| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
MetaboliteFeatureDeconvolution Class Reference
Analysis

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

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

Inheritance diagram for MetaboliteFeatureDeconvolution:

## 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

## Public Member Functions

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...
Constructors and Destructor s
| MetaboliteFeatureDeconvolution ()
| default constructor More...
| MetaboliteFeatureDeconvolution (const MetaboliteFeatureDeconvolution &source)
| Copy constructor. More...
MetaboliteFeatureDeconvolution & | operator= (const MetaboliteFeatureDeconvolution &source)
| Assignment operator. More...
| ~MetaboliteFeatureDeconvolution () 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...

## Protected Member Functions

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...
Protected Member Functions inherited from DefaultParamHandler
void | defaultsToParam_ ()
| Updates the parameters after the defaults have been set in the constructor. More...

## Protected Attributes

MassExplainer::AdductsType | potential_adducts_
| List of adducts used to explain mass differences. More...
Map< Size, String > | map_label_
| labeling table More...
Map< String, Size > | map_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...
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

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

## Member Typedef Documentation

## ◆ ClusterPointType

typedef DPosition<2> ClusterPointType

## ◆ CoordinateType

typedef FeatureMapType::FeatureType::CoordinateType CoordinateType

## ◆ FeatureMapType

typedef FeatureMap FeatureMapType

## ◆ FeatureType

typedef Feature FeatureType

## ◆ PairsType

typedef ILPDCWrapper::PairsType PairsType

## Member Enumeration Documentation

## ◆ CHARGEMODE

enum CHARGEMODE

Enumerator
QFROMFEATURE |
QHEURISTIC |
QALL |

## Constructor & Destructor Documentation

## ◆ MetaboliteFeatureDeconvolution() [1/2]

MetaboliteFeatureDeconvolution | ( |  | ) |

default constructor

## ◆ MetaboliteFeatureDeconvolution() [2/2]

MetaboliteFeatureDeconvolution | ( | const MetaboliteFeatureDeconvolution & | source | ) |

Copy constructor.

## ◆ ~MetaboliteFeatureDeconvolution()

~MetaboliteFeatureDeconvolution | ( |  | ) |

override

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_in | Input feature-map
  fm_out | Output 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
| ) |  |

inline protected

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=()

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

Assignment operator.

## ◆ printEdgesOfConnectedFeatures_()

void printEdgesOfConnectedFeatures_ | ( | Size | idx_1,
|  | Size | idx_2,
|  | const PairsType & | feature_relation
| ) |  |

protected

A function mostly for debugging.

## ◆ 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

## ◆ 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