Home  · Classes  · Annotated Classes  · Modules  · Members  · Namespaces  · Related Pages
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
FeatureFindingMetabo Class Reference

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

Inheritance diagram for FeatureFindingMetabo:
DefaultParamHandler ProgressLogger

Public Member Functions

 FeatureFindingMetabo ()
 Default constructor. More...
 
virtual ~FeatureFindingMetabo ()
 Default destructor. More...
 
void run (std::vector< MassTrace > &, FeatureMap &)
 main method of FeatureFindingMetabo 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...
 

Protected Member Functions

virtual void updateMembers_ ()
 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...
 

Private Member Functions

double computeOLSCoeff_ (const std::vector< double > &, const std::vector< double > &)
 private member functions More...
 
double computeCosineSim_ (const std::vector< double > &, const std::vector< double > &)
 
bool isLegalIsotopePattern_ (FeatureHypothesis &)
 
bool isLegalIsotopePattern2_ (FeatureHypothesis &)
 
void loadIsotopeModel_ (const String &)
 
double scoreMZ_ (const MassTrace &, const MassTrace &, Size, Size)
 
double scoreMZ2_ (const MassTrace &, const MassTrace &, Size, Size)
 
double scoreRT_ (const MassTrace &, const MassTrace &)
 
double computeAveragineSimScore_ (const std::vector< double > &, const double &)
 
void findLocalFeatures_ (std::vector< MassTrace * > &, std::vector< FeatureHypothesis > &)
 

Private Attributes

svm_model * isotope_filt_svm_
 
std::vector< doublesvm_feat_centers_
 
std::vector< doublesvm_feat_scales_
 
double total_intensity_
 
double local_rt_range_
 parameter stuff More...
 
double local_mz_range_
 
Size charge_lower_bound_
 
Size charge_upper_bound_
 
double chrom_fwhm_
 
bool report_summed_ints_
 
bool enable_RT_filtering_
 
bool disable_isotope_filtering_
 
String isotope_model_
 
String metabo_iso_noisemodel_
 
bool use_smoothed_intensities_
 

Additional Inherited Members

- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. 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_
 

Constructor & Destructor Documentation

Default constructor.

virtual ~FeatureFindingMetabo ( )
virtual

Default destructor.

Member Function Documentation

double computeAveragineSimScore_ ( const std::vector< double > &  ,
const double  
)
private
double computeCosineSim_ ( const std::vector< double > &  ,
const std::vector< double > &   
)
private
double computeOLSCoeff_ ( const std::vector< double > &  ,
const std::vector< double > &   
)
private

private member functions

void findLocalFeatures_ ( std::vector< MassTrace * > &  ,
std::vector< FeatureHypothesis > &   
)
private
bool isLegalIsotopePattern2_ ( FeatureHypothesis )
private
bool isLegalIsotopePattern_ ( FeatureHypothesis )
private
void loadIsotopeModel_ ( const String )
private
void run ( std::vector< MassTrace > &  ,
FeatureMap  
)

main method of FeatureFindingMetabo

double scoreMZ2_ ( const MassTrace ,
const MassTrace ,
Size  ,
Size   
)
private
double scoreMZ_ ( const MassTrace ,
const MassTrace ,
Size  ,
Size   
)
private
double scoreRT_ ( const MassTrace ,
const MassTrace  
)
private
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

Size charge_lower_bound_
private
Size charge_upper_bound_
private
double chrom_fwhm_
private
bool disable_isotope_filtering_
private
bool enable_RT_filtering_
private
svm_model* isotope_filt_svm_
private
String isotope_model_
private
double local_mz_range_
private
double local_rt_range_
private

parameter stuff

String metabo_iso_noisemodel_
private
bool report_summed_ints_
private
std::vector<double> svm_feat_centers_
private
std::vector<double> svm_feat_scales_
private
double total_intensity_
private
bool use_smoothed_intensities_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Thu Aug 20 2015 01:44:35 using doxygen 1.8.9.1