| affineGapalign_(Size xbegin, Size ybegin, Size xend, Size yend, const std::vector< MSSpectrum * > &pattern, std::vector< MSSpectrum * > &aligned, std::vector< int > &xcoordinate, std::vector< float > &ycoordinate, std::vector< int > &xcoordinatepattern) | MapAlignmentAlgorithmSpectrumAlignment | private |
| align(std::vector< PeakMap > &, std::vector< TransformationDescription > &) | MapAlignmentAlgorithmSpectrumAlignment | virtual |
| anchorPoints_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| bestk_(const std::vector< MSSpectrum * > &pattern, std::vector< MSSpectrum * > &aligned, std::map< Size, std::map< Size, float > > &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< float > &ycoordinate, std::vector< Int > &xcoordinatepattern) | MapAlignmentAlgorithmSpectrumAlignment | private |
| bucketsize_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| c1_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| check_defaults_ | DefaultParamHandler | protected |
| CMD enum value | ProgressLogger | |
| current_logger_ | ProgressLogger | mutableprotected |
| cutoffScore_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| debug_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| debugFileCreator_(const std::vector< MSSpectrum * > &pattern, std::vector< MSSpectrum * > &aligned) | MapAlignmentAlgorithmSpectrumAlignment | private |
| debugmatrix_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| debugscoreDistributionCalculation_(float score) | MapAlignmentAlgorithmSpectrumAlignment | private |
| debugscorematrix_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| debugtraceback_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| DefaultParamHandler(const String &name) | DefaultParamHandler | |
| DefaultParamHandler(const DefaultParamHandler &rhs) | DefaultParamHandler | |
| DefaultParamHandler() | DefaultParamHandler | private |
| defaults_ | DefaultParamHandler | protected |
| defaultsToParam_() | DefaultParamHandler | protected |
| e_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| endProgress() const | ProgressLogger | |
| error_name_ | DefaultParamHandler | protected |
| gap_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| getDefaults() const | DefaultParamHandler | |
| getLogType() const | ProgressLogger | |
| getName() const | DefaultParamHandler | |
| getParameters() const | DefaultParamHandler | |
| 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 | |
| logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
| MapAlignmentAlgorithmSpectrumAlignment() | MapAlignmentAlgorithmSpectrumAlignment | |
| MapAlignmentAlgorithmSpectrumAlignment(const MapAlignmentAlgorithmSpectrumAlignment &) | MapAlignmentAlgorithmSpectrumAlignment | private |
| mismatchscore_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| msFilter_(PeakMap &peakmap, std::vector< MSSpectrum * > &spectrum_pointer_container) | MapAlignmentAlgorithmSpectrumAlignment | private |
| nextProgress() const | ProgressLogger | |
| NONE enum value | ProgressLogger | |
| operator=(const MapAlignmentAlgorithmSpectrumAlignment &) | MapAlignmentAlgorithmSpectrumAlignment | private |
| OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs) | DefaultParamHandler | virtual |
| OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger | |
| operator==(const DefaultParamHandler &rhs) const | DefaultParamHandler | virtual |
| param_ | DefaultParamHandler | protected |
| prepareAlign_(const std::vector< MSSpectrum * > &pattern, PeakMap &aligned, std::vector< TransformationDescription > &transformation) | MapAlignmentAlgorithmSpectrumAlignment | private |
| ProgressLogger() | ProgressLogger | |
| ProgressLogger(const ProgressLogger &other) | ProgressLogger | |
| recursion_depth_ | ProgressLogger | protectedstatic |
| scoreCalculation_(Size i, Size j, Size patternbegin, Size alignbegin, const std::vector< MSSpectrum * > &pattern, std::vector< MSSpectrum * > &aligned, std::map< Size, std::map< Size, float > > &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 | |
| startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
| subsections_ | DefaultParamHandler | protected |
| threshold_ | MapAlignmentAlgorithmSpectrumAlignment | private |
| type_ | ProgressLogger | mutableprotected |
| updateMembers_() override | MapAlignmentAlgorithmSpectrumAlignment | privatevirtual |
| warn_empty_defaults_ | DefaultParamHandler | protected |
| writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &prefix="") | DefaultParamHandler | static |
| ~DefaultParamHandler() | DefaultParamHandler | virtual |
| ~MapAlignmentAlgorithmSpectrumAlignment() override | MapAlignmentAlgorithmSpectrumAlignment | |
| ~ProgressLogger() | ProgressLogger | |
1.8.16
