OpenMS  2.4.0
List of all members
MassDecompositionAlgorithm Class Reference

Mass decomposition algorithm, given a mass it suggests possible compositions. More...

#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/MassDecompositionAlgorithm.h>

Inheritance diagram for MassDecompositionAlgorithm:
DefaultParamHandler

Public Member Functions

constructors and destructor
 MassDecompositionAlgorithm ()
 Default constructor. More...
 
 ~MassDecompositionAlgorithm () 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 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...
 

Operators

ims::IMSAlphabetalphabet_
 
ims::RealMassDecomposerdecomposer_
 
void getDecompositions (std::vector< MassDecomposition > &decomps, double weight)
 returns the possible decompositions given the weight More...
 
void updateMembers_ () override
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
 MassDecompositionAlgorithm (const MassDecompositionAlgorithm &deco)
 Copy constructor. More...
 
MassDecompositionAlgorithmoperator= (const MassDecompositionAlgorithm &rhs)
 assignment operator More...
 

Additional Inherited Members

- Protected Member Functions inherited from DefaultParamHandler
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

Mass decomposition algorithm, given a mass it suggests possible compositions.

A mass decomposition algorithm decomposes a mass or a mass difference into possible amino acids and frequencies of them, which add up to the given mass. This class is a wrapper for the algorithm published in

Constructor & Destructor Documentation

◆ MassDecompositionAlgorithm() [1/2]

Default constructor.

◆ ~MassDecompositionAlgorithm()

Destructor.

◆ MassDecompositionAlgorithm() [2/2]

Copy constructor.

Member Function Documentation

◆ getDecompositions()

void getDecompositions ( std::vector< MassDecomposition > &  decomps,
double  weight 
)

returns the possible decompositions given the weight

◆ operator=()

MassDecompositionAlgorithm& operator= ( const MassDecompositionAlgorithm rhs)
private

assignment operator

◆ updateMembers_()

void updateMembers_ ( )
overrideprotectedvirtual

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

◆ alphabet_

ims::IMSAlphabet* alphabet_
protected

◆ decomposer_

ims::RealMassDecomposer* decomposer_
protected