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 |
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 |
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 | |
create() | MapAlignmentAlgorithmSpectrumAlignment | inlinestatic |
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 | |
defaults_ | DefaultParamHandler | protected |
defaultsToParam_() | DefaultParamHandler | protected |
e_ | MapAlignmentAlgorithmSpectrumAlignment | private |
endProgress() const | ProgressLogger | |
error_name_ | DefaultParamHandler | protected |
fitModel(const String &model_type, const Param ¶ms, std::vector< TransformationDescription > &trafos) | MapAlignmentAlgorithm | static |
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 | |
logTypeToFactoryName_(LogType type) | ProgressLogger | protectedstatic |
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 |
OpenMS::ProgressLogger::operator=(const ProgressLogger &other) | ProgressLogger | |
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 | |
ProgressLogger(const ProgressLogger &other) | 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, 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 | |
setReference(Size reference_index=0, const String &reference_file="") | MapAlignmentAlgorithm | virtual |
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
subsections_ | DefaultParamHandler | protected |
threshold_ | MapAlignmentAlgorithmSpectrumAlignment | private |
type_ | ProgressLogger | mutableprotected |
updateMembers_() | MapAlignmentAlgorithmSpectrumAlignment | privatevirtual |
warn_empty_defaults_ | DefaultParamHandler | protected |
~DefaultParamHandler() | DefaultParamHandler | virtual |
~MapAlignmentAlgorithm() | MapAlignmentAlgorithm | virtual |
~MapAlignmentAlgorithmSpectrumAlignment() | MapAlignmentAlgorithmSpectrumAlignment | virtual |
~ProgressLogger() | ProgressLogger | |