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MRMFeatureFinderScoring Class Reference

The MRMFeatureFinder finds and scores peaks of transitions that coelute. More...

#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>

Inheritance diagram for MRMFeatureFinderScoring:
DefaultParamHandler ProgressLogger

Public Types

typedef MSSpectrum
< ChromatogramPeak
RichPeakChromatogram
 Type definitions. More...
 
typedef OpenSwath::LightTransition TransitionType
 
typedef
OpenSwath::LightTargetedExperiment 
TargetedExpType
 
typedef OpenSwath::LightPeptide PeptideType
 
typedef OpenSwath::LightProtein ProteinType
 
typedef
OpenSwath::LightModification 
ModificationType
 
typedef MRMTransitionGroup
< MSSpectrum< ChromatogramPeak >
, TransitionType
MRMTransitionGroupType
 
typedef std::map< String,
MRMTransitionGroupType
TransitionGroupMapType
 
- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 

Public Member Functions

 MRMFeatureFinderScoring ()
 Constructor. More...
 
 ~MRMFeatureFinderScoring ()
 Destructor. More...
 
void pickExperiment (MSExperiment< Peak1D > &chromatograms, FeatureMap< Feature > &output, TargetedExperiment &transition_exp_, TransformationDescription trafo, MSExperiment< Peak1D > &swath_map)
 
void pickExperiment (OpenSwath::SpectrumAccessPtr input, FeatureMap< Feature > &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType &transition_group_map)
 
void mapExperimentToTransitionList (OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window)
 
void setStrictFlag (bool f)
 
- 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...
 
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...
 

Private Member Functions

template<typename SpectrumT , typename TransitionT >
void scorePeakgroups_ (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, TransformationDescription &trafo, OpenSwath::SpectrumAccessPtr swath_map, FeatureMap< Feature > &output)
 Score all peak groups. More...
 
OpenSwath::SpectrumPtr getAddedSpectra_ (OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add)
 Returns the addition of "nr_spectra_to_add" spectra around the given RT. More...
 
template<typename SpectrumT , typename TransitionT >
void calculateSwathScores_ (MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, MRMFeature &mrmfeature_, OpenSwath::SpectrumAccessPtr swath_map, std::vector< double > &normalized_library_intensity, OpenSwath_Scores scores)
 
void updateMembers_ ()
 Synchronize members with param class. More...
 

Private Attributes

DoubleReal rt_extraction_window_
 
DoubleReal quantification_cutoff_
 
bool use_coelution_score_
 
bool use_shape_score_
 
bool use_rt_score_
 
bool use_library_score_
 
bool use_elution_model_score_
 
bool use_intensity_score_
 
bool use_total_xic_score_
 
bool use_nr_peaks_score_
 
bool use_sn_score_
 
int stop_report_after_feature_
 
int add_up_spectra_
 
DoubleReal spacing_for_spectra_resampling_
 
bool write_convex_hull_
 
bool strict_
 
DoubleReal rt_normalization_factor_
 
std::map< OpenMS::String, doublePeptideRTMap_
 
std::map< OpenMS::String,
const PeptideType * > 
PeptideRefMap_
 
std::map< OpenMS::String,
const ProteinType * > 
ProteinRefMap_
 
OpenSwath::MRMScoring mrmscore_
 
OpenMS::DIAScoring diascoring_
 
OpenMS::EmgScoring emgscoring_
 

Additional Inherited Members

- Protected Member Functions inherited from DefaultParamHandler
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...
 
- Protected Attributes inherited from ProgressLogger
LogType type_
 
SignedSize begin_
 
SignedSize end_
 
SignedSize value_
 
QProgressDialog * dlg_
 
StopWatch stop_watch_
 
time_t last_invoke_
 
- Static Protected Attributes inherited from ProgressLogger
static int recursion_depth_
 

Detailed Description

The MRMFeatureFinder finds and scores peaks of transitions that coelute.

It does so using an internal peakpicker for each chromatogram and then creating consensus / meta-peaks (MRMFeatures) that contain the information of all corresponding chromatograms at the peak-position. It then goes on to score those MRMFeatures using different criteria described in the MRMScoring class.

Member Typedef Documentation

Type definitions.

Constructor & Destructor Documentation

Constructor.

Destructor.

Member Function Documentation

void calculateSwathScores_ ( MRMTransitionGroup< SpectrumT, TransitionT > &  transition_group,
MRMFeature mrmfeature_,
OpenSwath::SpectrumAccessPtr  swath_map,
std::vector< double > &  normalized_library_intensity,
OpenSwath_Scores  scores 
)
inlineprivate
OpenSwath::SpectrumPtr getAddedSpectra_ ( OpenSwath::SpectrumAccessPtr  swath_map,
double  RT,
int  nr_spectra_to_add 
)
inlineprivate

Returns the addition of "nr_spectra_to_add" spectra around the given RT.

References SpectrumAddition::addUpSpectra(), and OpenSwath::SpectrumPtr.

void mapExperimentToTransitionList ( OpenSwath::SpectrumAccessPtr  input,
OpenSwath::LightTargetedExperiment transition_exp,
TransitionGroupMapType transition_group_map,
TransformationDescription  trafo,
double  rt_extraction_window 
)
void pickExperiment ( MSExperiment< Peak1D > &  chromatograms,
FeatureMap< Feature > &  output,
TargetedExperiment transition_exp_,
TransformationDescription  trafo,
MSExperiment< Peak1D > &  swath_map 
)
inline
void pickExperiment ( OpenSwath::SpectrumAccessPtr  input,
FeatureMap< Feature > &  output,
OpenSwath::LightTargetedExperiment transition_exp,
TransformationDescription  trafo,
OpenSwath::SpectrumAccessPtr  swath_map,
TransitionGroupMapType transition_group_map 
)
inline
void scorePeakgroups_ ( MRMTransitionGroup< SpectrumT, TransitionT > &  transition_group,
TransformationDescription trafo,
OpenSwath::SpectrumAccessPtr  swath_map,
FeatureMap< Feature > &  output 
)
inlineprivate
void setStrictFlag ( bool  f)
inline
void updateMembers_ ( )
privatevirtual

Synchronize members with param class.

Reimplemented from DefaultParamHandler.

Member Data Documentation

int add_up_spectra_
private
OpenMS::DIAScoring diascoring_
private
OpenMS::EmgScoring emgscoring_
private
OpenSwath::MRMScoring mrmscore_
private
std::map<OpenMS::String, const PeptideType*> PeptideRefMap_
private
std::map<OpenMS::String, double> PeptideRTMap_
private
std::map<OpenMS::String, const ProteinType*> ProteinRefMap_
private
DoubleReal quantification_cutoff_
private
DoubleReal rt_extraction_window_
private
DoubleReal rt_normalization_factor_
private
DoubleReal spacing_for_spectra_resampling_
private
int stop_report_after_feature_
private
bool strict_
private
bool use_coelution_score_
private
bool use_elution_model_score_
private
bool use_intensity_score_
private
bool use_library_score_
private
bool use_nr_peaks_score_
private
bool use_rt_score_
private
bool use_shape_score_
private
bool use_sn_score_
private
bool use_total_xic_score_
private
bool write_convex_hull_
private

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5