Returns the name of this module.
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private |
Assignment operator not implemented => private.
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inlineprotected |
return the p-value at position x for the bi-Gaussian distribution with mean m and standard deviation sig1 (left) and sig2 (right)
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virtual |
Run the algorithm.
| Exception::IllegalArgument | is thrown if the input data is not valid. |
Implements BaseGroupFinder.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |