| 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 |  |