OpenMS
FeatureFinderAlgorithmMRM Class Reference

FeatureFinderAlgorithm for MRM experiments. More...

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

Inheritance diagram for FeatureFinderAlgorithmMRM:
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Collaboration diagram for FeatureFinderAlgorithmMRM:
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Type definitions

enum  { RT = Peak2D::RT , MZ = Peak2D::MZ }
 
typedef FeatureFinderAlgorithm::MapType MapType
 
typedef MapType::SpectrumType SpectrumType
 
typedef SpectrumType::FloatDataArrays FloatDataArrays
 
 FeatureFinderAlgorithmMRM ()
 default constructor More...
 
void run () override
 Main method for actual FeatureFinder. More...
 
static FeatureFinderAlgorithmcreate ()
 
static const String getProductName ()
 
double fitRT_ (std::vector< Peak1D > &rt_input_data, std::unique_ptr< InterpolationModel > &model) const
 
void updateMembers_ () override
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
FeatureMapfeatures_
 Output data pointer. More...
 
FeatureFinderff_
 Pointer to the calling FeatureFinder that is used to access the feature flags. More...
 
const MapTypemap_
 Input data pointer. More...
 

Additional Inherited Members

- 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 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...
 
DefaultParamHandleroperator= (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 ParamgetParameters () const
 Non-mutable access to the parameters. More...
 
const ParamgetDefaults () const
 Non-mutable access to the default parameters. More...
 
const StringgetName () 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 inherited from FeatureFinderAlgorithm
static void registerChildren ()
 register all derived classes here (see FeatureFinderAlgorithm_impl.h) More...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")
 Writes all parameters to meta values. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- Protected Attributes inherited from FeatureFinderAlgorithm
const MapTypemap_
 Input data pointer. More...
 
FeatureMapfeatures_
 Output data pointer. More...
 
FeatureFinderff_
 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< Stringsubsections_
 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:

NameTypeDefaultRestrictionsDescription
min_rt_distance float10.0 min: 0.0Minimal distance of MRM features in seconds.
min_num_peaks_per_feature int5 min: 1Minimal number of peaks which are needed for a single feature
min_signal_to_noise_ratio float2.0 min: 0.0Minimal 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 stringfalse true, falseIf set to true, for each feature a plot will be created, in the subdirectory 'debug'
resample_traces stringfalse true, falseIf 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 stringfalse true, falseIf 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

◆ MapType

◆ SpectrumType

Member Enumeration Documentation

◆ anonymous enum

anonymous enum
Enumerator
RT 
MZ 

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmMRM()

default constructor

Member Function Documentation

◆ create()

static FeatureFinderAlgorithm* create ( )
static

◆ fitRT_()

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

◆ getProductName()

static const String getProductName ( )
static

◆ run()

void run ( )
overridevirtual

Main method for actual FeatureFinder.

Implements FeatureFinderAlgorithm.

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

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_

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

◆ map_

const MapType* map_

Input data pointer.