| OpenMS 2.5.0

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

The LabeledPairFinder allows the matching of labeled features (features with a fixed distance). More...

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

Inheritance diagram for LabeledPairFinder:

## Public Member Functions

| LabeledPairFinder ()
| Default constructor. More...
| ~LabeledPairFinder () override
| Destructor. More...
void | run (const std::vector< ConsensusMap > &input_maps, ConsensusMap &result_map) override
| Run the algorithm. More...
Public Member Functions inherited from BaseGroupFinder
| BaseGroupFinder ()
| Default constructor. More...
| ~BaseGroupFinder () override
| 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 &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...
Public Member Functions inherited from ProgressLogger
| ProgressLogger ()
| Constructor. More...
| ~ProgressLogger ()
| Destructor. More...
| ProgressLogger (const ProgressLogger &other)
| Copy constructor. More...
ProgressLogger & | operator= (const ProgressLogger &other)
| Assignment Operator. 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...
void | nextProgress () const
| increment progress by 1 (according to range begin-end) 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

double | PValue_ (double x, double m, double sig1, double 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...
Static Protected Member Functions inherited from ProgressLogger
static String | logTypeToFactoryName_ (LogType type)
| Return the name of the factory product used for this log type. 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_
time_t | last_invoke_
ProgressLoggerImpl * | current_logger_
Static Protected Attributes inherited from ProgressLogger
static int | recursion_depth_

## Detailed Description

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 | -20.0 |  | 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.

Todo:

  Implement support for labeled 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)

## Constructor & Destructor Documentation

## ◆ LabeledPairFinder() [1/2]

LabeledPairFinder | ( |  | ) |

Default constructor.

## ◆ ~LabeledPairFinder()

~LabeledPairFinder | ( |  | ) |

inline override

Destructor.

## ◆ LabeledPairFinder() [2/2]

LabeledPairFinder | ( | const LabeledPairFinder & | source | ) |

private

Copy constructor not implemented => private.

## Member Function Documentation

## ◆ create()

static BaseGroupFinder* create | ( |  | ) |

inline static

Returns an instance of this class.

## ◆ getProductName()

static const String getProductName | ( |  | ) |

inline static

Returns the name of this module.

## ◆ operator=()

LabeledPairFinder& operator= | ( | const LabeledPairFinder & | source | ) |

private

Assignment operator not implemented => private.

## ◆ PValue_()

double PValue_ | ( | double | x,
|  | double | m,
|  | double | sig1,
|  | double | sig2
| ) |  |

inline protected

return the p-value at position x for the bi-Gaussian distribution with mean `m` and standard deviation `sig1` (left) and `sig2` (right)

## ◆ run()

void run | ( | const std::vector< ConsensusMap > & | input_maps,
|  | ConsensusMap & | result_map
| ) |  |

override virtual

Run 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 BaseGroupFinder.