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MassTraceDetection Class Reference

A mass trace extraction method that gathers peaks similar in m/z and moving along retention time. More...

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

Inheritance diagram for MassTraceDetection:
DefaultParamHandler ProgressLogger

Public Member Functions

 MassTraceDetection ()
 Default constructor. More...
 
virtual ~MassTraceDetection ()
 Default destructor. More...
 
Helper methods
void updateIterativeWeightedMeanMZ (const double &, const double &, double &, double &, double &)
 Allows the iterative computation of the intensity-weighted mean of a mass trace's centroid m/z. 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

double mass_error_ppm_
 
double noise_threshold_int_
 
double chrom_peak_snr_
 
String trace_termination_criterion_
 
Size trace_termination_outliers_
 
double min_sample_rate_
 
double min_trace_length_
 
double max_trace_length_
 
bool reestimate_mt_sd_
 
void run (const MSExperiment< Peak1D > &, std::vector< MassTrace > &)
 Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vector container. More...
 
void run (MSExperiment< Peak1D >::ConstAreaIterator &begin, MSExperiment< Peak1D >::ConstAreaIterator &end, std::vector< MassTrace > &found_masstraces)
 Invokes the run method (see above) on merely a subregion of a MSExperiment map. More...
 
virtual void updateMembers_ ()
 This method is used to update extra member variables at the end of the setParameters() method. More...
 

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

A mass trace extraction method that gathers peaks similar in m/z and moving along retention time.

Peaks of a MSExperiment are sorted by their intensity and stored in a list of potential chromatographic apex positions. Starting with these, mass traces are extended in- and decreasingly in retention time. During this extension phase, the centroid m/z is computed on-line as an intensity-weighted mean of peaks. The extension phase ends when the frequency of gathered peaks drops below a threshold (min_sample_rate, see MassTraceDetection parameters).

Constructor & Destructor Documentation

Default constructor.

virtual ~MassTraceDetection ( )
virtual

Default destructor.

Member Function Documentation

void run ( const MSExperiment< Peak1D > &  ,
std::vector< MassTrace > &   
)

Main method of MassTraceDetection. Extracts mass traces of a MSExperiment and gathers them into a vector container.

void run ( MSExperiment< Peak1D >::ConstAreaIterator &  begin,
MSExperiment< Peak1D >::ConstAreaIterator &  end,
std::vector< MassTrace > &  found_masstraces 
)

Invokes the run method (see above) on merely a subregion of a MSExperiment map.

void updateIterativeWeightedMeanMZ ( const double ,
const double ,
double ,
double ,
double  
)

Allows the iterative computation of the intensity-weighted mean of a mass trace's centroid m/z.

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_peak_snr_
private
double mass_error_ppm_
private
double max_trace_length_
private
double min_sample_rate_
private
double min_trace_length_
private
double noise_threshold_int_
private
bool reestimate_mt_sd_
private
String trace_termination_criterion_
private
Size trace_termination_outliers_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:40 using doxygen 1.8.9.1