| OpenMS 2.5.0

Public Types | Public Member Functions | Protected Member Functions | List of all members
CompNovoIonScoringCID Class Reference

run with CompNovoIonScoringCID More...

`#include <OpenMS/ANALYSIS/DENOVO/CompNovoIonScoringCID.h>`

Inheritance diagram for CompNovoIonScoringCID:

## Public Types

typedef CompNovoIonScoringBase::IsotopeType | IsotopeType
typedef CompNovoIonScoringBase::IonScore | IonScore
Public Types inherited from CompNovoIonScoringBase
enum | IsotopeType { PARENT = 0, CHILD = 1, LONE = 2 }

## Public Member Functions

CompNovoIonScoringCID & | operator= (const CompNovoIonScoringCID &source)
constructors and destructors
| CompNovoIonScoringCID ()
| default constructor More...
| CompNovoIonScoringCID (const CompNovoIonScoringCID &source)
| copy constructor More...
| ~CompNovoIonScoringCID () override
| destructor More...
Accessors
void | scoreSpectrum (Map< double, IonScore > &CID_ion_scores, PeakSpectrum &CID_spec, double precursor_weight, Size charge)
Public Member Functions inherited from CompNovoIonScoringBase
CompNovoIonScoringBase & | operator= (const CompNovoIonScoringBase &source)
| CompNovoIonScoringBase ()
| default constructor More...
| CompNovoIonScoringBase (const CompNovoIonScoringBase &source)
| copy constructor More...
| ~CompNovoIonScoringBase () override
| destructor More...
double | scoreIsotopes (const PeakSpectrum &CID_spec, PeakSpectrum::ConstIterator it, Size charge)
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 | scoreWitnessSet_ (Size charge, double precursor_weight, Map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec) override
Protected Member Functions inherited from CompNovoIonScoringBase
void | updateMembers_ () override
| update members method from DefaultParamHandler to update the members More...
IsotopeType | classifyIsotopes_ (const PeakSpectrum &spec, PeakSpectrum::ConstIterator it)
double | scoreIsotopes_ (const PeakSpectrum &spec, PeakSpectrum::ConstIterator it, Map< double, IonScore > &CID_nodes, Size charge=1)
void | addSingleChargedIons_ (Map< double, IonScore > &ion_scores, PeakSpectrum &CID_spec)
void | initIsotopeDistributions_ ()
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 CompNovoIonScoringBase
Map< Size, std::vector< double > > | isotope_distributions_
double | fragment_mass_tolerance_
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

run with CompNovoIonScoringCID

Parameters of this class are:

Name | Type | Default | Restrictions | Description
--- | --- | --- | --- | ---
fragment_mass_tolerance | float | 0.4 |  | fragment mass tolerance
decomp_weights_precision | float | 0.01 |  | precision used to calculate the decompositions, this only affects cache usage!
double_charged_iso_threshold | float | 0.9 |  | minimal isotope intensity correlation of doubly charged ions to be used to score the single scored ions
double_charged_iso_threshold_single | float | 0.99 |  | Isotope scoring threshold used for doubly charged ions to infer singly charged variants
max_isotope_to_score | int | 3 |  | max isotope peak to be considered in the scoring
max_decomp_weight | int | 600 |  | maximal m/z difference used to calculate the decompositions
max_isotope | int | 3 |  | max isotope used in the theoretical spectra to score
max_mz | float | 2000.0 |  | maximal m/z value used to calculate isotope distributions
precursor_mass_tolerance | float | 1.5 |  | precursor mass tolerance

Note:

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

## Member Typedef Documentation

## ◆ IonScore

typedef CompNovoIonScoringBase::IonScore IonScore

## ◆ IsotopeType

typedef CompNovoIonScoringBase::IsotopeType IsotopeType

## Constructor & Destructor Documentation

## ◆ CompNovoIonScoringCID() [1/2]

CompNovoIonScoringCID | ( |  | ) |

default constructor

## ◆ CompNovoIonScoringCID() [2/2]

CompNovoIonScoringCID | ( | const CompNovoIonScoringCID & | source | ) |

copy constructor

## ◆ ~CompNovoIonScoringCID()

~CompNovoIonScoringCID | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ operator=()

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

## ◆ scoreSpectrum()

void scoreSpectrum | ( | Map< double, IonScore > & | CID_ion_scores,
|  | PeakSpectrum & | CID_spec,
|  | double | precursor_weight,
|  | Size | charge
| ) |  |

## ◆ scoreWitnessSet_()

void scoreWitnessSet_ | ( | Size | charge,
|  | double | precursor_weight,
|  | Map< double, IonScore > & | CID_nodes,
|  | const PeakSpectrum & | CID_orig_spec
| ) |  |

override protected virtual

Implements CompNovoIonScoringBase.