| OpenMS 2.5.0

Classes | Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
CompNovoIonScoringBase Class Referenceabstract

run with CompNovoIonScoringBase More...

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

Inheritance diagram for CompNovoIonScoringBase:

## Classes

struct | IonScore

## Public Types

enum | IsotopeType { PARENT = 0, CHILD = 1, LONE = 2 }

## Public Member Functions

CompNovoIonScoringBase & | operator= (const CompNovoIonScoringBase &source)
constructors and destructors
| CompNovoIonScoringBase ()
| default constructor More...
| CompNovoIonScoringBase (const CompNovoIonScoringBase &source)
| copy constructor More...
| ~CompNovoIonScoringBase () override
| destructor More...
Accessors
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 | 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)
virtual void | scoreWitnessSet_ (Size charge, double precursor_weight, Map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec)=0
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...

## Protected Attributes

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 CompNovoIonScoringBase

## Member Enumeration Documentation

## ◆ IsotopeType

enum IsotopeType

Enumerator
PARENT |
CHILD |
LONE |

## Constructor & Destructor Documentation

## ◆ CompNovoIonScoringBase() [1/2]

CompNovoIonScoringBase | ( |  | ) |

default constructor

## ◆ CompNovoIonScoringBase() [2/2]

CompNovoIonScoringBase | ( | const CompNovoIonScoringBase & | source | ) |

copy constructor

## ◆ ~CompNovoIonScoringBase()

~CompNovoIonScoringBase | ( |  | ) |

override

destructor

## Member Function Documentation

## ◆ addSingleChargedIons_()

void addSingleChargedIons_ | ( | Map< double, IonScore > & | ion_scores,
|  | PeakSpectrum & | CID_spec
| ) |  |

protected

## ◆ classifyIsotopes_()

IsotopeType classifyIsotopes_ | ( | const PeakSpectrum & | spec,
|  | PeakSpectrum::ConstIterator | it
| ) |  |

protected

## ◆ initIsotopeDistributions_()

void initIsotopeDistributions_ | ( |  | ) |

protected

## ◆ operator=()

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

## ◆ scoreIsotopes()

double scoreIsotopes | ( | const PeakSpectrum & | CID_spec,
|  | PeakSpectrum::ConstIterator | it,
|  | Size | charge
| ) |  |

## ◆ scoreIsotopes_()

double scoreIsotopes_ | ( | const PeakSpectrum & | spec,
|  | PeakSpectrum::ConstIterator | it,
|  | Map< double, IonScore > & | CID_nodes,
|  | Size | charge = `1`
| ) |  |

protected

## ◆ scoreWitnessSet_()

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

protected pure virtual

Implemented in CompNovoIonScoring, and CompNovoIonScoringCID.

## ◆ updateMembers_()

void updateMembers_ | ( |  | ) |

override protected virtual

update members method from DefaultParamHandler to update the members

Reimplemented from DefaultParamHandler.

## Member Data Documentation

## ◆ fragment_mass_tolerance_

double fragment_mass_tolerance_

protected

## ◆ isotope_distributions_

Map<Size, std::vector<double> > isotope_distributions_

protected