| 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 | |