| OpenMS 2.5.0

Public Member Functions | Static Public Member Functions | Private Member Functions | List of all members
FeatureGroupingAlgorithmLabeled Class Reference
Analysis » FeatureGrouping

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

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

Inheritance diagram for FeatureGroupingAlgorithmLabeled:

## 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 &param)
| 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 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< 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...

## 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:

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 | -20.0 |  | optimal pair distance in RT [sec] from light to heavy feature
rt_dev_low | float | 15.0 | min: 0.0 | maximum allowed deviation below optimal retention time distance
rt_dev_high | float | 15.0 | min: 0.0 | maximum 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 | float | 0.05 | min: 0.0 | 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)

Note:

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

## Constructor & Destructor Documentation

## ◆ FeatureGroupingAlgorithmLabeled() [1/2]

FeatureGroupingAlgorithmLabeled | ( |  | ) |

Default constructor.

## ◆ ~FeatureGroupingAlgorithmLabeled()

~FeatureGroupingAlgorithmLabeled | ( |  | ) |

override

Destructor.

## ◆ FeatureGroupingAlgorithmLabeled() [2/2]

FeatureGroupingAlgorithmLabeled | ( | const FeatureGroupingAlgorithmLabeled & |  | ) |

private

Copy constructor is not implemented -> private.

## Member Function Documentation

## ◆ create()

static FeatureGroupingAlgorithm* create | ( |  | ) |

inline static

Creates a new instance of this class (for Factory)

## ◆ getProductName()

static String getProductName | ( |  | ) |

inline static

Returns the product name (for the Factory)

## ◆ group()

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

override virtual

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::IllegalArgument | is thrown if the input data is not valid.

Implements FeatureGroupingAlgorithm.

## ◆ operator=()

FeatureGroupingAlgorithmLabeled& operator= | ( | const FeatureGroupingAlgorithmLabeled & |  | ) |

private

Assignment operator is not implemented -> private.