| addModificationToPeptideHit_(Feature &feature, const String &modification) const | SILACLabeler | protected |
| applyLabelToProteinHit_(FeatureMapSim &protein_hit, const String &arginine_label, const String &lysine_label) const | SILACLabeler | protected |
| BaseLabeler() | BaseLabeler | |
| canModificationBeApplied_(const String &modification_id, const String &aa) const | SILACLabeler | protected |
| channel_description_ | BaseLabeler | protected |
| check_defaults_ | DefaultParamHandler | protected |
| consensus_ | BaseLabeler | protected |
| create() | SILACLabeler | inlinestatic |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| error_name_ | DefaultParamHandler | protected |
| getChannelIntensityName(const Size channel_index) const | BaseLabeler | |
| getConsensus() | BaseLabeler | |
| getDefaultParameters() const | BaseLabeler | virtual |
| getDefaults() const | DefaultParamHandler | |
| getDescription() const | BaseLabeler | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getProductName() | SILACLabeler | inlinestatic |
| getSubsections() const | DefaultParamHandler | |
| getUnmodifiedSequence_(const Feature &feature, const String &arginine_label, const String &lysine_label) const | SILACLabeler | protected |
| heavy_channel_arginine_label_ | SILACLabeler | protected |
| heavy_channel_lysine_label_ | SILACLabeler | protected |
| HEAVY_FEATURE_MAPID_ | SILACLabeler | privatestatic |
| LIGHT_FEATURE_MAPID_ | SILACLabeler | privatestatic |
| medium_channel_arginine_label_ | SILACLabeler | protected |
| medium_channel_lysine_label_ | SILACLabeler | protected |
| MEDIUM_FEATURE_MAPID_ | SILACLabeler | privatestatic |
| mergeAllChannelFeatures_(Feature &heavy_channel_feature, const String &unmodified_feature_sequence, Map< String, Feature > &light_channel_feature_index, Map< String, Feature > &medium_channel_feature_index) const | SILACLabeler | protected |
| mergeFeatures_(Feature &labeled_channel_feature, const String &unmodified_sequence, Map< String, Feature > &unlabeled_features_index, Int index_channel_id, Int labeled_channel_id) const | SILACLabeler | protected |
| mergeProteinAccessions_(Feature &target, const Feature &source) const | BaseLabeler | protected |
| mergeProteinIdentificationsMaps_(const FeatureMapSimVector &maps) | BaseLabeler | protected |
| operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| postDetectabilityHook(FeatureMapSimVector &) | SILACLabeler | virtual |
| postDigestHook(FeatureMapSimVector &) | SILACLabeler | virtual |
| postIonizationHook(FeatureMapSimVector &) | SILACLabeler | virtual |
| postRawMSHook(FeatureMapSimVector &) | SILACLabeler | virtual |
| postRawTandemMSHook(FeatureMapSimVector &, MSSimExperiment &) | SILACLabeler | virtual |
| postRTHook(FeatureMapSimVector &) | SILACLabeler | virtual |
| preCheck(Param &) const | SILACLabeler | virtual |
| recomputeConsensus_(const FeatureMapSim &simulated_features) | BaseLabeler | protected |
| registerChildren() | BaseLabeler | static |
| rng_ | BaseLabeler | protected |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setRnd(const SimRandomNumberGenerator &rng) | BaseLabeler | virtual |
| setUpHook(FeatureMapSimVector &) | SILACLabeler | virtual |
| SILACLabeler() | SILACLabeler | |
| subsections_ | DefaultParamHandler | protected |
| updateMembers_() | SILACLabeler | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| ~BaseLabeler() | BaseLabeler | virtual |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~SILACLabeler() | SILACLabeler | virtual |