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MRMFeatureFinderScoring Class Reference

The MRMFeatureFinder finds and scores peaks of transitions that co-elute. More...

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

Inheritance diagram for MRMFeatureFinderScoring:
DefaultParamHandler ProgressLogger

Public Types

typedef MSSpectrum< ChromatogramPeakRichPeakChromatogram
 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 >, TransitionTypeMRMTransitionGroupType
 
typedef std::map< String, MRMTransitionGroupTypeTransitionGroupMapType
 
- Public Types inherited from ProgressLogger
enum  LogType { CMD, GUI, NONE }
 Possible log types. More...
 

Public Member Functions

 MRMFeatureFinderScoring ()
 Constructor. More...
 
 ~MRMFeatureFinderScoring ()
 Destructor. More...
 
void scorePeakgroups (MRMTransitionGroupType &transition_group, TransformationDescription &trafo, OpenSwath::SpectrumAccessPtr swath_map, FeatureMap &output)
 Score all peak groups of a transition group. More...
 
void setStrictFlag (bool f)
 Set the flag for strict mapping. More...
 
void setMS1Map (OpenSwath::SpectrumAccessPtr ms1_map)
 Add an MS1 map containing spectra. More...
 
void mapExperimentToTransitionList (OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window)
 Map the chromatograms to the transitions. More...
 
void pickExperiment (MSExperiment< Peak1D > &chromatograms, FeatureMap &output, TargetedExperiment &transition_exp, TransformationDescription trafo, MSExperiment< Peak1D > &swath_map)
 Picker and prepare functions. More...
 
void pickExperiment (OpenSwath::SpectrumAccessPtr input, FeatureMap &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType &transition_group_map)
 Pick features in one experiment containing chromatogram. More...
 
void prepareProteinPeptideMaps_ (OpenSwath::LightTargetedExperiment &transition_exp)
 Prepares the internal mappings of peptides and proteins. 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...
 

Private Member Functions

void updateMembers_ ()
 Synchronize members with param class. More...
 

Private Attributes

double rt_extraction_window_
 
double quantification_cutoff_
 
int stop_report_after_feature_
 
bool write_convex_hull_
 
bool strict_
 
double rt_normalization_factor_
 
int add_up_spectra_
 
double spacing_for_spectra_resampling_
 
std::map< OpenMS::String, const PeptideType * > PeptideRefMap_
 
OpenSwath_Scores_Usage su_
 
OpenMS::DIAScoring diascoring_
 
OpenMS::EmgScoring emgscoring_
 
OpenSwath::SpectrumAccessPtr ms1_map_
 

Additional Inherited Members

- 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

The MRMFeatureFinder finds and scores peaks of transitions that co-elute.

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.

Internally, all peak group detection is performed in MRMTransitionGroupPicker which segments the data and determines consensus peaks across traces (MRMFeatures). All scoring is delegated to the OpenSwathScoring class which implements i) chromatographic scores, ii) library based scores and iii) full spectrum (DIA) scores. These scores are retrieved from the OpenSwathScoring class and added to the MRMFeatures found in this algorithm. Note that the OpenSwathScoring is a facade that can be used to communicate with the underlying actual scoring engines and assembles the scores inside a scoring object called OpenSwath_Scores where they are easy to retrieve.

Member Typedef Documentation

Type definitions.

Constructor & Destructor Documentation

Constructor.

Destructor.

Member Function Documentation

void mapExperimentToTransitionList ( OpenSwath::SpectrumAccessPtr  input,
OpenSwath::LightTargetedExperiment transition_exp,
TransitionGroupMapType transition_group_map,
TransformationDescription  trafo,
double  rt_extraction_window 
)

Map the chromatograms to the transitions.

Map an input chromatogram experiment (mzML) and transition list (TraML) onto each other when they share identifiers, e.g. if the transition id is the same as the chromatogram native id.

Parameters
inputThe input chromatograms
transition_expThe transition list describing the experiment
transition_group_mapMapping of transition groups
trafoOptional transformation of the experimental retention time to the normalized retention time space used in the transition list.
rt_extraction_windowThe used retention time extraction window
void pickExperiment ( MSExperiment< Peak1D > &  chromatograms,
FeatureMap output,
TargetedExperiment transition_exp,
TransformationDescription  trafo,
MSExperiment< Peak1D > &  swath_map 
)

Picker and prepare functions.

Pick features in one experiment containing chromatogram

Function for for wrapping in Python, only uses OpenMS datastructures and does not return the map.

Parameters
chromatogramsThe input chromatograms
outputThe output features with corresponding scores
transition_expThe transition list describing the experiment
trafoOptional transformation of the experimental retention time to the normalized retention time space used in the transition list
swath_mapOptional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted

Referenced by OpenSwathWorkflow::RTNormalization().

void pickExperiment ( OpenSwath::SpectrumAccessPtr  input,
FeatureMap output,
OpenSwath::LightTargetedExperiment transition_exp,
TransformationDescription  trafo,
OpenSwath::SpectrumAccessPtr  swath_map,
TransitionGroupMapType transition_group_map 
)

Pick features in one experiment containing chromatogram.

Parameters
inputThe input chromatograms
outputThe output features with corresponding scores
transition_expThe transition list describing the experiment
trafoOptional transformation of the experimental retention time to the normalized retention time space used in the transition list.
swath_mapOptional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted. Use empty map if no data is available.
transition_group_mapOutput mapping of transition groups
void prepareProteinPeptideMaps_ ( OpenSwath::LightTargetedExperiment transition_exp)

Prepares the internal mappings of peptides and proteins.

Calling this method _is_ required before calling scorePeakgroups.

Parameters
transition_expThe transition list describing the experiment

Referenced by OpenSwathWorkflow::scoreAllChromatograms().

void scorePeakgroups ( MRMTransitionGroupType transition_group,
TransformationDescription trafo,
OpenSwath::SpectrumAccessPtr  swath_map,
FeatureMap output 
)

Score all peak groups of a transition group.

Iterate through all features found along the chromatograms of the transition group and score each one individually.

Parameters
transition_groupThe MRMTransitionGroup to be scored (input)
trafoOptional transformation of the experimental retention time to the normalized retention time space used in the transition list.
swath_mapOptional SWATH-MS (DIA) map corresponding from which the chromatograms were extracted. Use empty map if no data is available.
outputThe output features with corresponding scores (the found features will be added to this FeatureMap).

Referenced by OpenSwathWorkflow::scoreAllChromatograms().

void setMS1Map ( OpenSwath::SpectrumAccessPtr  ms1_map)
inline

Add an MS1 map containing spectra.

For DIA (SWATH-MS), an optional MS1 map can be supplied which can be used to extract precursor ion signal and provides additional scores. If no MS1 map is provided, the respective scores are not calculated.

Parameters
ms1_mapThe raw mass spectrometric MS1 data

Referenced by OpenSwathWorkflow::scoreAllChromatograms().

void setStrictFlag ( bool  f)
inline

Set the flag for strict mapping.

Referenced by OpenSwathWorkflow::RTNormalization().

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::SpectrumAccessPtr ms1_map_
private
std::map<OpenMS::String, const PeptideType*> PeptideRefMap_
private
double quantification_cutoff_
private
double rt_extraction_window_
private
double rt_normalization_factor_
private
double spacing_for_spectra_resampling_
private
int stop_report_after_feature_
private
bool strict_
private
bool write_convex_hull_
private

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Nov 1 2016 16:34:46 using doxygen 1.8.11