The MRMFeatureFinder finds and scores peaks of transitions that coelute. More...
#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureFinderScoring.h>
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 DefaultParamHandler & | operator= (const DefaultParamHandler &rhs) |
| Assignment operator. More... | |
| virtual bool | operator== (const DefaultParamHandler &rhs) const |
| Equality operator. More... | |
| void | setParameters (const Param ¶m) |
| Sets the parameters. More... | |
| const Param & | getParameters () const |
| Non-mutable access to the parameters. More... | |
| const Param & | getDefaults () const |
| Non-mutable access to the default parameters. More... | |
| const String & | getName () 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, double > | PeptideRTMap_ |
| 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< String > | subsections_ |
| 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_ |
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.
| typedef OpenSwath::LightPeptide PeptideType |
| typedef OpenSwath::LightProtein ProteinType |
Type definitions.
| typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType |
Constructor.
Destructor.
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References MRMFeature::addScore(), OpenSwath_Scores::calculate_swath_lda_prescore(), OpenSwathDataAccessHelper::convertPeptideToAASequence(), Peak2D::getRT(), MRMTransitionGroup< SpectrumType, TransitionType >::getTransitions(), OpenSwath_Scores::isotope_correlation, OpenSwath_Scores::isotope_overlap, OpenSwath_Scores::massdev_score, Feature::setOverallQuality(), MRMTransitionGroup< SpectrumType, TransitionType >::size(), OpenSwath::SpectrumPtr, and OpenSwath_Scores::yseries_score.
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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 | ||
| ) |
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References MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms(), LightTargetedExperiment::getPeptides(), FeatureMap< FeatureT >::getProteinIdentifications(), LightTargetedExperiment::getProteins(), MRMTransitionGroup< SpectrumType, TransitionType >::getTransitions(), LightTargetedExperiment::getTransitions(), LightPeptide::id, LightProtein::id, MRMTransitionGroupPicker::pickTransitionGroup(), LightPeptide::rt, run_identifier, LightProtein::sequence, ProteinHit::setAccession(), ProteinIdentification::setHits(), ProteinIdentification::setIdentifier(), DefaultParamHandler::setParameters(), and ProteinHit::setSequence().
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Score all peak groups.
References PeptideHit::addProteinAccession(), TransformationDescription::apply(), OpenSwath_Scores::calculate_lda_prescore(), OpenSwath_Scores::elution_model_fit_score, OpenSwath_Scores::get_quick_lda_score(), LightPeptide::getChargeState(), MRMTransitionGroup< SpectrumType, TransitionType >::getChromatograms(), MRMTransitionGroup< SpectrumType, TransitionType >::getFeaturesMuteable(), MRMTransitionGroup< SpectrumType, TransitionType >::getLibraryIntensity(), LightTransition::getPeptideRef(), MRMTransitionGroup< SpectrumType, TransitionType >::getTransition(), MRMTransitionGroup< SpectrumType, TransitionType >::getTransitionGroupID(), MRMTransitionGroup< SpectrumType, TransitionType >::getTransitions(), LightProtein::id, PeptideIdentification::insertHit(), TransformationDescription::invert(), OpenSwath::ISignalToNoisePtr, OpenMS::Constants::k, OpenSwath_Scores::library_corr, OpenSwath_Scores::library_rmsd, OpenSwath_Scores::log_sn_score, OpenSwath_Scores::norm_rt_score, OpenSwath::normalize(), OpenSwath::Scoring::normalize_sum(), LightPeptide::protein_ref, run_identifier, LightPeptide::sequence, PeptideHit::setCharge(), PeptideIdentification::setIdentifier(), PeptideHit::setScore(), PeptideHit::setSequence(), MRMTransitionGroup< SpectrumType, TransitionType >::size(), OpenSwath_Scores::xcorr_coelution_score, and OpenSwath_Scores::xcorr_shape_score.
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Synchronize members with param class.
Reimplemented from DefaultParamHandler.
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |