| addModificationToPeptideHit_(Feature &feature, const String &modification, const Size &pos) const | ITRAQLabeler | protected |
| BaseLabeler() | BaseLabeler | |
| channel_description_ | BaseLabeler | protected |
| channel_map_ | ITRAQLabeler | protected |
| ChannelInfo typedef | ITRAQLabeler | |
| ChannelMapType typedef | ITRAQLabeler | |
| check_defaults_ | DefaultParamHandler | protected |
| consensus_ | BaseLabeler | protected |
| create() | ITRAQLabeler | 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 | |
| getItraqIntensity_(const Feature &f, const double MS2_RT_time) const | ITRAQLabeler | protected |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getProductName() | ITRAQLabeler | inlinestatic |
| getRTProfileIntensity_(const Feature &f, const double MS2_RT_time) const | ITRAQLabeler | protected |
| getSubsections() const | DefaultParamHandler | |
| isotope_corrections_ | ITRAQLabeler | protected |
| IsotopeMatrices typedef | ITRAQLabeler | |
| itraq_type_ | ITRAQLabeler | protected |
| ITRAQLabeler() | ITRAQLabeler | |
| labelPeptide_(const Feature &feature, SimTypes::FeatureMapSim &result) const | ITRAQLabeler | protected |
| mergeFeatures_(Feature &labeled_channel_feature, const AASequence &unmodified_sequence, std::map< AASequence, Feature > &unlabeled_features_index) const | ITRAQLabeler | protected |
| mergeProteinAccessions_(Feature &target, const Feature &source) const | BaseLabeler | protected |
| mergeProteinIdentificationsMaps_(const SimTypes::FeatureMapSimVector &maps) | BaseLabeler | protected |
| operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| postDetectabilityHook(SimTypes::FeatureMapSimVector &) | ITRAQLabeler | virtual |
| postDigestHook(SimTypes::FeatureMapSimVector &) | ITRAQLabeler | virtual |
| postIonizationHook(SimTypes::FeatureMapSimVector &) | ITRAQLabeler | virtual |
| postRawMSHook(SimTypes::FeatureMapSimVector &) | ITRAQLabeler | virtual |
| postRawTandemMSHook(SimTypes::FeatureMapSimVector &, SimTypes::MSSimExperiment &) | ITRAQLabeler | virtual |
| postRTHook(SimTypes::FeatureMapSimVector &) | ITRAQLabeler | virtual |
| preCheck(Param ¶m) const | ITRAQLabeler | virtual |
| recomputeConsensus_(const SimTypes::FeatureMapSim &simulated_features) | BaseLabeler | protected |
| registerChildren() | BaseLabeler | static |
| rng_ | BaseLabeler | protected |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setRnd(SimTypes::MutableSimRandomNumberGeneratorPtr rng) | BaseLabeler | virtual |
| setUpHook(SimTypes::FeatureMapSimVector &) | ITRAQLabeler | virtual |
| subsections_ | DefaultParamHandler | protected |
| updateMembers_() | ITRAQLabeler | protectedvirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| y_labeling_efficiency_ | ITRAQLabeler | protected |
| ~BaseLabeler() | BaseLabeler | virtual |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~ITRAQLabeler() | ITRAQLabeler | virtual |