add_up_spectra_ | MRMFeatureFinderScoring | private |
begin_ | ProgressLogger | mutableprotected |
calculateSwathScores_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, MRMFeature &mrmfeature_, OpenSwath::SpectrumAccessPtr swath_map, std::vector< double > &normalized_library_intensity, OpenSwath_Scores scores) | MRMFeatureFinderScoring | inlineprivate |
check_defaults_ | DefaultParamHandler | protected |
CMD enum value | ProgressLogger | |
DefaultParamHandler(const String &name) | DefaultParamHandler | |
DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
defaults_ | DefaultParamHandler | protected |
defaultsToParam_() | DefaultParamHandler | protected |
diascoring_ | MRMFeatureFinderScoring | private |
dlg_ | ProgressLogger | mutableprotected |
emgscoring_ | MRMFeatureFinderScoring | private |
end_ | ProgressLogger | mutableprotected |
endProgress() const | ProgressLogger | |
error_name_ | DefaultParamHandler | protected |
getAddedSpectra_(OpenSwath::SpectrumAccessPtr swath_map, double RT, int nr_spectra_to_add) | MRMFeatureFinderScoring | inlineprivate |
getDefaults() const | DefaultParamHandler | |
getLogType() const | ProgressLogger | |
getName() const | DefaultParamHandler | |
getParameters() const | DefaultParamHandler | |
getSubsections() const | DefaultParamHandler | |
GUI enum value | ProgressLogger | |
last_invoke_ | ProgressLogger | mutableprotected |
LogType enum name | ProgressLogger | |
mapExperimentToTransitionList(OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment &transition_exp, TransitionGroupMapType &transition_group_map, TransformationDescription trafo, double rt_extraction_window) | MRMFeatureFinderScoring | |
ModificationType typedef | MRMFeatureFinderScoring | |
MRMFeatureFinderScoring() | MRMFeatureFinderScoring | |
mrmscore_ | MRMFeatureFinderScoring | private |
MRMTransitionGroupType typedef | MRMFeatureFinderScoring | |
NONE enum value | ProgressLogger | |
operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
param_ | DefaultParamHandler | protected |
PeptideRefMap_ | MRMFeatureFinderScoring | private |
PeptideRTMap_ | MRMFeatureFinderScoring | private |
PeptideType typedef | MRMFeatureFinderScoring | |
pickExperiment(MSExperiment< Peak1D > &chromatograms, FeatureMap< Feature > &output, TargetedExperiment &transition_exp_, TransformationDescription trafo, MSExperiment< Peak1D > &swath_map) | MRMFeatureFinderScoring | inline |
pickExperiment(OpenSwath::SpectrumAccessPtr input, FeatureMap< Feature > &output, OpenSwath::LightTargetedExperiment &transition_exp, TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType &transition_group_map) | MRMFeatureFinderScoring | inline |
ProgressLogger() | ProgressLogger | |
ProteinRefMap_ | MRMFeatureFinderScoring | private |
ProteinType typedef | MRMFeatureFinderScoring | |
quantification_cutoff_ | MRMFeatureFinderScoring | private |
recursion_depth_ | ProgressLogger | protectedstatic |
RichPeakChromatogram typedef | MRMFeatureFinderScoring | |
rt_extraction_window_ | MRMFeatureFinderScoring | private |
rt_normalization_factor_ | MRMFeatureFinderScoring | private |
scorePeakgroups_(MRMTransitionGroup< SpectrumT, TransitionT > &transition_group, TransformationDescription &trafo, OpenSwath::SpectrumAccessPtr swath_map, FeatureMap< Feature > &output) | MRMFeatureFinderScoring | inlineprivate |
setLogType(LogType type) const | ProgressLogger | |
setName(const String &name) | DefaultParamHandler | |
setParameters(const Param ¶m) | DefaultParamHandler | |
setProgress(SignedSize value) const | ProgressLogger | |
setStrictFlag(bool f) | MRMFeatureFinderScoring | inline |
spacing_for_spectra_resampling_ | MRMFeatureFinderScoring | private |
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
stop_report_after_feature_ | MRMFeatureFinderScoring | private |
stop_watch_ | ProgressLogger | mutableprotected |
strict_ | MRMFeatureFinderScoring | private |
subsections_ | DefaultParamHandler | protected |
TargetedExpType typedef | MRMFeatureFinderScoring | |
TransitionGroupMapType typedef | MRMFeatureFinderScoring | |
TransitionType typedef | MRMFeatureFinderScoring | |
type_ | ProgressLogger | mutableprotected |
updateMembers_() | MRMFeatureFinderScoring | privatevirtual |
use_coelution_score_ | MRMFeatureFinderScoring | private |
use_elution_model_score_ | MRMFeatureFinderScoring | private |
use_intensity_score_ | MRMFeatureFinderScoring | private |
use_library_score_ | MRMFeatureFinderScoring | private |
use_nr_peaks_score_ | MRMFeatureFinderScoring | private |
use_rt_score_ | MRMFeatureFinderScoring | private |
use_shape_score_ | MRMFeatureFinderScoring | private |
use_sn_score_ | MRMFeatureFinderScoring | private |
use_total_xic_score_ | MRMFeatureFinderScoring | private |
value_ | ProgressLogger | mutableprotected |
warn_empty_defaults_ | DefaultParamHandler | protected |
write_convex_hull_ | MRMFeatureFinderScoring | private |
~DefaultParamHandler() | DefaultParamHandler | virtual |
~MRMFeatureFinderScoring() | MRMFeatureFinderScoring | |
~ProgressLogger() | ProgressLogger | |