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FeatureFindingMetabo Class Reference

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

Inheritance diagram for FeatureFindingMetabo:
DefaultParamHandler ProgressLogger

List of all members.

Public Member Functions

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

Protected Member Functions

virtual void updateMembers_ ()

Private Member Functions

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

Private Attributes

svm_model * isotope_filt_svm_
std::vector< DoubleReal > svm_feat_centers_
std::vector< DoubleReal > svm_feat_scales_
DoubleReal total_intensity_
DoubleReal local_rt_range_
 parameter stuff
DoubleReal local_mz_range_
Size charge_lower_bound_
Size charge_upper_bound_
DoubleReal chrom_fwhm_
bool report_summed_ints_
bool disable_isotope_filtering_
String isotope_model_
bool use_smoothed_intensities_

Constructor & Destructor Documentation

FeatureFindingMetabo (  ) 

Default constructor.

virtual ~FeatureFindingMetabo (  )  [virtual]

Default destructor.

Member Function Documentation

DoubleReal computeAveragineSimScore_ ( const std::vector< DoubleReal > &  ,
const DoubleReal &   
) [private]
DoubleReal computeCosineSim_ ( const std::vector< DoubleReal > &  ,
const std::vector< DoubleReal > &   
) [private]
DoubleReal computeOLSCoeff_ ( const std::vector< DoubleReal > &  ,
const std::vector< DoubleReal > &   
) [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

DoubleReal scoreMZ_ ( const MassTrace &  ,
const MassTrace &  ,
Size  ,
Size   
) [private]
DoubleReal scoreRT_ ( const MassTrace &  ,
const MassTrace &   
) [private]
virtual void updateMembers_ (  )  [protected, virtual]

Member Data Documentation

Size charge_lower_bound_ [private]
Size charge_upper_bound_ [private]
DoubleReal chrom_fwhm_ [private]
bool disable_isotope_filtering_ [private]
svm_model* isotope_filt_svm_ [private]
String isotope_model_ [private]
DoubleReal local_mz_range_ [private]
DoubleReal local_rt_range_ [private]

parameter stuff

bool report_summed_ints_ [private]
std::vector<DoubleReal> svm_feat_centers_ [private]
std::vector<DoubleReal> svm_feat_scales_ [private]
DoubleReal total_intensity_ [private]
bool use_smoothed_intensities_ [private]
OpenMS / TOPP release 1.10.0 Documentation generated on Thu Mar 7 2013 09:42:53 using doxygen 1.7.1