OpenMS
MapAlignmentAlgorithmSpectrumAlignment Member List

This is the complete list of members for MapAlignmentAlgorithmSpectrumAlignment, including all inherited members.

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)MapAlignmentAlgorithmSpectrumAlignmentprivate
align(std::vector< PeakMap > &, std::vector< TransformationDescription > &)MapAlignmentAlgorithmSpectrumAlignmentvirtual
anchorPoints_MapAlignmentAlgorithmSpectrumAlignmentprivate
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)MapAlignmentAlgorithmSpectrumAlignmentprivate
bucketFilter_(const std::vector< MSSpectrum * > &pattern, std::vector< MSSpectrum * > &aligned, std::vector< Int > &xcoordinate, std::vector< float > &ycoordinate, std::vector< Int > &xcoordinatepattern)MapAlignmentAlgorithmSpectrumAlignmentprivate
bucketsize_MapAlignmentAlgorithmSpectrumAlignmentprivate
c1_MapAlignmentAlgorithmSpectrumAlignmentprivate
check_defaults_DefaultParamHandlerprotected
CMD enum valueProgressLogger
current_logger_ProgressLoggermutableprotected
cutoffScore_MapAlignmentAlgorithmSpectrumAlignmentprivate
debug_MapAlignmentAlgorithmSpectrumAlignmentprivate
debugFileCreator_(const std::vector< MSSpectrum * > &pattern, std::vector< MSSpectrum * > &aligned)MapAlignmentAlgorithmSpectrumAlignmentprivate
debugmatrix_MapAlignmentAlgorithmSpectrumAlignmentprivate
debugscoreDistributionCalculation_(float score)MapAlignmentAlgorithmSpectrumAlignmentprivate
debugscorematrix_MapAlignmentAlgorithmSpectrumAlignmentprivate
debugtraceback_MapAlignmentAlgorithmSpectrumAlignmentprivate
DefaultParamHandler(const String &name)DefaultParamHandler
DefaultParamHandler(const DefaultParamHandler &rhs)DefaultParamHandler
DefaultParamHandler()DefaultParamHandlerprivate
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
e_MapAlignmentAlgorithmSpectrumAlignmentprivate
endProgress() constProgressLogger
error_name_DefaultParamHandlerprotected
gap_MapAlignmentAlgorithmSpectrumAlignmentprivate
getDefaults() constDefaultParamHandler
getLogType() constProgressLogger
getName() constDefaultParamHandler
getParameters() constDefaultParamHandler
getSubsections() constDefaultParamHandler
GUI enum valueProgressLogger
insideBand_(Size i, Size j, Size n, Size m, Int k_)MapAlignmentAlgorithmSpectrumAlignmentprivate
last_invoke_ProgressLoggermutableprotected
LogType enum nameProgressLogger
logTypeToFactoryName_(LogType type)ProgressLoggerprotectedstatic
MapAlignmentAlgorithmSpectrumAlignment()MapAlignmentAlgorithmSpectrumAlignment
MapAlignmentAlgorithmSpectrumAlignment(const MapAlignmentAlgorithmSpectrumAlignment &)MapAlignmentAlgorithmSpectrumAlignmentprivate
mismatchscore_MapAlignmentAlgorithmSpectrumAlignmentprivate
msFilter_(PeakMap &peakmap, std::vector< MSSpectrum * > &spectrum_pointer_container)MapAlignmentAlgorithmSpectrumAlignmentprivate
nextProgress() constProgressLogger
NONE enum valueProgressLogger
operator=(const MapAlignmentAlgorithmSpectrumAlignment &)MapAlignmentAlgorithmSpectrumAlignmentprivate
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)DefaultParamHandler
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) constDefaultParamHandlervirtual
param_DefaultParamHandlerprotected
prepareAlign_(const std::vector< MSSpectrum * > &pattern, PeakMap &aligned, std::vector< TransformationDescription > &transformation)MapAlignmentAlgorithmSpectrumAlignmentprivate
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
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)MapAlignmentAlgorithmSpectrumAlignmentprivate
scoredistribution_MapAlignmentAlgorithmSpectrumAlignmentprivate
scoring_(const MSSpectrum &a, MSSpectrum &b)MapAlignmentAlgorithmSpectrumAlignmentprivate
setLogType(LogType type) constProgressLogger
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) constProgressLogger
startProgress(SignedSize begin, SignedSize end, const String &label) constProgressLogger
subsections_DefaultParamHandlerprotected
threshold_MapAlignmentAlgorithmSpectrumAlignmentprivate
type_ProgressLoggermutableprotected
updateMembers_() overrideMapAlignmentAlgorithmSpectrumAlignmentprivatevirtual
warn_empty_defaults_DefaultParamHandlerprotected
writeParametersToMetaValues(const Param &write_this, MetaInfoInterface &write_here, const String &key_prefix="")DefaultParamHandlerstatic
~DefaultParamHandler()DefaultParamHandlervirtual
~MapAlignmentAlgorithmSpectrumAlignment() overrideMapAlignmentAlgorithmSpectrumAlignment
~ProgressLogger()ProgressLoggervirtual