OpenMS  2.8.0
Public Member Functions | Static Public Member Functions | List of all members
IsotopeMarker Class Reference

IsotopeMarker marks peak pairs which could represent an ion and its isotope. More...

#include <OpenMS/FILTERING/TRANSFORMERS/IsotopeMarker.h>

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

 IsotopeMarker ()
 default constructor More...
 
 IsotopeMarker (const IsotopeMarker &source)
 copy constructor More...
 
 ~IsotopeMarker () override
 destructor More...
 
IsotopeMarkeroperator= (const IsotopeMarker &source)
 assignment operator More...
 
template<typename SpectrumType >
void apply (std::map< double, bool > &marked, SpectrumType &spectrum)
 
- Public Member Functions inherited from PeakMarker
 PeakMarker ()
 default constructor More...
 
 PeakMarker (const PeakMarker &source)
 copy constructor More...
 
 ~PeakMarker () override
 destructor More...
 
PeakMarkeroperator= (const PeakMarker &source)
 assignment operator More...
 
template<typename SpectrumType >
void apply (std::map< double, bool > &, SpectrumType &)
 method to mark peaks 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...
 

Static Public Member Functions

static PeakMarkercreate ()
 
static const String getProductName ()
 
- Static Public Member Functions inherited from PeakMarker
static const String getProductName ()
 
- 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...
 

Additional Inherited Members

- 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

IsotopeMarker marks peak pairs which could represent an ion and its isotope.

Todo:
implement a real isotope marking here with isotopedistributions and fitting (Andreas)
Parameters of this class are:

NameTypeDefaultRestrictionsDescription
marks int1  How often a peak must be marked to be reported
mz_variation float0.1  variation in m/z direction
in_variation float0.5  variation in intensity

Note:

Constructor & Destructor Documentation

◆ IsotopeMarker() [1/2]

default constructor

◆ IsotopeMarker() [2/2]

IsotopeMarker ( const IsotopeMarker source)

copy constructor

◆ ~IsotopeMarker()

~IsotopeMarker ( )
override

destructor

Member Function Documentation

◆ apply()

void apply ( std::map< double, bool > &  marked,
SpectrumType spectrum 
)
inline

◆ create()

static PeakMarker* create ( )
inlinestatic

◆ getProductName()

static const String getProductName ( )
inlinestatic

◆ operator=()

IsotopeMarker& operator= ( const IsotopeMarker source)

assignment operator