OpenMS
DeNovoAlgorithm Class Referenceabstract

Base class for ion scoring implementation for de novo algorithms. More...

#include <OpenMS/ANALYSIS/DENOVO/DeNovoAlgorithm.h>

Inheritance diagram for DeNovoAlgorithm:
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Collaboration diagram for DeNovoAlgorithm:
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Public Member Functions

Constructors and destructors
 DeNovoAlgorithm ()
 default constructor More...
 
 ~DeNovoAlgorithm () override
 destructor More...
 
 DeNovoAlgorithm (const DeNovoAlgorithm &rhs)
 copy constructor More...
 
DeNovoAlgorithmoperator= (const DeNovoAlgorithm &rhs)
 assignment operator More...
 
virtual void generateCandidates (std::vector< PeptideIdentification > &candidates, const std::vector< std::vector< DeNovoIonScoring::IonScore > > &ion_scores, const PeakMap &exp)=0
 
virtual void generateCandidates (PeptideIdentification &candidates, std::vector< DeNovoIonScoring::IonScore > &ion_scores, const PeakSpectrum &spec)=0
 
- 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...
 
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...
 

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...
 
- Protected Member Functions inherited from DefaultParamHandler
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
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

Base class for ion scoring implementation for de novo algorithms.

Constructor & Destructor Documentation

◆ DeNovoAlgorithm() [1/2]

default constructor

◆ ~DeNovoAlgorithm()

~DeNovoAlgorithm ( )
override

destructor

◆ DeNovoAlgorithm() [2/2]

DeNovoAlgorithm ( const DeNovoAlgorithm rhs)

copy constructor

Member Function Documentation

◆ generateCandidates() [1/2]

virtual void generateCandidates ( PeptideIdentification candidates,
std::vector< DeNovoIonScoring::IonScore > &  ion_scores,
const PeakSpectrum spec 
)
pure virtual

◆ generateCandidates() [2/2]

virtual void generateCandidates ( std::vector< PeptideIdentification > &  candidates,
const std::vector< std::vector< DeNovoIonScoring::IonScore > > &  ion_scores,
const PeakMap exp 
)
pure virtual

◆ operator=()

DeNovoAlgorithm& operator= ( const DeNovoAlgorithm rhs)

assignment operator