| affineGapalign_(Size xbegin, Size ybegin, Size xend, Size yend, const std::vector< MSSpectrum<> * > &pattern, std::vector< MSSpectrum<> * > &aligned, std::vector< int > &xcoordinate, std::vector< Real > &ycoordinate, std::vector< int > &xcoordinatepattern) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | alignCompactFeatureMaps(std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithm | virtual | 
  | alignConsensusMaps(std::vector< ConsensusMap > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithm | virtual | 
  | alignFeatureMaps(std::vector< FeatureMap<> > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithm | virtual | 
  | alignPeakMaps(std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithmSpectrumAlignment | virtual | 
  | alignPeptideIdentifications(std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithm | virtual | 
  | anchorPoints_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | begin_ | ProgressLogger | mutableprotected | 
  | bestk_(const std::vector< MSSpectrum<> * > &pattern, std::vector< MSSpectrum<> * > &aligned, std::map< Size, std::map< Size, Real > > &buffer, bool column_row_orientation, Size xbegin, Size xend, Size ybegin, Size yend) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | bucketFilter_(const std::vector< MSSpectrum<> * > &pattern, std::vector< MSSpectrum<> * > &aligned, std::vector< Int > &xcoordinate, std::vector< Real > &ycoordinate, std::vector< Int > &xcoordinatepattern) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | bucketsize_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | c1_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | check_defaults_ | DefaultParamHandler | protected | 
  | CMD enum value | ProgressLogger |  | 
  | create() | MapAlignmentAlgorithmSpectrumAlignment | inlinestatic | 
  | cutoffScore_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | debug_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | debugFileCreator_(const std::vector< MSSpectrum<> * > &pattern, std::vector< MSSpectrum<> * > &aligned) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | debugmatrix_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | debugscoreDistributionCalculation_(Real score) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | debugscorematrix_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | debugtraceback_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | DefaultParamHandler(const String &name) | DefaultParamHandler |  | 
  | DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler |  | 
  | defaults_ | DefaultParamHandler | protected | 
  | defaultsToParam_() | DefaultParamHandler | protected | 
  | dlg_ | ProgressLogger | mutableprotected | 
  | e_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | end_ | ProgressLogger | mutableprotected | 
  | endProgress() const | ProgressLogger |  | 
  | eraseFloatDataArrayEntry_(std::vector< MSSpectrum<> * > &spectrum_pointer_container) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | error_name_ | DefaultParamHandler | protected | 
  | fitModel(const String &model_type, const Param ¶ms, std::vector< TransformationDescription > &trafos) | MapAlignmentAlgorithm | static | 
  | fourierActivation_(std::vector< MSSpectrum<> * > &spectrum_pointer_container) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | gap_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | getDefaults() const | DefaultParamHandler |  | 
  | getLogType() const | ProgressLogger |  | 
  | getName() const | DefaultParamHandler |  | 
  | getParameters() const | DefaultParamHandler |  | 
  | getProductName() | MapAlignmentAlgorithmSpectrumAlignment | inlinestatic | 
  | getSubsections() const | DefaultParamHandler |  | 
  | GUI enum value | ProgressLogger |  | 
  | insideBand_(Size i, Size j, Size n, Size m, Int k_) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | last_invoke_ | ProgressLogger | mutableprotected | 
  | LogType enum name | ProgressLogger |  | 
  | MapAlignmentAlgorithm() | MapAlignmentAlgorithm |  | 
  | MapAlignmentAlgorithmSpectrumAlignment() | MapAlignmentAlgorithmSpectrumAlignment |  | 
  | MapAlignmentAlgorithmSpectrumAlignment(const MapAlignmentAlgorithmSpectrumAlignment &) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | mismatchscore_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | msFilter_(MSExperiment<> &peakmap, std::vector< MSSpectrum<> * > &spectrum_pointer_container) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | NONE enum value | ProgressLogger |  | 
  | operator=(const MapAlignmentAlgorithmSpectrumAlignment &) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual | 
  | operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual | 
  | param_ | DefaultParamHandler | protected | 
  | prepareAlign_(const std::vector< MSSpectrum<> * > &pattern, MSExperiment<> &aligned, std::vector< TransformationDescription > &transformation) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | ProgressLogger() | ProgressLogger |  | 
  | recursion_depth_ | ProgressLogger | protectedstatic | 
  | registerChildren() | MapAlignmentAlgorithm | static | 
  | scoreCalculation_(Size i, Size j, Size patternbegin, Size alignbegin, const std::vector< MSSpectrum<> * > &pattern, std::vector< MSSpectrum<> * > &aligned, std::map< Size, std::map< Size, Real > > &buffer, bool column_row_orientation) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | scoredistribution_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | scoring_(const MSSpectrum<> &a, MSSpectrum<> &b) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | 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="") | MapAlignmentAlgorithm | virtual | 
  | startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger |  | 
  | stop_watch_ | ProgressLogger | mutableprotected | 
  | subsections_ | DefaultParamHandler | protected | 
  | threshold_ | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | transform_(MSSpectrum<> &spec) | MapAlignmentAlgorithmSpectrumAlignment | private | 
  | type_ | ProgressLogger | mutableprotected | 
  | updateMembers_() | MapAlignmentAlgorithmSpectrumAlignment | privatevirtual | 
  | value_ | ProgressLogger | mutableprotected | 
  | warn_empty_defaults_ | DefaultParamHandler | protected | 
  | ~DefaultParamHandler() | DefaultParamHandler | virtual | 
  | ~MapAlignmentAlgorithm() | MapAlignmentAlgorithm | virtual | 
  | ~MapAlignmentAlgorithmSpectrumAlignment() | MapAlignmentAlgorithmSpectrumAlignment | virtual | 
  | ~ProgressLogger() | ProgressLogger |  |