OpenMS  2.7.0
Public Types | List of all members
MetaboliteFeatureDeconvolution Class Reference

An algorithm to decharge small molecule features (i.e. as found by FeatureFinder). More...

#include <OpenMS/ANALYSIS/DECHARGING/MetaboliteFeatureDeconvolution.h>

Inheritance diagram for MetaboliteFeatureDeconvolution:
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Collaboration diagram for MetaboliteFeatureDeconvolution:
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Public Types

enum  CHARGEMODE { QFROMFEATURE = 1 , QHEURISTIC , QALL }
 
typedef FeatureMap FeatureMapType
 
typedef Feature FeatureType
 
typedef DPosition< 2 > ClusterPointType
 
typedef FeatureMapType::FeatureType::CoordinateType CoordinateType
 
typedef ILPDCWrapper::PairsType PairsType
 

Constructors and Destructor s

MassExplainer::AdductsType potential_adducts_
 List of adducts used to explain mass differences. More...
 
Map< Size, Stringmap_label_
 labeling table More...
 
Map< String, Sizemap_label_inverse_
 labeling table inverse More...
 
bool enable_intensity_filter_
 status of intensity filter for edges More...
 
bool negative_mode_
 status of ionization mode More...
 
CHARGEMODE q_try_
 status of charge discovery More...
 
Int verbose_level_
 amount of debug information displayed More...
 
 MetaboliteFeatureDeconvolution ()
 default constructor More...
 
 MetaboliteFeatureDeconvolution (const MetaboliteFeatureDeconvolution &source)
 Copy constructor. More...
 
MetaboliteFeatureDeconvolutionoperator= (const MetaboliteFeatureDeconvolution &source)
 Assignment operator. More...
 
 ~MetaboliteFeatureDeconvolution () override
 destructor More...
 
void compute (const FeatureMapType &fm_in, FeatureMapType &fm_out, ConsensusMap &cons_map, ConsensusMap &cons_map_p)
 Compute a zero-charge feature map from a set of charged features. More...
 
void updateMembers_ () override
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void checkSolution_ (const ConsensusMap &cons_map) const
 
void inferMoreEdges_ (PairsType &edges, Map< Size, std::set< CmpInfo_ > > &feature_adducts)
 
void candidateEdges_ (FeatureMapType &fm_out, const Adduct &default_adduct, PairsType &feature_relation, Map< Size, std::set< CmpInfo_ > > &feature_adducts)
 
void annotate_feature_ (FeatureMapType &fm_out, Adduct &default_adduct, Compomer &c, const Size f_idx, const UInt side, const Int new_q, const Int old_q)
 
void printEdgesOfConnectedFeatures_ (Size idx_1, Size idx_2, const PairsType &feature_relation)
 A function mostly for debugging. More...
 
bool intensityFilterPassed_ (const Int q1, const Int q2, const Compomer &cmp, const FeatureType &f1, const FeatureType &f2)
 returns true if the intensity filter was passed or switched off More...
 
bool chargeTestworthy_ (const Int feature_charge, const Int putative_charge, const bool other_unchanged) const
 determines if we should test a putative feature charge More...
 

Additional Inherited Members

- 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...
 
- Static Public Member Functions inherited from DefaultParamHandler
static void writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &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 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

An algorithm to decharge small molecule features (i.e. as found by FeatureFinder).

Member Typedef Documentation

◆ ClusterPointType

◆ CoordinateType

typedef FeatureMapType::FeatureType::CoordinateType CoordinateType

◆ FeatureMapType

◆ FeatureType

◆ PairsType

Member Enumeration Documentation

◆ CHARGEMODE

enum CHARGEMODE
Enumerator
QFROMFEATURE 
QHEURISTIC 
QALL 

Constructor & Destructor Documentation

◆ MetaboliteFeatureDeconvolution() [1/2]

default constructor

◆ MetaboliteFeatureDeconvolution() [2/2]

Copy constructor.

◆ ~MetaboliteFeatureDeconvolution()

destructor

Member Function Documentation

◆ annotate_feature_()

void annotate_feature_ ( FeatureMapType fm_out,
Adduct default_adduct,
Compomer c,
const Size  f_idx,
const UInt  side,
const Int  new_q,
const Int  old_q 
)
protected

◆ candidateEdges_()

void candidateEdges_ ( FeatureMapType fm_out,
const Adduct default_adduct,
PairsType feature_relation,
Map< Size, std::set< CmpInfo_ > > &  feature_adducts 
)
protected

◆ chargeTestworthy_()

bool chargeTestworthy_ ( const Int  feature_charge,
const Int  putative_charge,
const bool  other_unchanged 
) const
protected

determines if we should test a putative feature charge

Answer query given the internal status of q_try. Features with q<=0 always return true.

◆ checkSolution_()

void checkSolution_ ( const ConsensusMap cons_map) const
protected

◆ compute()

void compute ( const FeatureMapType fm_in,
FeatureMapType fm_out,
ConsensusMap cons_map,
ConsensusMap cons_map_p 
)

Compute a zero-charge feature map from a set of charged features.

Find putative ChargePairs, then score them and hand over to ILP.

Parameters
fm_inInput feature-map
fm_outOutput feature-map (sorted by position and augmented with user params)
cons_map[out] Output of grouped features belonging to a charge group
cons_map_p[out] Output of paired features connected by an edge

◆ inferMoreEdges_()

void inferMoreEdges_ ( PairsType edges,
Map< Size, std::set< CmpInfo_ > > &  feature_adducts 
)
protected

test if "simple" edges have alternative (more difficult explanation) supported by neighboring edges e.g. (.) -> (H+) might be augmented to (Na+) -> (H+Na+)

◆ intensityFilterPassed_()

bool intensityFilterPassed_ ( const Int  q1,
const Int  q2,
const Compomer cmp,
const FeatureType f1,
const FeatureType f2 
)
inlineprotected

returns true if the intensity filter was passed or switched off

Filter for adding an edge only when the two features connected by it, fulfill the intensity criterion.

◆ operator=()

Assignment operator.

◆ printEdgesOfConnectedFeatures_()

void printEdgesOfConnectedFeatures_ ( Size  idx_1,
Size  idx_2,
const PairsType feature_relation 
)
protected

A function mostly for debugging.

◆ 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

◆ enable_intensity_filter_

bool enable_intensity_filter_
protected

status of intensity filter for edges

◆ map_label_

Map<Size, String> map_label_
protected

labeling table

◆ map_label_inverse_

Map<String, Size> map_label_inverse_
protected

labeling table inverse

◆ negative_mode_

bool negative_mode_
protected

status of ionization mode

◆ potential_adducts_

MassExplainer::AdductsType potential_adducts_
protected

List of adducts used to explain mass differences.

◆ q_try_

CHARGEMODE q_try_
protected

status of charge discovery

◆ verbose_level_

Int verbose_level_
protected

amount of debug information displayed