| alignCompactFeatureMaps(std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithm | virtual |
| alignConsensusMaps(std::vector< ConsensusMap > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithmIdentification | virtual |
| alignFeatureMaps(std::vector< FeatureMap<> > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithmIdentification | virtual |
| alignMaps(std::vector< MapType > &maps, std::vector< TransformationDescription > &transformations) | MapAlignmentAlgorithmIdentification | inline |
| alignPeakMaps(std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithmIdentification | virtual |
| alignPeptideIdentifications(std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithmIdentification | virtual |
| begin_ | ProgressLogger | mutableprotected |
| check_defaults_ | DefaultParamHandler | protected |
| checkParameters_(const Size runs) | MapAlignmentAlgorithmIdentification | protected |
| CMD enum value | ProgressLogger | |
| computeMedians_(SeqToList &rt_data, SeqToValue &medians, bool sorted=false) | MapAlignmentAlgorithmIdentification | protected |
| computeTransformations_(std::vector< SeqToList > &rt_data, std::vector< TransformationDescription > &transforms, bool sorted=false) | MapAlignmentAlgorithmIdentification | protected |
| create() | MapAlignmentAlgorithmIdentification | inlinestatic |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| dlg_ | ProgressLogger | mutableprotected |
| end_ | ProgressLogger | mutableprotected |
| endProgress() const | ProgressLogger | |
| error_name_ | DefaultParamHandler | protected |
| fitModel(const String &model_type, const Param ¶ms, std::vector< TransformationDescription > &trafos) | MapAlignmentAlgorithm | static |
| getDefaults() const | DefaultParamHandler | |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| getProductName() | MapAlignmentAlgorithmIdentification | inlinestatic |
| getReference_() | MapAlignmentAlgorithmIdentification | protected |
| getRetentionTimes_(std::vector< PeptideIdentification > &peptides, SeqToList &rt_data) | MapAlignmentAlgorithmIdentification | protected |
| getRetentionTimes_(MSExperiment<> &experiment, SeqToList &rt_data) | MapAlignmentAlgorithmIdentification | protected |
| getRetentionTimes_(MapType &features, SeqToList &rt_data) | MapAlignmentAlgorithmIdentification | protected |
| getSubsections() const | DefaultParamHandler | |
| GUI enum value | ProgressLogger | |
| hasGoodHit_(PeptideIdentification &peptide) | MapAlignmentAlgorithmIdentification | protected |
| last_invoke_ | ProgressLogger | mutableprotected |
| LogType enum name | ProgressLogger | |
| MapAlignmentAlgorithm() | MapAlignmentAlgorithm | |
| MapAlignmentAlgorithmIdentification() | MapAlignmentAlgorithmIdentification | |
| MapAlignmentAlgorithmIdentification(const MapAlignmentAlgorithmIdentification &) | MapAlignmentAlgorithmIdentification | private |
| min_run_occur_ | MapAlignmentAlgorithmIdentification | protected |
| NONE enum value | ProgressLogger | |
| operator=(const MapAlignmentAlgorithmIdentification &) | MapAlignmentAlgorithmIdentification | private |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| ProgressLogger() | ProgressLogger | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| reference_ | MapAlignmentAlgorithmIdentification | protected |
| reference_index_ | MapAlignmentAlgorithmIdentification | protected |
| registerChildren() | MapAlignmentAlgorithm | static |
| score_threshold_ | MapAlignmentAlgorithmIdentification | protected |
| SeqToList typedef | MapAlignmentAlgorithmIdentification | protected |
| SeqToValue typedef | MapAlignmentAlgorithmIdentification | protected |
| setLogType(LogType type) const | ProgressLogger | |
| setName(const String &name) | DefaultParamHandler | |
| setParameters(const Param ¶m) | DefaultParamHandler | |
| setProgress(SignedSize value) const | ProgressLogger | |
| setReference(Size reference_index=0, const String &reference_file="") | MapAlignmentAlgorithmIdentification | virtual |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| stop_watch_ | ProgressLogger | mutableprotected |
| subsections_ | DefaultParamHandler | protected |
| type_ | ProgressLogger | mutableprotected |
| updateMembers_() | DefaultParamHandler | protectedvirtual |
| value_ | ProgressLogger | mutableprotected |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~MapAlignmentAlgorithm() | MapAlignmentAlgorithm | virtual |
| ~MapAlignmentAlgorithmIdentification() | MapAlignmentAlgorithmIdentification | virtual |
| ~ProgressLogger() | ProgressLogger | |