OpenMS  2.8.0
Classes | Public Member Functions | Protected Types | Protected Member Functions | Protected Attributes | List of all members
FeatureFinderAlgorithmMetaboIdent Class Reference

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

Inheritance diagram for FeatureFinderAlgorithmMetaboIdent:
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Collaboration diagram for FeatureFinderAlgorithmMetaboIdent:
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Classes

struct  FeatureCompare
 Comparison functor for features. More...
 
struct  FeatureFilterQuality
 Predicate for filtering features by overall quality. More...
 
struct  FeatureFinderMetaboIdentCompound
 represents a compound in the assay library More...
 
struct  MassTraceBounds
 Boundaries for a mass trace in a feature. More...
 

Public Member Functions

 FeatureFinderAlgorithmMetaboIdent ()
 default constructor More...
 
void run (const std::vector< FeatureFinderMetaboIdentCompound > &metaboIdentTable, FeatureMap &features, String spectra_file="")
 perform targeted feature extraction of compounds from More...
 
PeakMapgetMSData ()
 Retrieve chromatograms (empty if run was not executed) More...
 
const PeakMapgetMSData () const
 
void setMSData (const PeakMap &m)
 Set spectra. More...
 
void setMSData (PeakMap &&m)
 
const PeakMapgetChromatograms () const
 Retrieve chromatograms (empty if run was not executed) More...
 
PeakMapgetChromatograms ()
 
const TargetedExperimentgetLibrary () const
 Retrieve the assay library (e.g., to store as TraML, empty if run was not executed) More...
 
const TransformationDescriptiongetTransformations () const
 Retrieve deviations between provided coordinates and extracted ones (e.g., to store as TrafoXML or for plotting) More...
 
size_t getNShared () const
 Retrieve number of features with shared identifications. More...
 
String prettyPrintCompound (const TargetedExperiment::Compound &compound)
 
- 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 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...
 

Protected Types

typedef std::map< UInt64, std::vector< MassTraceBounds > > FeatureBoundsMap
 Boundaries for all mass traces per feature. More...
 
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTrace MassTrace
 
typedef FeatureFinderAlgorithmPickedHelperStructs::MassTraces MassTraces
 
typedef std::vector< Feature * > FeatureGroup
 group of (overlapping) features More...
 

Protected Member Functions

void extractTransformations_ (const FeatureMap &features)
 
void addTargetToLibrary_ (const String &name, const String &formula, double mass, const std::vector< Int > &charges, const std::vector< double > &rts, std::vector< double > rt_ranges, const std::vector< double > &iso_distrib)
 Add a target (from the input file) to the assay library. More...
 
Size addTargetAnnotations_ (FeatureMap &features)
 Add "peptide" identifications with information about targets to features. More...
 
void addTargetRT_ (TargetedExperiment::Compound &target, double rt)
 
double calculateMZ_ (double mass, Int charge) const
 Calculate mass-to-charge ratio from mass and charge. More...
 
void generateTransitions_ (const String &target_id, double mz, Int charge, const IsotopeDistribution &iso_dist)
 
bool hasOverlappingBounds_ (const std::vector< MassTraceBounds > &mtb1, const std::vector< MassTraceBounds > &mtb2) const
 Check if two sets of mass trace boundaries overlap. More...
 
void getFeatureBounds_ (const FeatureMap &features, FeatureBoundsMap &feature_bounds)
 
bool hasOverlappingFeature_ (const Feature &feature, const FeatureGroup &group, const FeatureBoundsMap &feature_bounds) const
 
void findOverlappingFeatures_ (FeatureMap &features, const FeatureBoundsMap &feature_bounds, std::vector< FeatureGroup > &overlap_groups)
 
void resolveOverlappingFeatures_ (FeatureGroup &group, const FeatureBoundsMap &feature_bounds)
 
void annotateFeatures_ (FeatureMap &features)
 
void ensureConvexHulls_ (Feature &feature) const
 
void selectFeaturesFromCandidates_ (FeatureMap &features)
 
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...
 

Protected Attributes

struct OpenMS::FeatureFinderAlgorithmMetaboIdent::FeatureFilterQuality feature_filter_
 
struct OpenMS::FeatureFinderAlgorithmMetaboIdent::FeatureCompare feature_compare_
 
double rt_window_
 RT window width. More...
 
double mz_window_
 m/z window width More...
 
bool mz_window_ppm_
 m/z window width is given in PPM (not Da)? More...
 
double isotope_pmin_
 min. isotope probability for peptide assay More...
 
Size n_isotopes_
 number of isotopes for peptide assay More...
 
double peak_width_
 
double min_peak_width_
 
double signal_to_noise_
 
String elution_model_
 
String candidates_out_
 
Size debug_level_
 
PeakMap ms_data_
 input LC-MS data More...
 
PeakMap chrom_data_
 accumulated chromatograms (XICs) More...
 
MRMFeatureFinderScoring feat_finder_
 OpenSWATH feature finder. More...
 
TargetedExperiment library_
 accumulated assays for targets More...
 
TransformationDescription trafo_
 
CoarseIsotopePatternGenerator iso_gen_
 isotope pattern generator More...
 
std::map< String, double > isotope_probs_
 isotope probabilities of transitions More...
 
std::map< String, double > target_rts_
 RTs of targets (assays) More...
 
size_t n_shared_ = 0
 
- 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...
 

Additional Inherited Members

- 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...
 

Class Documentation

◆ OpenMS::FeatureFinderAlgorithmMetaboIdent::MassTraceBounds

struct OpenMS::FeatureFinderAlgorithmMetaboIdent::MassTraceBounds

Boundaries for a mass trace in a feature.

Collaboration diagram for FeatureFinderAlgorithmMetaboIdent::MassTraceBounds:
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Class Members
double mz_max
double mz_min
double rt_max
double rt_min
Size sub_index

Member Typedef Documentation

◆ FeatureBoundsMap

typedef std::map<UInt64, std::vector<MassTraceBounds> > FeatureBoundsMap
protected

Boundaries for all mass traces per feature.

◆ FeatureGroup

typedef std::vector<Feature*> FeatureGroup
protected

group of (overlapping) features

◆ MassTrace

◆ MassTraces

Constructor & Destructor Documentation

◆ FeatureFinderAlgorithmMetaboIdent()

default constructor

Member Function Documentation

◆ addTargetAnnotations_()

Size addTargetAnnotations_ ( FeatureMap features)
protected

Add "peptide" identifications with information about targets to features.

◆ addTargetRT_()

void addTargetRT_ ( TargetedExperiment::Compound target,
double  rt 
)
protected

◆ addTargetToLibrary_()

void addTargetToLibrary_ ( const String name,
const String formula,
double  mass,
const std::vector< Int > &  charges,
const std::vector< double > &  rts,
std::vector< double >  rt_ranges,
const std::vector< double > &  iso_distrib 
)
protected

Add a target (from the input file) to the assay library.

◆ annotateFeatures_()

void annotateFeatures_ ( FeatureMap features)
protected

◆ calculateMZ_()

double calculateMZ_ ( double  mass,
Int  charge 
) const
protected

Calculate mass-to-charge ratio from mass and charge.

◆ ensureConvexHulls_()

void ensureConvexHulls_ ( Feature feature) const
protected

◆ extractTransformations_()

void extractTransformations_ ( const FeatureMap features)
protected

◆ findOverlappingFeatures_()

void findOverlappingFeatures_ ( FeatureMap features,
const FeatureBoundsMap feature_bounds,
std::vector< FeatureGroup > &  overlap_groups 
)
protected

◆ generateTransitions_()

void generateTransitions_ ( const String target_id,
double  mz,
Int  charge,
const IsotopeDistribution iso_dist 
)
protected

◆ getChromatograms() [1/2]

PeakMap& getChromatograms ( )
inline

◆ getChromatograms() [2/2]

const PeakMap& getChromatograms ( ) const
inline

Retrieve chromatograms (empty if run was not executed)

◆ getFeatureBounds_()

void getFeatureBounds_ ( const FeatureMap features,
FeatureBoundsMap feature_bounds 
)
protected

◆ getLibrary()

const TargetedExperiment& getLibrary ( ) const
inline

Retrieve the assay library (e.g., to store as TraML, empty if run was not executed)

◆ getMSData() [1/2]

PeakMap& getMSData ( )
inline

Retrieve chromatograms (empty if run was not executed)

◆ getMSData() [2/2]

const PeakMap& getMSData ( ) const
inline

◆ getNShared()

size_t getNShared ( ) const
inline

Retrieve number of features with shared identifications.

◆ getTransformations()

const TransformationDescription& getTransformations ( ) const
inline

Retrieve deviations between provided coordinates and extracted ones (e.g., to store as TrafoXML or for plotting)

◆ hasOverlappingBounds_()

bool hasOverlappingBounds_ ( const std::vector< MassTraceBounds > &  mtb1,
const std::vector< MassTraceBounds > &  mtb2 
) const
protected

Check if two sets of mass trace boundaries overlap.

◆ hasOverlappingFeature_()

bool hasOverlappingFeature_ ( const Feature feature,
const FeatureGroup group,
const FeatureBoundsMap feature_bounds 
) const
protected

◆ prettyPrintCompound()

String prettyPrintCompound ( const TargetedExperiment::Compound compound)

◆ resolveOverlappingFeatures_()

void resolveOverlappingFeatures_ ( FeatureGroup group,
const FeatureBoundsMap feature_bounds 
)
protected

◆ run()

void run ( const std::vector< FeatureFinderMetaboIdentCompound > &  metaboIdentTable,
FeatureMap features,
String  spectra_file = "" 
)

perform targeted feature extraction of compounds from

Parameters
metaboIdentTableand stores them in
feature.If spectra_file is provided it will be used as a fall-back to setPrimaryMSRunPath in the feature map in case a proper primaryMSRunPath is not annotated in the MSExperiment.

◆ selectFeaturesFromCandidates_()

void selectFeaturesFromCandidates_ ( FeatureMap features)
protected

◆ setMSData() [1/2]

void setMSData ( const PeakMap m)

Set spectra.

◆ setMSData() [2/2]

void setMSData ( PeakMap &&  m)

◆ 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

◆ candidates_out_

String candidates_out_
protected

◆ chrom_data_

PeakMap chrom_data_
protected

accumulated chromatograms (XICs)

◆ debug_level_

Size debug_level_
protected

◆ elution_model_

String elution_model_
protected

◆ feat_finder_

MRMFeatureFinderScoring feat_finder_
protected

OpenSWATH feature finder.

◆ feature_compare_

◆ feature_filter_

◆ iso_gen_

CoarseIsotopePatternGenerator iso_gen_
protected

isotope pattern generator

◆ isotope_pmin_

double isotope_pmin_
protected

min. isotope probability for peptide assay

◆ isotope_probs_

std::map<String, double> isotope_probs_
protected

isotope probabilities of transitions

◆ library_

TargetedExperiment library_
protected

accumulated assays for targets

◆ min_peak_width_

double min_peak_width_
protected

◆ ms_data_

PeakMap ms_data_
protected

input LC-MS data

◆ mz_window_

double mz_window_
protected

m/z window width

◆ mz_window_ppm_

bool mz_window_ppm_
protected

m/z window width is given in PPM (not Da)?

◆ n_isotopes_

Size n_isotopes_
protected

number of isotopes for peptide assay

◆ n_shared_

size_t n_shared_ = 0
protected

◆ peak_width_

double peak_width_
protected

◆ rt_window_

double rt_window_
protected

RT window width.

◆ signal_to_noise_

double signal_to_noise_
protected

◆ target_rts_

std::map<String, double> target_rts_
protected

RTs of targets (assays)

◆ trafo_

TransformationDescription trafo_
protected