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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
alignCompactFeatureMaps(std::vector< std::vector< Peak2D > > &, std::vector< TransformationDescription > &)MapAlignmentAlgorithmvirtual
alignConsensusMaps(std::vector< ConsensusMap > &, std::vector< TransformationDescription > &)MapAlignmentAlgorithmvirtual
alignFeatureMaps(std::vector< FeatureMap > &, std::vector< TransformationDescription > &)MapAlignmentAlgorithmvirtual
alignPeakMaps(std::vector< MSExperiment<> > &, std::vector< TransformationDescription > &)MapAlignmentAlgorithmSpectrumAlignmentvirtual
alignPeptideIdentifications(std::vector< std::vector< PeptideIdentification > > &, std::vector< TransformationDescription > &)MapAlignmentAlgorithmvirtual
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
create()MapAlignmentAlgorithmSpectrumAlignmentinlinestatic
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
defaults_DefaultParamHandlerprotected
defaultsToParam_()DefaultParamHandlerprotected
e_MapAlignmentAlgorithmSpectrumAlignmentprivate
endProgress() const ProgressLogger
error_name_DefaultParamHandlerprotected
fitModel(const String &model_type, const Param &params, std::vector< TransformationDescription > &trafos)MapAlignmentAlgorithmstatic
gap_MapAlignmentAlgorithmSpectrumAlignmentprivate
getDefaults() const DefaultParamHandler
getLogType() const ProgressLogger
getName() const DefaultParamHandler
getParameters() const DefaultParamHandler
getProductName()MapAlignmentAlgorithmSpectrumAlignmentinlinestatic
getSubsections() const DefaultParamHandler
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
MapAlignmentAlgorithm()MapAlignmentAlgorithm
MapAlignmentAlgorithmSpectrumAlignment()MapAlignmentAlgorithmSpectrumAlignment
MapAlignmentAlgorithmSpectrumAlignment(const MapAlignmentAlgorithmSpectrumAlignment &)MapAlignmentAlgorithmSpectrumAlignmentprivate
mismatchscore_MapAlignmentAlgorithmSpectrumAlignmentprivate
msFilter_(MSExperiment<> &peakmap, std::vector< MSSpectrum<> * > &spectrum_pointer_container)MapAlignmentAlgorithmSpectrumAlignmentprivate
NONE enum valueProgressLogger
operator=(const MapAlignmentAlgorithmSpectrumAlignment &)MapAlignmentAlgorithmSpectrumAlignmentprivate
OpenMS::DefaultParamHandler::operator=(const DefaultParamHandler &rhs)DefaultParamHandlervirtual
OpenMS::ProgressLogger::operator=(const ProgressLogger &other)ProgressLogger
operator==(const DefaultParamHandler &rhs) const DefaultParamHandlervirtual
param_DefaultParamHandlerprotected
prepareAlign_(const std::vector< MSSpectrum<> * > &pattern, MSExperiment<> &aligned, std::vector< TransformationDescription > &transformation)MapAlignmentAlgorithmSpectrumAlignmentprivate
ProgressLogger()ProgressLogger
ProgressLogger(const ProgressLogger &other)ProgressLogger
recursion_depth_ProgressLoggerprotectedstatic
registerChildren()MapAlignmentAlgorithmstatic
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) const ProgressLogger
setName(const String &name)DefaultParamHandler
setParameters(const Param &param)DefaultParamHandler
setProgress(SignedSize value) const ProgressLogger
setReference(Size reference_index=0, const String &reference_file="")MapAlignmentAlgorithmvirtual
startProgress(SignedSize begin, SignedSize end, const String &label) const ProgressLogger
subsections_DefaultParamHandlerprotected
threshold_MapAlignmentAlgorithmSpectrumAlignmentprivate
type_ProgressLoggermutableprotected
updateMembers_()MapAlignmentAlgorithmSpectrumAlignmentprivatevirtual
warn_empty_defaults_DefaultParamHandlerprotected
~DefaultParamHandler()DefaultParamHandlervirtual
~MapAlignmentAlgorithm()MapAlignmentAlgorithmvirtual
~MapAlignmentAlgorithmSpectrumAlignment()MapAlignmentAlgorithmSpectrumAlignmentvirtual
~ProgressLogger()ProgressLogger

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:39 using doxygen 1.8.9.1