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ElutionPeakDetection Class Reference

Extracts chromatographic peaks from a mass trace. More...

#include <OpenMS/FILTERING/DATAREDUCTION/ElutionPeakDetection.h>

Inheritance diagram for ElutionPeakDetection:
DefaultParamHandler ProgressLogger

Public Member Functions

 ElutionPeakDetection ()
 Default Constructor. More...
 
virtual ~ElutionPeakDetection ()
 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...
 
- Public Member Functions inherited from ProgressLogger
 ProgressLogger ()
 Constructor. More...
 
 ~ProgressLogger ()
 Destructor. More...
 
 ProgressLogger (const ProgressLogger &other)
 Copy constructor. More...
 
ProgressLoggeroperator= (const ProgressLogger &other)
 Assignment Operator. More...
 
void setLogType (LogType type) const
 Sets the progress log that should be used. The default type is NONE! More...
 
LogType getLogType () const
 Returns the type of progress log being used. More...
 
void startProgress (SignedSize begin, SignedSize end, const String &label) const
 Initializes the progress display. More...
 
void setProgress (SignedSize value) const
 Sets the current progress. More...
 
void endProgress () const
 Ends the progress display. More...
 

Main computation methods

Getter & setter methods

double chrom_fwhm_
 
double chrom_peak_snr_
 
double noise_threshold_int_
 
double min_fwhm_
 
double max_fwhm_
 
String pw_filtering_
 
bool mt_snr_filtering_
 
void detectPeaks (MassTrace &mt, std::vector< MassTrace > &single_mtraces)
 Extracts chromatographic peaks from a single MassTrace and stores the splits into a vector of new mass traces. More...
 
void detectPeaks (std::vector< MassTrace > &mt_vec, std::vector< MassTrace > &single_mtraces)
 
void filterByPeakWidth (std::vector< MassTrace > &, std::vector< MassTrace > &)
 
double computeMassTraceNoise (const MassTrace &)
 
double computeMassTraceSNR (const MassTrace &)
 
double computeApexSNR (const MassTrace &)
 
void findLocalExtrema (const MassTrace &, const Size &, std::vector< Size > &, std::vector< Size > &)
 
void smoothData (MassTrace &mt, int win_size) const
 adds smoothed_intensities to internal data of mt More...
 
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 
void detectElutionPeaks_ (MassTrace &, std::vector< MassTrace > &)
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 
- Protected Member Functions inherited from DefaultParamHandler
void defaultsToParam_ ()
 Updates the parameters after the defaults have been set in the constructor. More...
 
- Static Protected Member Functions inherited from ProgressLogger
static String logTypeToFactoryName_ (LogType type)
 Return the name of the factory product used for this log type. 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...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
time_t last_invoke_
 
ProgressLoggerImplcurrent_logger_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

Extracts chromatographic peaks from a mass trace.

Mass traces may consist of several consecutively (partly overlapping) eluting peaks, e.g., stemming from isomeric compounds with exactly the same mass but different retentional behaviour. This method first applies smoothing on the mass trace's intensities, then detects local minima/maxima in order to separate the chromatographic peaks from each other. This results in a vector that gathers the splitted mass traces (see ElutionPeakDetection parameters).

Constructor & Destructor Documentation

Default Constructor.

virtual ~ElutionPeakDetection ( )
virtual

Destructor.

Member Function Documentation

double computeApexSNR ( const MassTrace )
double computeMassTraceNoise ( const MassTrace )
double computeMassTraceSNR ( const MassTrace )
void detectElutionPeaks_ ( MassTrace ,
std::vector< MassTrace > &   
)
private
void detectPeaks ( MassTrace mt,
std::vector< MassTrace > &  single_mtraces 
)

Extracts chromatographic peaks from a single MassTrace and stores the splits into a vector of new mass traces.

void detectPeaks ( std::vector< MassTrace > &  mt_vec,
std::vector< MassTrace > &  single_mtraces 
)

Applies the aforementioned detection method on a series of mass traces as input Smoothed intensities are added to mt_vec

void filterByPeakWidth ( std::vector< MassTrace > &  ,
std::vector< MassTrace > &   
)
void findLocalExtrema ( const MassTrace ,
const Size ,
std::vector< Size > &  ,
std::vector< Size > &   
)
void smoothData ( MassTrace mt,
int  win_size 
) const

adds smoothed_intensities to internal data of mt

virtual void updateMembers_ ( )
protectedvirtual

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

double chrom_fwhm_
private
double chrom_peak_snr_
private
double max_fwhm_
private
double min_fwhm_
private
bool mt_snr_filtering_
private
double noise_threshold_int_
private
String pw_filtering_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:37 using doxygen 1.8.9.1