| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Member Functions | Public Attributes | Protected Member Functions | List of all members
FeatureFinderAlgorithmMRM Class Reference
Analysis » FeatureFinder

FeatureFinderAlgorithm for MRM experiments. More...

`#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/FeatureFinderAlgorithmMRM.h>`

Inheritance diagram for FeatureFinderAlgorithmMRM:

## Public Types

enum | { RT = Peak2D::RT, MZ = Peak2D::MZ }
Type definitions
typedef FeatureFinderAlgorithm::MapType | MapType
typedef MapType::SpectrumType | SpectrumType
typedef SpectrumType::FloatDataArrays | FloatDataArrays
Public Types inherited from FeatureFinderAlgorithm
typedef PeakMap | MapType
| Input map type. More...
typedef MapType::CoordinateType | CoordinateType
| Coordinate/Position type of peaks. More...
typedef MapType::IntensityType | IntensityType
| Intensity type of peaks. More...
Public Types inherited from FeatureFinderDefs
enum | Flag { UNUSED, USED }
| Flags that indicate if a peak is already used in a feature. More...
typedef IsotopeCluster::IndexPair | IndexPair
| Index to peak consisting of two UInts (scan index / peak index) More...
typedef IsotopeCluster::ChargedIndexSet | ChargedIndexSet
| Index to peak consisting of two UInts (scan index / peak index) with charge information. More...
typedef IsotopeCluster::IndexSet | IndexSet
| A set of peak indices. More...

## Public Member Functions

| FeatureFinderAlgorithmMRM ()
| default constructor More...
void | run () override
| Main method for actual FeatureFinder. More...
Public Member Functions inherited from FeatureFinderAlgorithm
| FeatureFinderAlgorithm ()
| default constructor More...
| ~FeatureFinderAlgorithm () override
| destructor More...
virtual Param | getDefaultParameters () const
| Returns the default parameters. Reimplement. More...
void | setData (const MapType &map, FeatureMap &features, FeatureFinder &ff)
| Sets a reference to the calling FeatureFinder. More...
virtual void | setSeeds (const FeatureMap &seeds)
| Sets a reference to the calling FeatureFinder. 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 FeatureFinderAlgorithm * | create ()
static const String | getProductName ()
Static Public Member Functions inherited from FeatureFinderAlgorithm
static void | registerChildren ()
| register all derived classes here (see FeatureFinderAlgorithm_impl.h) More...

## Public Attributes

FeatureMap * | features_
| Output data pointer. More...
FeatureFinder * | ff_
| Pointer to the calling FeatureFinder that is used to access the feature flags. More...
const MapType * | map_
| Input data pointer. More...

## Protected Member Functions

double | fitRT_ (std::vector< Peak1D > &rt_input_data, InterpolationModel *&model) const
void | updateMembers_ () override
| This method is used to update extra member variables at the end of the setParameters() method. More...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Additional Inherited Members

Protected Attributes inherited from FeatureFinderAlgorithm
const MapType * | map_
| Input data pointer. More...
FeatureMap * | features_
| Output data pointer. More...
FeatureFinder * | ff_
| Pointer to the calling FeatureFinder that is used to access the feature flags. 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

FeatureFinderAlgorithm for MRM experiments.

Experimental classes:
  This tool has not been tested thoroughly and might behave not as expected!

This very simple algorithm has mainly been tested on data generated on an ABI/SCIEX QTrap 4000. Maybe this algorithm cannot be directly applied on data generated by other mass spectrometers.

Precursor m/z information (Q1) is stored in the "MZ" metavalue of each feature! The feature's m/z itself is the Q3's ion m/z.

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
min_rt_distance | float | 10.0 | min: 0.0 | Minimal distance of MRM features in seconds.
min_num_peaks_per_feature | int | 5 | min: 1 | Minimal number of peaks which are needed for a single feature
min_signal_to_noise_ratio | float | 2.0 | min: 0.0 | Minimal S/N ratio a peak must have to be taken into account. Set to zero if the MRM-traces contains mostly signals, and no noise.
write_debug_files | string | false | true, false | If set to true, for each feature a plot will be created, in the subdirectory 'debug'
resample_traces | string | false | true, false | If set to true, each trace, which is in this case a part of the MRM monitoring trace with signal is resampled, using the minimal distance of two data points in RT dimension
write_debuginfo | string | false | true, false | If set to true, debug messages are written, the output can be somewhat lengthy.

Note:

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

## Member Typedef Documentation

## ◆ FloatDataArrays

typedef SpectrumType::FloatDataArrays FloatDataArrays

## ◆ MapType

typedef FeatureFinderAlgorithm::MapType MapType

## ◆ SpectrumType

typedef MapType::SpectrumType SpectrumType

## Member Enumeration Documentation

## ◆ anonymous enum

anonymous enum

Enumerator
RT |
MZ |

## Constructor & Destructor Documentation

## ◆ FeatureFinderAlgorithmMRM()

FeatureFinderAlgorithmMRM | ( |  | ) |

default constructor

## Member Function Documentation

## ◆ create()

static FeatureFinderAlgorithm* create | ( |  | ) |

static

## ◆ fitRT_()

double fitRT_ | ( | std::vector< Peak1D > & | rt_input_data,
|  | InterpolationModel *& | model
| ) |  | const

protected

## ◆ getProductName()

static const String getProductName | ( |  | ) |

static

## ◆ run()

void run | ( |  | ) |

override virtual

Main method for actual FeatureFinder.

Implements FeatureFinderAlgorithm.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

This method is used to update extra member variables at the end of the setParameters() method.

Also call it at the end of the derived classes' copy constructor and assignment operator.

The default implementation is empty.

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ features_

FeatureMap* features_

Output data pointer.

## ◆ ff_

FeatureFinder* ff_

Pointer to the calling FeatureFinder that is used to access the feature flags.

## ◆ map_

const MapType* map_

Input data pointer.