OpenMS
BaseModel< D > Class Template Referenceabstract

Abstract base class for all D-dimensional models. More...

#include <OpenMS/TRANSFORMATIONS/FEATUREFINDER/BaseModel.h>

Inheritance diagram for BaseModel< D >:
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Collaboration diagram for BaseModel< D >:
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Public Types

typedef double IntensityType
 
typedef double CoordinateType
 
typedef DPosition< D > PositionType
 
typedef DPeak< D >::Type PeakType
 
typedef std::vector< PeakTypeSamplesType
 

Public Member Functions

 BaseModel ()
 Default constructor. More...
 
 BaseModel (const BaseModel &source)
 copy constructor More...
 
 ~BaseModel () override
 Destructor. More...
 
BaseModeloperator= (const BaseModel &source)
 assignment operator More...
 
virtual IntensityType getIntensity (const PositionType &pos) const =0
 access model predicted intensity at position pos More...
 
virtual bool isContained (const PositionType &pos) const
 check if position pos is part of the model regarding the models cut-off. More...
 
template<typename PeakType >
void fillIntensity (PeakType &peak) const
 Convenience function to set the intensity of a peak to the predicted intensity at its current position, calling virtual void getIntensity(). More...
 
template<class PeakIterator >
void fillIntensities (PeakIterator begin, PeakIterator end) const
 Convenience function that applies fillIntensity() to an iterator range. More...
 
virtual IntensityType getCutOff () const
 get cutoff value More...
 
virtual void setCutOff (IntensityType cut_off)
 set cutoff value More...
 
virtual void getSamples (SamplesType &cont) const =0
 get reasonable set of samples from the model (i.e. for printing) More...
 
virtual void getSamples (std::ostream &os)
 fill stream with reasonable set of samples from the model (i.e. for printing) More...
 
void registerChildren ()
 
void registerChildren ()
 
- 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...
 

Static Public Member Functions

static void registerChildren ()
 register all derived classes here (implemented in file BaseModel_impl.h) More...
 
- 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

void updateMembers_ () override
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 

Protected Attributes

IntensityType cut_off_
 
- 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

template<UInt D>
class OpenMS::BaseModel< D >

Abstract base class for all D-dimensional models.

Every derived class has to implement the static functions "T* create()" and "const String getProductName()" (see DefaultParamHandler for details)

Member Typedef Documentation

◆ CoordinateType

typedef double CoordinateType

◆ IntensityType

typedef double IntensityType

◆ PeakType

typedef DPeak<D>::Type PeakType

◆ PositionType

typedef DPosition<D> PositionType

◆ SamplesType

typedef std::vector<PeakType> SamplesType

Constructor & Destructor Documentation

◆ BaseModel() [1/2]

BaseModel ( )
inline

Default constructor.

References DefaultParamHandler::defaults_, and Param::setValue().

◆ BaseModel() [2/2]

BaseModel ( const BaseModel< D > &  source)
inline

copy constructor

◆ ~BaseModel()

~BaseModel ( )
inlineoverride

Destructor.

Member Function Documentation

◆ fillIntensities()

void fillIntensities ( PeakIterator  begin,
PeakIterator  end 
) const
inline

Convenience function that applies fillIntensity() to an iterator range.

References BaseModel< D >::fillIntensity().

◆ fillIntensity()

void fillIntensity ( PeakType peak) const
inline

Convenience function to set the intensity of a peak to the predicted intensity at its current position, calling virtual void getIntensity().

References BaseModel< D >::getIntensity().

Referenced by BaseModel< D >::fillIntensities().

◆ getCutOff()

virtual IntensityType getCutOff ( ) const
inlinevirtual

get cutoff value

References BaseModel< D >::cut_off_.

◆ getIntensity()

virtual IntensityType getIntensity ( const PositionType pos) const
pure virtual

access model predicted intensity at position pos

Implemented in ProductModel< 2 >.

Referenced by BaseModel< D >::fillIntensity(), and BaseModel< D >::isContained().

◆ getSamples() [1/2]

virtual void getSamples ( SamplesType cont) const
pure virtual

get reasonable set of samples from the model (i.e. for printing)

Implemented in ProductModel< 2 >, and InterpolationModel.

Referenced by BaseModel< D >::getSamples().

◆ getSamples() [2/2]

virtual void getSamples ( std::ostream &  os)
inlinevirtual

fill stream with reasonable set of samples from the model (i.e. for printing)

References BaseModel< D >::getSamples().

◆ isContained()

virtual bool isContained ( const PositionType pos) const
inlinevirtual

check if position pos is part of the model regarding the models cut-off.

References BaseModel< D >::cut_off_, and BaseModel< D >::getIntensity().

◆ operator=()

BaseModel& operator= ( const BaseModel< D > &  source)
inline

◆ registerChildren() [1/3]

static void registerChildren ( )
static

register all derived classes here (implemented in file BaseModel_impl.h)

◆ registerChildren() [2/3]

void registerChildren ( )

◆ registerChildren() [3/3]

void registerChildren ( )

◆ setCutOff()

virtual void setCutOff ( IntensityType  cut_off)
inlinevirtual

◆ updateMembers_()

void updateMembers_ ( )
inlineoverrideprotectedvirtual

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.

References BaseModel< D >::cut_off_, Param::getValue(), and DefaultParamHandler::param_.

Referenced by InterpolationModel::updateMembers_(), and ProductModel< 2 >::updateMembers_().

Member Data Documentation

◆ cut_off_