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GammaDistributionFitResult() :
GammaDistributionFitter::GammaDistributionFitResult
GammaDistributionFitter() :
GammaDistributionFitter
gammaDistributionFitterdf_() :
GammaDistributionFitter
gammaDistributionFitterf_() :
GammaDistributionFitter
gammaDistributionFitterfdf_() :
GammaDistributionFitter
GaussFilter() :
GaussFilter
GaussFilterAlgorithm() :
GaussFilterAlgorithm
GaussFitter() :
GaussFitter
GaussFitter1D() :
GaussFitter1D
gaussFitterdf_() :
GaussFitter
gaussFitterf_() :
GaussFitter
gaussFitterfdf_() :
GaussFitter
GaussModel() :
GaussModel
GaussTraceFitter() :
GaussTraceFitter< PeakType >
GBdeltaright_() :
AAIndex
GBleft_() :
AAIndex
GBsidechain_() :
AAIndex
genCord_() :
LocalLinearMap
generateCandidates() :
DeNovoAlgorithm
generateClusterConsensusByCluster() :
SILACAnalyzer
generateClusterConsensusByPattern() :
SILACAnalyzer
generateClusterDebug() :
SILACAnalyzer
generateClusterFeatureByCluster() :
SILACAnalyzer
generateDecoys() :
MRMDecoy
generateDescriptorSet_() :
SvmTheoreticalSpectrumGenerator
generateDistributionImage_() :
IDDecoyProbability
generateFilterConsensusByPattern() :
SILACAnalyzer
generateModel() :
PILISNeutralLossModel
generateMSESpectra_() :
RawTandemMSSignalSimulation
generateMzTabMetaDataSection_() :
MzTabFile
generateMzTabPeptideHeader_() :
MzTabFile
generateMzTabPeptideSection_() :
MzTabFile
generateMzTabPeptideSectionRow_() :
MzTabFile
generateMzTabProteinHeader_() :
MzTabFile
generateMzTabProteinSection_() :
MzTabFile
generateMzTabProteinSectionRow_() :
MzTabFile
generateMzTabSmallMoleculeHeader_() :
MzTabFile
generateMzTabSmallMoleculeSection_() :
MzTabFile
generateMzTabSmallMoleculeSectionRow_() :
MzTabFile
generateParameters_() :
PILISCrossValidation
generatePrecursorSpectra_() :
RawTandemMSSignalSimulation
generateRawSignals() :
RawMSSignalSimulation
generateRawTandemSignals() :
RawTandemMSSignalSimulation
generateRTMapping() :
MascotXMLFile
generateSeedList() :
SeedListGenerator
generateSeedLists() :
SeedListGenerator
generateSingleConsensusByPattern() :
SILACAnalyzer
generateTrieDB() :
InspectOutfile
get() :
MzTabInteger
,
MzTabBoolean
,
MzTabString
,
MzTabParameterList
,
MzTabStringList
,
MzTabModificationList
,
CentroidData
,
RawData
,
TOPPASResources
,
Date
,
DateTime
,
MzTabDouble
,
MzTabDoubleList
get1stLayerIndex() :
SpectrumAlignmentDialog
get2DData() :
MSExperiment< PeakT, ChromatogramPeakT >
get2ndLayerIndex() :
SpectrumAlignmentDialog
get3CharsNumber_() :
TOPPASVertex
get_AC() :
MS2Info
,
SHFeature
get_alignment_error() :
LCMS
get_alignment_error_down() :
SHFeature
get_alignment_error_up() :
SHFeature
get_ALL_AC() :
MS2Info
get_ALL_AC_END() :
MS2Info
get_ALL_AC_START() :
MS2Info
get_ALL_peak() :
LCMSCData
get_ALL_peak_ordered() :
LCMSCData
get_apex_intensity() :
LCElutionPeak
get_apex_MZ() :
LCElutionPeak
get_apex_peak_intensity() :
SHFeature
get_apex_retention_time() :
LCElutionPeak
get_best_MS2_SCAN() :
SHFeature
get_charge_state() :
LCElutionPeak
,
MSPeak
,
SHFeature
get_CHRG() :
MS2Info
get_Chrg() :
MSPeak
get_DATA_end() :
LCMSCData
get_DATA_start() :
LCMSCData
get_DELTA_CN() :
MS2Info
get_end_retention_time() :
LCElutionPeak
get_end_scan() :
LCElutionPeak
get_feature() :
SHFeature
get_feature_ID() :
SHFeature
get_feature_list() :
LCMS
get_feature_list_begin() :
LCMS
get_feature_list_end() :
LCMS
get_feature_list_reference() :
LCMS
get_feature_match_status() :
SHFeature
get_FEATURE_PI() :
SHFeature
get_feature_profile() :
SHFeature
get_ID() :
MS2Info
get_intensity() :
LCElutionPeak
,
MSPeak
get_isotopic_peaks() :
MSPeak
get_isotopic_peaks_end() :
MSPeak
get_isotopic_peaks_start() :
MSPeak
get_LC_elution_peak_counter() :
ProcessData
get_MASTER_ID() :
LCMS
,
SHFeature
get_match_list() :
SHFeature
get_match_list_end() :
SHFeature
get_match_list_REFERENCE() :
SHFeature
get_match_list_start() :
SHFeature
get_MATCHED_peak_area() :
SHFeature
get_matching_nb() :
SHFeature
get_MOD_SQ() :
MS2Info
,
SHFeature
get_Modification_list() :
MS2Info
get_Modification_list_end() :
MS2Info
get_Modification_list_start() :
MS2Info
get_Molecular_Mass() :
SHFeature
get_MONO_AA_MASS() :
MS2Info
get_MONO_H() :
SHFeature
get_MONO_MZ() :
MS2Info
get_MS2_info() :
SHFeature
get_MS2_scan() :
SHFeature
get_MS2_SCAN_LIST() :
SHFeature
get_MS2_SCAN_LIST_END() :
SHFeature
get_MS2_SCAN_LIST_START() :
SHFeature
get_MS2_SCAN_MAP() :
SHFeature
get_MS2_SCANS_END() :
SHFeature
get_MS2_SCANS_SIZE() :
SHFeature
get_MS2_SCANS_START() :
SHFeature
get_MS2_TYPE_TAG() :
MS2Info
,
SHFeature
get_MZ() :
LCElutionPeak
,
MSPeak
,
ProcessData
,
SHFeature
get_MZ_by_iterator() :
LCMSCData
get_MZ_END() :
SHFeature
get_MZ_list() :
LCMSCData
get_MZ_LIST_end() :
ProcessData
get_MZ_LIST_start() :
ProcessData
get_MZ_lower_bound() :
ProcessData
get_MZ_START() :
SHFeature
get_nb_common_match() :
SHFeature
get_nb_common_peaks() :
LCMS
get_nb_features() :
LCMS
get_nb_identified_features() :
LCMS
get_nb_ms_peaks() :
LCElutionPeak
get_nb_MZ_cluster_elements() :
ProcessData
get_nb_raw_specs() :
LCMS
get_NEUTRAL_MR() :
MS2Info
get_nr_isotopes() :
MSPeak
get_peak_area() :
SHFeature
get_peak_score() :
SHFeature
get_pep_prob() :
SHFeature
get_PEP_PROB() :
MS2Info
get_PREV_AA() :
MS2Info
get_profile_Molecular_Mass() :
SHFeature
get_profile_retention_time() :
SHFeature
get_PROTEO_TYPE() :
MS2Info
get_quick_lda_score() :
OpenSwath_Scores
get_raw_MZ() :
SHFeature
get_raw_retention_time_apex() :
SHFeature
get_raw_spec_name() :
LCMS
get_raw_spec_name_end() :
LCMS
get_raw_spec_name_map() :
LCMS
get_raw_spec_name_start() :
LCMS
get_replicate_intensity_sum() :
SHFeature
get_replicate_match_nb() :
SHFeature
get_retention_time() :
MSPeak
,
SHFeature
get_retention_time_END() :
SHFeature
get_retention_time_START() :
SHFeature
get_SCAN() :
MS2Info
get_Scan() :
MSPeak
get_scan_apex() :
LCElutionPeak
get_scan_end() :
SHFeature
get_SCAN_END() :
MS2Info
get_scan_number() :
MSPeak
,
SHFeature
get_scan_start() :
SHFeature
get_SCAN_START() :
MS2Info
get_score() :
MSPeak
get_SCORE_HOLDER() :
SHFeature
get_signal_list_end() :
LCElutionPeak
get_signal_list_start() :
LCElutionPeak
get_spec_name() :
LCMS
get_spectrum_ID() :
LCMS
,
SHFeature
get_SQ() :
MS2Info
,
SHFeature
get_start_retention_time() :
LCElutionPeak
get_start_scan() :
LCElutionPeak
get_target_file() :
FTPeakDetectController
get_THEO_MZ() :
MS2Info
,
SHFeature
get_total_peak_area() :
LCElutionPeak
get_TOTAL_SQ() :
MS2Info
,
SHFeature
get_TRYPTIC_STATE() :
MS2Info
get_XCORR() :
MS2Info
getAAAfter() :
PeptideHit
getAABefore() :
PeptideHit
getAAFrequencies() :
AASequence
getAbsoluteMZTolerance_() :
IDMapper
getAbundance() :
IMSIsotopeDistribution
getAbundances() :
IMSIsotopeDistribution
getACAndACType() :
InspectOutfile
,
SequestOutfile
getAcceptableAbsolute() :
FuzzyStringComparator
getAcceptableRelative() :
FuzzyStringComparator
getAccession() :
CVMappingTerm
,
MzTabParameter
,
CVTerm
,
ProteinHit
getAccession_() :
PeptideAndProteinQuant
getAccuracy() :
MassAnalyzer
getAcquisitionInfo() :
ChromatogramSettings
,
SpectrumSettings
getAcquisitionMode() :
IonDetector
getActionMode() :
SpectrumCanvas
,
SpectrumWidget
,
TOPPASScene
getActivationEnergy() :
Precursor
getActivationMethods() :
Precursor
getActive1DWidget() :
TOPPViewBase
getActive2DWidget() :
TOPPViewBase
getActive3DWidget() :
TOPPViewBase
getActiveCanvas() :
TOPPViewBase
getActiveSpectrumWidget() :
TOPPViewBase
getADCSamplingFrequency() :
IonDetector
getAddedSpectra_() :
MRMFeatureFinderScoring
getAddress() :
ContactPerson
getAdductBase() :
MassExplainer
getAdductMass() :
AccurateMassSearchResult
getAdductsAsString() :
Compomer
getAffectedAminoAcids() :
Modification
getAIonToFull() :
Residue
getAIonToFullAverageWeight() :
Residue
getAIonToFullMonoWeight() :
Residue
getAlignedPeaksIndices() :
Spectrum1DCanvas
getAlignmentScore() :
Spectrum1DCanvas
getAlignmentSize() :
Spectrum1DCanvas
getAlignmentTraceback() :
PeakAlignment
getAllChildTerms() :
ControlledVocabulary
getAllDecompositions() :
IntegerMassDecomposer< ValueType, DecompositionValueType >
,
MassDecomposer< ValueType, DecompositionValueType >
getAllIntensities() :
FeatureHypothesis
getAllowChildren() :
CVMappingTerm
getAllSearchModifications() :
ModificationsDB
getAlphabetMass() :
Weights
getAlphaBoundaries_() :
EGHTraceFitter< PeakType >
getAmount() :
Adduct
getAnalysisSummary() :
MSQuantifications
getAnnotation_() :
PeptideAndProteinQuant
getAnnotations() :
GridFeature
,
QTCluster
,
LayerData
getAnnotationState() :
BaseFeature
getAnnotationStatistics() :
FeatureMap< FeatureT >
getApexScan() :
MS2ConsensusSpectrum
,
MS2Fragment
getArchAsString() :
OpenMSOSInfo
getARGP820102() :
AAIndex
getAssayRT_() :
ConfidenceScoring
getAssays() :
MSQuantifications
getAtomicNumber() :
Element
getAtomicNumbers() :
ElementDB
getAutoId() :
DBConnection
getAvailableBackboneCharge_() :
PILISModel
getAverageMass() :
IMSElement
,
IMSIsotopeDistribution
,
ResidueModification
getAverageMasses() :
IMSAlphabet
getAverageWeight() :
AASequence
,
Element
,
EmpiricalFormula
,
Residue
getAveragine() :
IsotopeWavelet
getAvgMZ() :
FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >
getAvIntens_() :
IsotopeWaveletTransform< PeakType >
getAvMZSpacing_() :
IsotopeWaveletTransform< PeakType >
getAxisMaximum() :
AxisWidget
getAxisMinimum() :
AxisWidget
getBackboneBasicityLeft() :
Residue
getBackboneBasicityRight() :
Residue
getBackgroundIntensityBinsIntens() :
SuperHirnParameters
getBackgroundIntensityBinsMinBinCount() :
SuperHirnParameters
getBackgroundIntensityBinsMZ() :
SuperHirnParameters
getBackgroundIntensityBinsTR() :
SuperHirnParameters
getBackgroundLevel() :
BackgroundControl
getBackgroundNoiseLevel() :
SHFeature
getBackwardVariable_() :
HiddenMarkovModel
getBase_() :
UniqueIdIndexer< RandomAccessContainer >
getBestHitSequence_() :
StablePairFinder
getBigString() :
BigString
getBinNumber() :
BinnedSpectrum
getBins() :
BinnedSpectrum
getBinSize() :
BinnedSpectrum
getBinSpread() :
BinnedSpectrum
getBIonToFull() :
Residue
getBIonToFullAverageWeight() :
Residue
getBIonToFullMonoWeight() :
Residue
getBlind() :
InspectInfile
getBothGnuplotFormula() :
PosteriorErrorProbabilityModel
getBoundary() :
MascotInfile
getBoundingBox() :
ConvexHull2D
getC13MassError() :
DeconvPeak
getCalculatedMassToCharge() :
IdentificationHit
getCandidates() :
SuffixArrayPeptideFinder
getCategory() :
ToolHandler
getCenter() :
EGHModel
,
BiGaussModel
,
EGHTraceFitter< PeakType >
,
EmgModel
,
ExtendedIsotopeModel
,
GaussModel
,
GaussTraceFitter< PeakType >
,
InterpolationModel
,
IsotopeModel
,
LmaGaussModel
,
LmaIsotopeModel
,
TraceFitter< PeakType >
getCenterMZ() :
QTCluster
getCenterRT() :
QTCluster
getCentroidMZ() :
FeatureHypothesis
,
MassTrace
getCentroidRT() :
FeatureHypothesis
,
MassTrace
getCentroidSD() :
MassTrace
getCentroidWindowWidth() :
SuperHirnParameters
getChannelInformation() :
IsobaricQuantitationMethod
,
ItraqEightPlexQuantitationMethod
,
ItraqFourPlexQuantitationMethod
,
TMTSixPlexQuantitationMethod
getChannelIntensityName() :
BaseLabeler
getCharge() :
AccurateMassSearchResult
,
EmpiricalFormula
,
Adduct
,
ChargePair
,
FeatureHypothesis
,
SILACFilter
,
BaseFeature
,
FeatureHandle
,
IdentificationHit
,
PeptideHit
,
Precursor
,
ExtendedIsotopeModel
,
IsotopeModel
,
LmaIsotopeModel
,
DeconvPeak
,
OptimizePeakDeconvolution
getChargeConsensus() :
MSSim
getChargeContribution_() :
RTSimulation
getCharges() :
MascotInfile
getChargeState() :
LightPeptide
,
Peptide
,
TraMLProduct
getChargeStateIntensities() :
ProtonDistributionModel
getChecksum() :
SourceFile
getChecksumType() :
SourceFile
getChildWithName_() :
MzIdentMLHandler
,
MzMLHandler< MapType >
,
MzQuantMLHandler
,
TraMLHandler
getChiSquared() :
LinearRegression
getCHRG() :
MS2Fragment
getChromatogram() :
MRMTransitionGroup< SpectrumType, TransitionType >
,
MSExperiment< PeakT, ChromatogramPeakT >
getChromatogramById() :
SpectrumAccessOpenMS
,
SpectrumAccessOpenMSCached
,
ISpectrumAccess
,
IChromatogramsReader
getChromatogramByPrecursorMZ() :
IChromatogramsReader
getChromatogramData() :
LayerData
getChromatogramIndex() :
CachedmzML
getChromatogramMetaById() :
IChromatogramsReader
getChromatogramMetaInfo() :
SpectrumAccessOpenMS
,
SpectrumAccessOpenMSCached
getChromatogramNativeID() :
SpectrumAccessOpenMS
,
SpectrumAccessOpenMSCached
,
ISpectrumAccess
getChromatograms() :
MRMTransitionGroup< SpectrumType, TransitionType >
,
MSExperiment< PeakT, ChromatogramPeakT >
getChromatogramType() :
ChromatogramSettings
getCIDSpectrum_() :
CompNovoIdentificationBase
getCIDSpectrumLight_() :
CompNovoIdentificationBase
getCIonMinusOneToFull() :
Residue
getCIonMinusOneToFullAverageWeight() :
Residue
getCIonMinusOneToFullMonoWeight() :
Residue
getCIonPlusOneToFull() :
Residue
getCIonPlusOneToFullAverageWeight() :
Residue
getCIonPlusOneToFullMonoWeight() :
Residue
getCIonPlusTwoToFull() :
Residue
getCIonPlusTwoToFullAverageWeight() :
Residue
getCIonPlusTwoToFullMonoWeight() :
Residue
getCIonToFull() :
Residue
getCIonToFullAverageWeight() :
Residue
getCIonToFullMonoWeight() :
Residue
getCleavage() :
MascotInfile
getClockTime() :
StopWatch
getClosedBoxes() :
IsotopeWaveletTransform< PeakType >
getCodebooks() :
LocalLinearMap
getColor() :
Annotation1DPeakItem
,
ColorSelector
getColumn() :
HPLC
getColumnIndex() :
LPWrapper
getColumnLowerBound() :
LPWrapper
getColumnName() :
LPWrapper
getColumns() :
SequestOutfile
getColumnType() :
LPWrapper
getColumnUpperBound() :
LPWrapper
getColumnValue() :
LPWrapper
getCombinationsLogic() :
CVMappingRule
getComboBox() :
SpectraViewWidget
getComment() :
ChromatogramSettings
,
ExperimentalSettings
,
HPLC
,
Sample
,
SampleTreatment
,
SpectrumSettings
getCompletionTime() :
DataProcessing
getCompomer() :
ChargePair
getCompomerById() :
MassExplainer
getComponent() :
Compomer
getCompoundRef() :
ReactionMonitoringTransition
,
IncludeExcludeTarget
getCompounds() :
TargetedExperiment
getCompression() :
PeakFileOptions
getConcentration() :
Sample
getConfigSetByName_() :
LogConfigHandler
getConfigurationList() :
TraMLProduct
getConfigurations() :
IncludeExcludeTarget
getConsensIsotopeIteratorEnd() :
ConsensusIsotopePattern
getConsensIsotopeIteratorStart() :
ConsensusIsotopePattern
getConsensus() :
BaseLabeler
getConsensusMap() :
LayerData
getConsensusMaps() :
MSQuantifications
getContactInfo() :
ContactPerson
getContacts() :
TargetedExperiment
,
ExperimentalSettings
getContainer() :
IsotopeDistribution
getContaminants() :
MSSim
getContentType() :
Bzip2InputStream
,
GzipInputStream
getConvexHull() :
Feature
getConvexhull() :
MassTrace
,
FeatureFinderAlgorithmPickedHelperStructs::MassTrace< PeakType >
getConvexHulls() :
FeatureHypothesis
,
Feature
getCord() :
LocalLinearMap
getCorrectlyAssignedFitResult() :
PosteriorErrorProbabilityModel
getCoverage() :
ProteinHit
getCPUTime() :
StopWatch
getCreationDate() :
Identification
getCTerminalModification() :
AASequence
getCTerminalToFull() :
Residue
getCTerminalToFullAverageWeight() :
Residue
getCTerminalToFullMonoWeight() :
Residue
getCurrentAnnotations() :
LayerData
getCurrentLayer() :
TOPPViewBase
,
SpectrumCanvas
getCurrentLayer_() :
SpectrumCanvas
getCurrentLayerIndex() :
SpectrumCanvas
getCurrentMaxIntensity() :
SpectrumCanvas
getCurrentMinIntensity() :
SpectrumCanvas
getCurrentSpectrum() :
LayerData
getCurrentSpectrumIndex() :
LayerData
getCustomizations() :
Instrument
getCutOff() :
BaseModel< D >
getCVIdentifierRef() :
CVMappingTerm
,
CVTerm
getCVLabel() :
MzTabParameter
getCVReferences() :
CVMappings
getCVs() :
TargetedExperiment
getCVTerm_() :
SemanticValidator
getCVTerms() :
CVMappingRule
,
CVTermList
getData() :
BilinearInterpolation< Key, Value >
,
LinearInterpolation< Key, Value >
getDatabase() :
SequestInfile
getDataPoints() :
TransformationDescription
getDataProcessing() :
ConsensusMap
,
FeatureMap< FeatureT >
,
ChromatogramSettings
,
MetaInfoDescription
,
SpectrumSettings
getDataProcessingList() :
MSQuantifications
getDataRange() :
MSExperiment< PeakT, ChromatogramPeakT >
,
SpectrumCanvas
getDate() :
DateTime
getDateTime() :
ExperimentalSettings
,
ProteinIdentification
getDb() :
InspectInfile
getDB() :
MascotInfile
getDB_() :
DBConnection
getDBSequenceRef() :
PeptideEvidence
getDecisionValues() :
SVMWrapper
getDecomposition() :
IntegerMassDecomposer< ValueType, DecompositionValueType >
,
MassDecomposer< ValueType, DecompositionValueType >
getDecompositions() :
RealMassDecomposer
,
MassDecompositionAlgorithm
getDecompositions_() :
CompNovoIdentificationBase
getDecompositionsDAC_() :
CompNovoIdentification
,
CompNovoIdentificationCID
getDeconvPeaks() :
Deisotoper
getDecoyIon() :
MRMDecoy
getDecoyTransitionType() :
ReactionMonitoringTransition
getDefaultGradientLinearIntensityMode() :
MultiGradient
getDefaultGradientLogarithmicIntensityMode() :
MultiGradient
getDefaultParameters() :
TransformationModel
,
TransformationModelLinear
,
TransformationModelInterpolated
,
TransformationModelBSpline
,
BaseLabeler
,
FeatureFinderAlgorithm< PeakType, FeatureType >
,
FeatureFinderAlgorithmSimple< PeakType, FeatureType >
,
FeatureFinderAlgorithmSimplest< PeakType, FeatureType >
getDefaultParameters_() :
TOPPBase
getDefaultParametersFilename() :
XTandemInfile
getDefaults() :
DefaultParamHandler
,
EmgScoring
getDescription() :
Param
,
MetaInfoRegistry
,
BaseLabeler
,
TOPPASScene
getDetectableIsotopeFactor() :
SuperHirnParameters
getDFSColor() :
TOPPASVertex
getDFSParent() :
TOPPASVertex
getDiffAverageMass() :
ResidueModification
getDiffFormula() :
ResidueModification
getDiffMonoMass() :
ResidueModification
getDigestionTime() :
Digestion
getDirectory() :
TOPPASOutputFilesDialog
getDistance_() :
QTClusterFinder
getDocumentIDTagger_() :
TOPPBase
getDoubleList_() :
TOPPBase
getDoubleOption_() :
TOPPBase
getDoubleParameter() :
SVMWrapper
getDoubleValue() :
DBConnection
getDrawMode() :
Spectrum1DCanvas
getEdgeScore() :
ChargePair
getEdgeStatus() :
TOPPASEdge
getElement() :
ElementDB
,
EmpiricalFormula
,
IMSAlphabet
,
LPWrapper
getElementDB() :
EmpiricalFormula
getElementIndex() :
ChargePair
getElementPath() :
CVMappingRule
getElements() :
IMSAlphabetParser< AlphabetElementType, Container, InputSource >
,
IMSAlphabetTextParser
,
QTCluster
,
SILACFilter
getEluents() :
Gradient
getElutionPeakDistance() :
ProcessData
getElutionPeakExtraInfo() :
LCElutionPeak
getEmail() :
ContactPerson
getEnd() :
PeptideEvidence
getEndPoint() :
Annotation1DDistanceItem
getEndScan() :
MS2ConsensusSpectrum
,
MS2Fragment
getEndTR() :
MS2ConsensusSpectrum
,
MS2Fragment
getEntry() :
Param
getEntry_() :
Param
getEnzyme() :
EnzymaticDigestion
,
InspectInfile
,
Digestion
getEnzymeByName() :
EnzymaticDigestion
getEnzymeInfo_() :
SequestInfile
getEnzymeInfoAsString() :
SequestInfile
getEnzymeName() :
SequestInfile
getEnzymeNumber() :
SequestInfile
getErrorMessage() :
MascotRemoteQuery
getErrorPPM() :
AccurateMassSearchResult
getETDSpectrum_() :
CompNovoIdentification
getExcludeTargets() :
TargetedExperiment
getExecutablePath() :
File
getExpectedMzShifts() :
SILACFilter
getExperiment() :
InspectOutfile
,
MSSim
getExperimentalMassToCharge() :
IdentificationHit
getExperimentalSettings() :
MSExperiment< PeakT, ChromatogramPeakT >
getExperimentType() :
ConsensusMap
getExpTableMaxIndex() :
IsotopeWavelet
getExternalToolConfigFiles_() :
ToolHandler
getExternalTools_() :
ToolHandler
getExternalToolsPath() :
ToolHandler
getExtraPeakInfo() :
CentroidPeak
,
MSPeak
getFactor_() :
SpectrumAlignmentScore
,
ZhangSimilarityScore
getFactory() :
SingletonRegistry
getFastaFile() :
EdwardsLippertIterator
,
PepIterator
,
TrypticIterator
,
FastaIterator
,
FastaIteratorIntern
getFAUJ880111() :
AAIndex
getFeature() :
MRMFeatureOpenMS
,
IMRMFeature
,
MockMRMFeature
,
GridFeature
,
MRMFeature
,
PeakIndex
,
FeatureEditDialog
getFeatureExtraInformation() :
SHFeature
getFeatureIDs() :
MRMFeature
getFeatureIndex() :
GridFeature
getFeatureIntensityContribution() :
EGHTraceFitter< PeakType >
,
GaussTraceFitter< PeakType >
,
TraceFitter< PeakType >
getFeatureMap() :
LayerData
getFeatureMaps() :
MSQuantifications
getFeatureMassErrorAtPPMLevel() :
SHFeature
getFeatureNumber() :
Spectrum2DGoToDialog
getFeatures() :
ConsensusFeature
,
MRMFeature
,
MRMTransitionGroup< SpectrumType, TransitionType >
getFeatureScaledIntensity_() :
RawMSSignalSimulation
getFeaturesMuteable() :
MRMTransitionGroup< SpectrumType, TransitionType >
getFile() :
BaseException
getFileDescriptions() :
ConsensusMap
getFileList_() :
TOPPViewBase
getFilename() :
TOPPASInputFileDialog
getFilenames() :
TOPPASInputFilesDialog
getFileNames() :
TOPPASVertex
getFilenamesOfOpenFiles_() :
TOPPViewBase
getFileSize() :
SourceFile
getFileType() :
SourceFile
getFilledBinNumber() :
BinnedSpectrum
getFINA770101() :
AAIndex
getFinalIdentification_() :
PILISIdentification
getFinalMSExponent() :
MassAnalyzer
getFirstColumn() :
FuzzyStringComparator
getFirstIsotopeRelativeIntensities_() :
DIAScoring
getFirstName() :
ContactPerson
getFitParameter_() :
PILISScoring
getFittedIntensity() :
CentroidPeak
getFixedModificationNames() :
ModificationDefinitionsSet
getFixedModifications() :
PrecursorIonSelectionPreprocessing
,
ModificationDefinitionsSet
getFlag_() :
TOPPBase
getFlags() :
Annotation1DTextItem
getFloatDataArrays() :
MSChromatogram< PeakT >
,
MSSpectrum< PeakT >
getFlux() :
HPLC
getFormat() :
SaveImageDialog
getFormula() :
AASequence
,
Residue
,
ResidueModification
,
Adduct
,
IsotopeModel
getFormulaString() :
AccurateMassSearchResult
getFormVersion() :
MascotInfile
getForwardVariable_() :
HiddenMarkovModel
getFoundAdduct() :
AccurateMassSearchResult
getFoundMass() :
AccurateMassSearchResult
getFractionIdentifier() :
ExperimentalSettings
getFragmentMassErrorUnit() :
XTandemInfile
getFragmentMassTolerance() :
XTandemInfile
getFragmentMz() :
MS2Fragment
getFragmentPeakArea() :
MS2Fragment
getFrame() :
PeptideEvidence
getFullId() :
ResidueModification
getFullName() :
ResidueModification
getFullOutputDirectory() :
TOPPASOutputFileListVertex
,
TOPPASToolVertex
getFunction() :
BaseException
getFWHM() :
FeatureHypothesis
,
MassTrace
,
EGHTraceFitter< PeakType >
,
GaussTraceFitter< PeakType >
,
TraceFitter< PeakType >
,
PeakShape
getFWHMborders() :
MassTrace
getGammaTableMaxIndex() :
IsotopeWavelet
getGauss() :
PosteriorErrorProbabilityModel
getGaussGnuplotFormula() :
PosteriorErrorProbabilityModel
getGaussMu() :
PrecursorIonSelectionPreprocessing
getGaussSigma() :
PrecursorIonSelectionPreprocessing
getGnuplotFormula() :
GammaDistributionFitter
,
GaussFitter
,
GumbelDistributionFitter
,
EGHTraceFitter< PeakType >
,
GaussTraceFitter< PeakType >
,
TraceFitter< PeakType >
getGradient() :
HPLC
getGradientTime() :
RTSimulation
getGslStatus_() :
LevMarqFitter1D
getGumbel() :
PosteriorErrorProbabilityModel
getGumbelGnuplotFormula() :
PosteriorErrorProbabilityModel
getHeight() :
EGHTraceFitter< PeakType >
,
GaussTraceFitter< PeakType >
,
TraceFitter< PeakType >
getHits() :
MascotInfile
,
PeptideIdentification
,
ProteinIdentification
,
SpectrumIdentification
getHMM() :
PILISNeutralLossModel
getHorizontalProjection() :
Spectrum2DWidget
getHoveringEdge() :
TOPPASScene
getHPLC() :
ExperimentalSettings
getHTTPPeakListEnclosure() :
MascotGenericFile
getHullPoints() :
ConvexHull2D
getId() :
ResidueModification
,
DBConnection
,
IdentificationHit
,
PeptideEvidence
getID() :
Compomer
,
GridFeature
,
MS2Feature
getID_() :
DocumentIDTagger
getIDDetails_() :
IDMapper
getIdentification() :
CompNovoIdentification
,
CompNovoIdentificationCID
,
DeNovoIdentification
,
PILISIdentification
getIdentificationMZ_() :
SpectrumCanvas
getIdentifications() :
CompNovoIdentification
,
CompNovoIdentificationBase
,
CompNovoIdentificationCID
,
DeNovoIdentification
,
PILISIdentification
getIdentifier() :
CVMappingRule
,
CVReference
,
Acquisition
,
DocumentIdentifier
,
PeptideIdentification
,
ProteinIdentification
getIncludeTargets() :
TargetedExperiment
getIncorrectlyAssignedFitResult() :
PosteriorErrorProbabilityModel
getIndex() :
FidHandler
,
MetaInfoRegistry
,
IsotopicDist
getIndex_() :
BigString
getIndistinguishableProteins() :
ProteinIdentification
getIndividualIntensities() :
AccurateMassSearchResult
getInfo() :
UniqueIdGenerator
getIniLocation_() :
TOPPBase
getInitialTransitionProbabilities_() :
PILISModel
getInitialTrTolerance() :
SuperHirnParameters
getInletType() :
IonSource
getInput() :
ToolsDialog
getInputFilename() :
XTandemInfile
getInputParameters() :
TOPPASToolVertex
getInsideReferencePoint() :
LinearInterpolation< Key, Value >
getInsideReferencePoint_0() :
BilinearInterpolation< Key, Value >
getInsideReferencePoint_1() :
BilinearInterpolation< Key, Value >
getInstance() :
ElementDB
,
ModificationsDB
,
ResidueDB
,
GlobalExceptionHandler
,
LogConfigHandler
,
IsotopeWavelet
getInstance_() :
UniqueIdGenerator
getInstitution() :
ContactPerson
getInstrument() :
InspectInfile
,
MascotInfile
,
ExperimentalSettings
,
HPLC
getInstruments() :
TargetedExperiment
getInstrumentSettings() :
ChromatogramSettings
,
SpectrumSettings
getIntegerDataArrays() :
MSChromatogram< PeakT >
,
MSSpectrum< PeakT >
getIntensitiesFromSpectrum_() :
PILISNeutralLossModel
getIntensity() :
FeatureOpenMS
,
MRMFeatureOpenMS
,
IFeature
,
IMRMFeature
,
MockFeature
,
MockMRMFeature
,
FidHandler
,
ChromatogramPeak
,
MassTrace
,
Peak1D
,
Peak2D
,
BaseModel< D >
,
InterpolationModel
,
cudaHelp
,
ProductModel< 2 >
,
CentroidPeak
getIntensity32Bit() :
PeakFileOptions
getIntensityArray() :
Chromatogram
,
Spectrum
,
Chromatogram
,
Spectrum
getIntensityCV() :
SuperHirnParameters
getIntensityFloor() :
SuperHirnParameters
getIntensityHist() :
BackgroundIntensityBin
getIntensityMap() :
BackgroundIntensityBin
getIntensityMode() :
SpectrumCanvas
getIntensityRange() :
FeatureFileOptions
,
PeakFileOptions
,
ConsensusFeature
getIntensityThreshold() :
SuperHirnParameters
getIntercept() :
LinearRegression
getIntermediateProducts() :
ReactionMonitoringTransition
getInternalToFull() :
Residue
getInternalToFullAverageWeight() :
Residue
getInternalToFullMonoWeight() :
Residue
getInternalToolConfigFiles_() :
ToolHandler
getInternalTools_() :
ToolHandler
getInternalToolsPath() :
ToolHandler
getInterpolatedValue_() :
ContinuousWaveletTransform
getInterpolation() :
InterpolationModel
getInterpolationMode() :
MultiGradient
,
MultiGradientSelector
getInterpretationList() :
TraMLProduct
getInterpretations() :
IncludeExcludeTarget
getIntList_() :
TOPPBase
getIntOption_() :
TOPPBase
getIntParameter() :
SVMWrapper
getIntValue() :
DBConnection
getInvTableSteps() :
IsotopeWavelet
getIonCutoffPercentage() :
SequestInfile
getIonDetectors() :
Instrument
getIonizationMethod() :
IonSource
getIonMass() :
IMSElement
getIonOptics() :
Instrument
getIons() :
PILISNeutralLossModel
getIons_() :
PILISNeutralLossModel
getIonScores() :
DeNovoIonScoring
getIonSeries() :
MRMDecoy
getIonSeriesWeights() :
SequestInfile
getIonSources() :
Instrument
getIonTypes() :
SvmTheoreticalSpectrumGenerator
getIsDecoy() :
PeptideEvidence
getIsolationWidth() :
MassAnalyzer
getIsolationWindowLowerOffset() :
Precursor
,
Product
getIsolationWindowUpperOffset() :
Precursor
,
Product
getIsOpen() :
Bzip2InputStream
,
GzipInputStream
getIsotopeCorrectionMatrix() :
IsobaricQuantitationMethod
,
ItraqEightPlexQuantitationMethod
,
ItraqFourPlexQuantitationMethod
,
TMTSixPlexQuantitationMethod
getIsotopeDistribution() :
Element
,
EmpiricalFormula
,
IMSElement
,
IsotopeDistributionCache
,
IsotopeModel
getIsotopeDistribution_() :
FeatureFinderAlgorithmPicked< PeakType, FeatureType >
getIsotopeMatrixAsStringList() :
ItraqConstants
getIsotopesSimScore() :
AccurateMassSearchResult
getIsotopicPeaks() :
DeconvPeak
getIsotopIdx() :
CentroidPeak
getIsRepeatable() :
CVMappingTerm
getItemAt() :
Annotations1DContainer
getItraqIntensity_() :
ITRAQLabeler
getKey() :
TOPPASInputFileListVertex
getKeys() :
MetaInfo
,
MetaInfoInterface
getKHAG800101() :
AAIndex
getLabel() :
Adduct
,
FeatureHypothesis
,
MassTrace
getLabelingConsensus() :
MSSim
getLabels() :
SVMWrapper
,
Compomer
,
FeatureHypothesis
,
InspectOutfile
getLambdaL() :
IsotopeWavelet
getLastLCelutionSignal() :
FeatureLCProfile
getLastName() :
ContactPerson
getLayer() :
SpectrumCanvas
getLayer_() :
SpectrumCanvas
getLayerCount() :
SpectrumCanvas
getLayerFlag() :
SpectrumCanvas
getLayerName() :
SpectrumCanvas
getLCElutionPeakSimilarity() :
MS2ConsensusSpectrum
getLCelutionProfile() :
SHFeature
getLCelutionSignalMap() :
FeatureLCProfile
getLCelutionSignalsEnd() :
FeatureLCProfile
getLCelutionSignalsStart() :
FeatureLCProfile
getLCMS() :
FTPeakDetectController
getLCP_() :
SuffixArrayTrypticCompressed
getLeftAndRightGBValues_() :
ProtonDistributionModel
getLeftEndpoint() :
PeakShape
getLeftPaddingIndex() :
ContinuousWaveletTransform
getLeftSplitter() :
HistogramDialog
,
HistogramWidget
getLegend() :
AxisWidget
getLevel() :
LogStreamBuf
,
LogStream
getLibraryIntensities() :
TransitionGroupOpenMS< SpectrumT, TransitionT >
,
ITransitionGroup
,
MockTransitionGroup
getLibraryIntensity() :
ReactionMonitoringTransition
,
LightTransition
,
MRMTransitionGroup< SpectrumType, TransitionType >
getLine() :
BaseException
getLinearInterpolation() :
IsotopeWaveletTransform< PeakType >
getList() :
ListEditor
,
ListTable
getListToolStatus_() :
TOPPASEdge
getLLMParam() :
LocalLinearMap
getLoadConvexHull() :
FeatureFileOptions
getLoadedFilePath() :
DocumentIdentifier
getLoadedFileType() :
DocumentIdentifier
getLoadSubordinates() :
FeatureFileOptions
getLocalFile() :
TOPPASResource
getLogDestination() :
FuzzyStringComparator
getLogP() :
Compomer
getLogProb() :
Adduct
getLogScore_() :
ILPDCWrapper
getLogStreamByName_() :
LogConfigHandler
getLogThreshold() :
EnzymaticDigestion
getLogType() :
ProgressLogger
getLossFormulas() :
Residue
getLossNames() :
Residue
getLower() :
LinearRegression
getLowerRTBound() :
EGHTraceFitter< PeakType >
,
GaussTraceFitter< PeakType >
,
TraceFitter< PeakType >
getLowIntensityMSSignalThreshold() :
SuperHirnParameters
getLowMassIons() :
Residue
getLPSolver() :
OfflinePrecursorIonSelection
,
PrecursorIonSelection
,
PSLPFormulation
getMagneticFieldStrength() :
MassAnalyzer
getMapIndex() :
GridFeature
,
FeatureHandle
getMappingRules() :
CVMappings
getMascotXMLResponse() :
MascotRemoteQuery
getMass() :
IMSAlphabet
,
IMSElement
,
IMSIsotopeDistribution
,
Compomer
,
Modification
,
Sample
,
CentroidPeak
getMassAnalyzers() :
Instrument
getMassDiff() :
ChargePair
getMassErrorAtPPMLevel() :
SuperHirnUtil
getMasses() :
PrecursorIonSelectionPreprocessing
,
IMSAlphabet
,
IMSIsotopeDistribution
getMassRanges() :
OfflinePrecursorIonSelection
getMassSeparations() :
SILACFilter
getMassShift() :
Tagging
getMassShifts() :
SILACAnalyzer
getMassTolDa() :
SuperHirnParameters
getMassTolPpm() :
SuperHirnParameters
getMassType() :
MascotInfile
getMassTypeFragment() :
SequestInfile
getMassTypeParent() :
SequestInfile
getMatchingHMDBids() :
AccurateMassSearchResult
getMatchingIndex() :
AccurateMassSearchResult
getMatchingPeaks() :
IsotopicDist
getMatchPeakAllowedError() :
SequestInfile
getMatchPeakCount() :
SequestInfile
getMatchPeakTolerance() :
SequestInfile
getMatrixA() :
LocalLinearMap
getMatrixRow() :
LPWrapper
getMax() :
IsotopeDistribution
,
RangeManager< D >
,
Spectrum1DGoToDialog
getMaxAAPerModPerPeptide() :
SequestInfile
getMaxAbsError() :
OptimizePick
,
TwoDOptimization
getMaxCharge() :
IsotopeWavelet
getMaxFeatureChrg() :
SuperHirnParameters
getMaxFeatureMZ() :
SuperHirnParameters
getMaxInt() :
RangeManager< D >
getMaxIntensity() :
MassTrace
,
SpectrumCanvas
getMaxInternalCleavageSites() :
SequestInfile
getMaxInterScanRetentionTimeDistance() :
SuperHirnParameters
getMaxIsotope() :
IsotopeDistribution
getMaxIterations() :
TwoDOptimization
getMaxModificationMasses() :
ModifierRep
getMaxModifications() :
ModificationDefinitionsSet
getMaxModsPerPeptide() :
SequestInfile
getMaxMZ() :
MSExperiment< PeakT, ChromatogramPeakT >
,
Spectrum2DGoToDialog
getMaxOccurences() :
ModificationDefinition
getMaxPeakDistance() :
TwoDOptimization
getMaxPosition_() :
PeakPickerCWT
getMaxPrecursorCharge() :
XTandemInfile
getMaxPTMsize() :
InspectInfile
getMaxRelError() :
OptimizePick
,
TwoDOptimization
getMaxRoundingError() :
Weights
getMaxRT() :
MSExperiment< PeakT, ChromatogramPeakT >
,
Spectrum2DGoToDialog
getMaxScanDistance() :
ProcessData
getMaxScanSize() :
IsotopeWaveletTransform< PeakType >
getMaxScore() :
PrecursorIonSelection
getMaxTR() :
SuperHirnParameters
getMaxValidEValue() :
XTandemInfile
getMean() :
BackgroundIntensityBin
getMeanRes() :
LinearRegression
getMergeLayer() :
TOPPViewOpenDialog
getMessage() :
BaseException
getMetaData() :
MzTab
getMetadataOnly() :
FeatureFileOptions
,
PeakFileOptions
getMetaValue() :
MetaInfoInterface
getMethodOfCombination() :
AcquisitionInfo
getMin() :
IsotopeDistribution
,
RangeManager< D >
,
Spectrum1DGoToDialog
getMinElement() :
SparseVector< Value >
getMinElementCoordinates() :
DistanceMatrix< Value >
getMinFeatureChrg() :
SuperHirnParameters
getMinFeatureMZ() :
SuperHirnParameters
getMinimalIntensityLevel() :
ProcessData
getMinInt() :
RangeManager< D >
getMinIntensity() :
SuperHirnParameters
,
SpectrumCanvas
getMinMZ() :
MSExperiment< PeakT, ChromatogramPeakT >
,
Spectrum2DGoToDialog
getMinNbClusterMembers() :
SuperHirnParameters
getMinPeakGroupSize() :
Deisotoper
getMinRoundingError() :
Weights
getMinRT() :
Spectrum2DGoToDialog
,
MSExperiment< PeakT, ChromatogramPeakT >
getMinSpacing() :
IsotopeWaveletTransform< PeakType >
getMinTR() :
SuperHirnParameters
getMissedCleavages() :
MascotInfile
,
EnzymaticDigestion
,
PeptideEvidence
getML1s() :
TOFCalibration
getML2s() :
TOFCalibration
getML3s() :
TOFCalibration
getModel() :
PILISModelGenerator
,
Instrument
,
ProductModel< 2 >
getModelDescription() :
Feature
getModelParameters() :
TransformationDescription
getModelType() :
TransformationDescription
getModelTypes() :
TransformationDescription
getModification() :
ModificationsDB
,
ModificationDefinition
,
ModificationsDB
,
Residue
getModificationNames() :
ModificationDefinitionsSet
getModificationOutputMethod() :
SuffixArrayPeptideFinder
getModifications() :
SequestInfile
,
ModificationDefinitionsSet
,
InspectInfile
,
MascotInfile
,
PepNovoInfile
,
XTandemInfile
getModificationsByDiffMonoMass() :
ModificationsDB
getModificationsForMass() :
ModifierRep
getModificationsPerPeptide() :
InspectInfile
getModificationTable() :
ModifierRep
getModifiedAASequence_() :
CompNovoIdentificationBase
getModifiedResidue() :
ResidueDB
getModifiedStringFromAASequence_() :
CompNovoIdentificationBase
getModOrSubstIdentifier() :
MzTabModification
getMonoisotopicFeatureIntensity() :
FeatureHypothesis
getMonoisotopicPeaks_() :
TOFCalibration
getMonoMass() :
ResidueModification
getMonoWeight() :
AASequence
,
Element
,
EmpiricalFormula
,
Residue
getMs1FeatureMergingTrTolerance() :
SuperHirnParameters
getMs1PeakAreaTrResolution() :
SuperHirnParameters
getMS1TRResolution() :
SuperHirnParameters
getMS2Feature() :
SHFeature
getMS2FragmentMap() :
MS2ConsensusSpectrum
getMS2FragmentPeakEnd() :
MS2ConsensusSpectrum
getMS2FragmentPeakStart() :
MS2ConsensusSpectrum
getMSFile() :
MzTabSpectraRef
getMSLevel() :
MSSpectrum< PeakT >
getMSLevels() :
PeakFileOptions
,
MSExperiment< PeakT, ChromatogramPeakT >
getMulticharge() :
InspectInfile
getMZ() :
Peak2D
,
GridFeature
,
ChromatogramPeak
,
MSChromatogram< PeakT >
,
Peak1D
,
Product
,
cudaHelp
,
IsotopeWaveletTransform< PeakType >::TransSpectrum
getMz32Bit() :
PeakFileOptions
getMZArray() :
Spectrum
getMzPeakCutOffAtMonoPos() :
IsotopeWavelet
getMZRange() :
FeatureFileOptions
,
PeakFileOptions
getMZTolerance() :
TwoDOptimization
getMzTolPpm() :
SuperHirnParameters
getNADH010106() :
AAIndex
getNADH010107() :
AAIndex
getName() :
IsobaricQuantitationMethod
,
HMMState
,
ReactionMonitoringTransition
,
ItraqEightPlexQuantitationMethod
,
ItraqFourPlexQuantitationMethod
,
TMTSixPlexQuantitationMethod
,
Element
,
IMSAlphabet
,
IMSElement
,
Residue
,
ResidueModification
,
BaseException
,
CVReference
,
Param::ParamIterator
,
MzTabParameter
,
MSChromatogram< PeakT >
,
CVTerm
,
IdentificationHit
,
Instrument
,
MetaInfoRegistry
,
PeptideEvidence
,
Sample
,
Software
,
ModelDescription< D >
,
TOPPASVertexNameDialog
,
TOPPASMergerVertex
,
TOPPASOutputFileListVertex
,
TOPPASToolVertex
,
IncludeExcludeTarget
,
TOPPASVertex
,
TOPPASInputFileListVertex
,
MetaInfoDescription
,
MSSpectrum< PeakT >
,
DefaultParamHandler
getNameMapping() :
INIUpdater
getNameOfFile() :
SourceFile
getNames() :
ElementDB
getNativeID() :
LightTransition
,
ChromatogramSettings
,
SpectrumSettings
,
ReactionMonitoringTransition
getNativeIDs() :
TransitionGroupOpenMS< SpectrumT, TransitionT >
,
ITransitionGroup
,
MockTransitionGroup
getNativeIDType() :
SourceFile
getNativeScanId() :
FeatureFinderAlgorithmSH< PeakType, FeatureType >
getNbLCelutionSignals() :
FeatureLCProfile
getNbMS2Fragments() :
MS2ConsensusSpectrum
getNbMSTraces() :
ProcessData
getNegativeCharges() :
Compomer
getNegativePrior() :
PosteriorErrorProbabilityModel
getNeighbors() :
QTCluster
getNetCharge() :
Compomer
getNeutralLossAverageMass() :
ResidueModification
getNeutralLossDiffFormula() :
ResidueModification
getNeutralLossesForIons() :
SequestInfile
getNeutralLossMonoMass() :
ResidueModification
getNewToolName() :
INIUpdater
getNextLogCounter_() :
LogStreamBuf
getNextMz() :
FeaFiModule< PeakType, FeatureType >
getNextPeakGroup() :
CentroidData
getNextPrecursors() :
PrecursorIonSelection
getNextPrecursorsSeq() :
PrecursorIonSelection
getNextRt() :
FeaFiModule< PeakType, FeatureType >
getNextSep_() :
SuffixArrayTrypticCompressed
getNextSpectrum_() :
MascotGenericFile
,
MascotInfile
getNoise() :
CentroidData
getNominalMass() :
IMSIsotopeDistribution
,
IMSElement
getNonReferencingHits() :
PeptideIdentification
getNormalizeXcorr() :
SequestInfile
getNrChromatograms() :
SpectrumAccessOpenMS
,
SpectrumAccessOpenMSCached
,
ISpectrumAccess
,
IChromatogramsReader
getNrIsotopes() :
DeconvPeak
getNrSpectra() :
SpectrumAccessOpenMS
,
ISpectrumAccess
,
ISpectraReader
,
SpectrumAccessOpenMSCached
getNTerminalModification() :
AASequence
getNTerminalToFull() :
Residue
getNTerminalToFullAverageWeight() :
Residue
getNTerminalToFullMonoWeight() :
Residue
getNTermLossFormulas() :
Residue
getNTermLossNames() :
Residue
getNucleotideReadingFrame() :
SequestInfile
getNumber() :
Sample
getNumberIterations() :
OptimizePick
getNumberOf() :
AASequence
,
EmpiricalFormula
getNumberOfAtoms() :
EmpiricalFormula
getNumberOfChannels() :
IsobaricQuantitationMethod
,
ItraqEightPlexQuantitationMethod
,
TMTSixPlexQuantitationMethod
,
ItraqFourPlexQuantitationMethod
getNumberOfColumns() :
LPWrapper
getNumberOfDecompositions() :
IntegerMassDecomposer< ValueType, DecompositionValueType >
,
MassDecomposer< ValueType, DecompositionValueType >
,
RealMassDecomposer
getNumberOfEnclosedPoints_() :
SVMWrapper
getNumberOfFixedModifications() :
ModificationDefinitionsSet
getNumberOfMaxAA() :
MassDecomposition
getNumberOfMissedCleavages() :
XTandemInfile
getNumberOfModifications() :
ModificationDefinitionsSet
,
ModificationsDB
,
SuffixArray
,
SuffixArrayPeptideFinder
,
SuffixArraySeqan
,
SuffixArrayTrypticCompressed
,
ModifierRep
getNumberOfModifiedResidues() :
ResidueDB
getNumberOfNonZeroEntriesInRow() :
LPWrapper
getNumberOfPeaks_() :
OptimizePeakDeconvolution
,
PeakPickerCWT
getNumberOfPrecsInSpectrum_() :
PSLPFormulation
getNumberOfProtIds() :
PSProteinInference
getNumberOfProtIdsPeptideRule() :
PSProteinInference
getNumberOfResidues() :
ResidueDB
getNumberOfRows() :
LPWrapper
getNumberOfSpectraScan() :
ClusteredMS2ConsensusSpectrum
getNumberOfStates() :
HiddenMarkovModel
getNumberOfThreads() :
XTandemInfile
getNumberOfVariableModifications() :
ModificationDefinitionsSet
getNumFeatPoints() :
FeatureHypothesis
getNumJobs() :
TOPPASOutputFilesDialog
getNumPeakCutOff() :
IsotopeWavelet
getObjective() :
LPWrapper
getObjectiveSense() :
LPWrapper
getObjectiveValue() :
LPWrapper
getObservedIntensity() :
AccurateMassSearchResult
getObservedRT() :
AccurateMassSearchResult
getOffset() :
LinearInterpolation< Key, Value >
,
ExtendedIsotopeModel
,
IsotopeModel
,
LmaIsotopeModel
getOffset_0() :
BilinearInterpolation< Key, Value >
getOffset_1() :
BilinearInterpolation< Key, Value >
getOneLetterCode() :
Residue
getOOBM850104() :
AAIndex
getOpenMSDataPath() :
File
getOptimizedParameters_() :
EGHTraceFitter< PeakType >
,
GaussTraceFitter< PeakType >
,
TraceFitter< PeakType >
getOptions() :
ConsensusXMLFile
,
DBAdapter
,
DTA2DFile
,
FeatureXMLFile
,
FileHandler
,
MzDataFile
,
MzMLFile
,
MzXMLFile
,
MzDataFile
,
FeatureXMLFile
,
DBAdapter
getOrder() :
IonDetector
,
IonSource
,
MassAnalyzer
getOrganism() :
Sample
getOrgIntensity() :
CentroidPeak
getOrigin() :
ResidueModification
getOSAsString() :
OpenMSOSInfo
getOutDir() :
TOPPASScene
getOutlierDetectionAttribute() :
MS2Fragment
getOutput() :
ToolsDialog
getOutputDir() :
TOPPASOutputFileListVertex
,
TOPPASToolVertex
getOutputFilename() :
XTandemInfile
getOutputFiles() :
TOPPASVertex
getOutputLines() :
SequestInfile
getOutputParameters() :
TOPPASToolVertex
getOutsideReferencePoint() :
LinearInterpolation< Key, Value >
getOutsideReferencePoint_0() :
BilinearInterpolation< Key, Value >
getOutsideReferencePoint_1() :
BilinearInterpolation< Key, Value >
getOverallQuality() :
Feature
getParam() :
AcqusHandler
,
ModelDescription< D >
,
TOPPASToolVertex
getParam_() :
TOPPBase
getParamArgument_() :
TOPPBase
getParamAsBool_() :
TOPPBase
getParamAsDouble_() :
TOPPBase
getParamAsDoubleList_() :
TOPPBase
getParamAsInt_() :
TOPPBase
getParamAsIntList_() :
TOPPBase
getParamAsString_() :
TOPPBase
getParamAsStringList_() :
TOPPBase
getParameterByName_() :
TOPPBase
getParameters() :
TransformationModelLinear
,
DefaultParamHandler
,
MSSim
,
FeatureFinder
,
TransformationModel
getParameters_() :
TOPPASToolVertex
getParentMass() :
Weights
getPartialSequence() :
SequestInfile
getPassThreshold() :
IdentificationHit
getPath_() :
MzMLValidator
,
SemanticValidator
getPathToFile() :
SourceFile
getPeak() :
PeakIndex
getPeakArea_() :
PeakPickerCWT
getPeakCentroid_() :
PeakPickerCWT
getPeakCount() :
FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >
getPeakData() :
LayerData
getPeakEndPoints_() :
PeakPickerCWT
getPeakFlag() :
FeatureFinder
getPeakIndex() :
AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
getPeakIntensity() :
FeaFiModule< PeakType, FeatureType >
getPeakIntensitySum() :
ProcessData
getPeakMap() :
MSSim
,
SpectrumCheapDPCorr
getPeakMassTolerance() :
InspectInfile
,
MascotInfile
,
SequestInfile
getPeakMz() :
FeaFiModule< PeakType, FeatureType >
getPeakPosition() :
Annotation1DPeakItem
getPeakPositions() :
SILACFilter
getPeakRt() :
FeaFiModule< PeakType, FeatureType >
getPeakWidth_() :
RawMSSignalSimulation
getPen() :
Annotations1DContainer
getPenalties() :
OptimizePeakDeconvolution
,
OptimizePick
,
TwoDOptimization
,
OptimizePick
getPeptide() :
BigString
getPeptideByRef() :
TargetedExperiment
getPeptideGroupLabel() :
Peptide
getPeptideHit() :
ProteinResolver
getPeptideIdentification() :
ProteinResolver
getPeptideIdentifications() :
BaseFeature
,
SpectrumSettings
getPeptideMassUnit() :
SequestInfile
getPeptideOptionalColumnNames() :
MzTab
getPeptideProbabilityThreshold() :
SuperHirnParameters
getPeptideProteinCounter() :
PrecursorIonSelection
getPeptideRef() :
ReactionMonitoringTransition
,
LightTransition
,
IncludeExcludeTarget
getPeptideResults() :
PeptideAndProteinQuant
getPeptides() :
LightTargetedExperiment
,
TargetedExperiment
getPeptideSectionData() :
MzTab
getPercentage() :
Gradient
getPercentageFactor() :
SpectrumCanvas
getPercentageIntensityElutionBorderVariation() :
SuperHirnParameters
getPercentages() :
Gradient
getPermut() :
CompNovoIdentificationBase::Permut
getPersistenceId() :
PersistentObject
getPh() :
Digestion
getPILISModel_() :
PILISIdentification
getPiValue() :
Residue
getPka() :
Residue
getPkb() :
Residue
getPkc() :
Residue
getPoints() :
IDEvaluationBase
getPolarity() :
InstrumentSettings
,
IonSource
getPoolFile() :
DocumentIDTagger
getPos() :
ChromatogramPeak
,
Peak1D
getPosition() :
Annotation1DPeakItem
,
AveragePosition< D >
,
ChromatogramPeak
,
Peak2D
,
Peak1D
,
AcqusHandler
,
ChromatogramPeak
,
Peak2D
,
Annotation1DTextItem
,
Peak1D
getPositionRange() :
ConsensusFeature
getPositionsAndParameters() :
MzTabModification
getPositiveCharges() :
Compomer
getPossibleChargeStates() :
Precursor
getPost() :
PeptideEvidence
getPPMs_() :
IsotopeWaveletTransform< PeakType >
getPpmToleranceForMZClustering() :
SuperHirnParameters
getPre() :
PeptideEvidence
getPrecision() :
Weights
getPrecursor() :
ChromatogramSettings
getPrecursorActivation() :
MSPeak
getPrecursorChrg() :
MS2ConsensusSpectrum
getPrecursorCHRG() :
MSPeak
,
MS2Fragment
getPrecursorCVTermList() :
ReactionMonitoringTransition
,
IncludeExcludeTarget
getPrecursorErrorType() :
XTandemInfile
getPrecursorMassErrorUnit() :
XTandemInfile
getPrecursorMassTolerance() :
MascotInfile
,
InspectInfile
,
SequestInfile
getPrecursorMassToleranceMinus() :
XTandemInfile
getPrecursorMassTolerancePlus() :
XTandemInfile
getPrecursorMZ() :
MS2Fragment
,
MSPeak
,
MS2ConsensusSpectrum
,
ReactionMonitoringTransition
,
IncludeExcludeTarget
,
LightTransition
getPrecursorRTandMZ() :
InspectOutfile
getPrecursors() :
SpectrumSettings
getPrecursorSpectrum() :
MSExperiment< PeakT, ChromatogramPeakT >
getPredecessorStates() :
HMMState
getPrediction() :
ReactionMonitoringTransition
,
IncludeExcludeTarget
getPrefix() :
AASequence
getPreIdentification_() :
PILISIdentification
getPressure() :
HPLC
getPrevMz() :
FeaFiModule< PeakType, FeatureType >
getPrevRt() :
FeaFiModule< PeakType, FeatureType >
getPrintDuplicateReferences() :
SequestInfile
getProbability_() :
IDDecoyProbability
getProcessedData() :
ProcessData
getProcessingActions() :
DataProcessing
getProcessingInfo_() :
TOPPBase
getProduct() :
ChromatogramSettings
,
ReactionMonitoringTransition
getProductChargeState() :
LightTransition
getProductCVTermList() :
IncludeExcludeTarget
getProductMZ() :
LightTransition
,
ReactionMonitoringTransition
,
IncludeExcludeTarget
getProductName() :
ComplementFilter
,
IsotopeFitter1D
,
ComplementMarker
,
ProductModel< 2 >
,
GoodDiffFilter
,
GaussModel
,
FeatureFinderAlgorithmPicked< PeakType, FeatureType >
,
GaussFitter1D
,
ExtendedIsotopeModel
,
ExtendedIsotopeFitter1D
,
LabelFreeLabeler
,
FastaIteratorIntern
,
ITRAQLabeler
,
LabeledPairFinder
,
SpectrumCheapDPCorr
,
PeakSpectrumCompareFunctor
,
PeakAlignment
,
CompleteLinkage
,
StablePairFinder
,
AverageLinkage
,
PoseClusteringAffineSuperimposer
,
FeatureGroupingAlgorithmUnlabeled
,
FeatureGroupingAlgorithmQT
,
NeutralLossMarker
,
PoseClusteringShiftSuperimposer
,
EdwardsLippertIterator
,
BinnedSpectrumCompareFunctor
,
FeatureGroupingAlgorithmLabeled
,
MapAlignmentAlgorithmIdentification
,
MapAlignmentAlgorithmPoseClustering
,
MapAlignmentAlgorithmSpectrumAlignment
,
MapAlignmentEvaluationAlgorithmRecall
,
PeakMarker
,
SimplePairFinder
,
TrypticIterator
,
BinnedSharedPeakCount
,
BinnedSpectralContrastAngle
,
CompareFouriertransform
,
SpectrumAlignmentScore
,
SpectrumPrecursorComparator
,
ZhangSimilarityScore
,
IntensityBalanceFilter
,
IsotopeDiffFilter
,
IsotopeMarker
,
NeutralLossDiffFilter
,
FastaIterator
,
EGHFitter1D
,
ICPLLabeler
,
SILACLabeler
,
BiGaussFitter1D
,
BiGaussModel
,
EmgModel
,
FeatureFinderAlgorithmMRM< PeakType, FeatureType >
,
FeatureFinderAlgorithmSH< PeakType, FeatureType >
,
FeatureFinderAlgorithmSimplest< PeakType, FeatureType >
,
IsotopeModel
,
LmaGaussFitter1D
,
LmaGaussModel
,
LmaIsotopeModel
,
MapAlignmentEvaluationAlgorithmPrecision
,
FeatureGroupingAlgorithmIdentification
,
QTClusterFinder
,
EdwardsLippertIteratorTryptic
,
SingleLinkage
,
BinnedSumAgreeingIntensities
,
SpectraSTSimilarityScore
,
SteinScottImproveScore
,
MarkerMower
,
TICFilter
,
EGHModel
,
O18Labeler
,
LmaIsotopeFitter1D
,
EmgFitter1D
,
FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >
,
FeatureFinderAlgorithmSimple< PeakType, FeatureType >
getProducts() :
SpectrumSettings
getPropertyVector_() :
PeakIntensityPredictor
getProteinAccessions() :
PeptideHit
getProteinAccessions_() :
IDRipper
getProteinByRef() :
TargetedExperiment
getProteinGroups() :
ProteinIdentification
getProteinGroups_() :
IdXMLFile
getProteinHits_() :
IDRipper
getProteinIdentification_() :
IDRipper
getProteinIdentifications() :
FeatureMap< FeatureT >
,
ExperimentalSettings
,
ConsensusMap
,
FeatureMap< FeatureT >
getProteinMassFilter() :
SequestInfile
getProteinOptionalColumnNames() :
MzTab
getProteinPeptideSequenceMap() :
PrecursorIonSelectionPreprocessing
getProteinProbability() :
PSProteinInference
getProteinPTMap() :
PrecursorIonSelectionPreprocessing
getProteinResults() :
PeptideAndProteinQuant
getProteinRTMap() :
PrecursorIonSelectionPreprocessing
getProteins() :
LightTargetedExperiment
,
TargetedExperiment
getProteinSectionData() :
MzTab
getProtMasses() :
PrecursorIonSelectionPreprocessing
getProtonDistribution() :
ProtonDistributionModel
getPseudoCounts() :
HiddenMarkovModel
getPSIMODAccession() :
ResidueModification
getPT() :
PrecursorIonSelectionPreprocessing
getPublications() :
TargetedExperiment
getPValue() :
SVMWrapper
getQuality() :
BaseFeature
,
QTCluster
,
Feature
getQuantiles_() :
TransformationModelBSpline
getQueryMass() :
AccurateMassSearchResult
getRank() :
ProteinHit
,
PeptideHit
,
IdentificationHit
getRatios() :
ConsensusFeature
getReagentName() :
Modification
getReference_() :
MapAlignmentAlgorithmIdentification
getReferenceChannel() :
ItraqFourPlexQuantitationMethod
,
TMTSixPlexQuantitationMethod
,
ItraqEightPlexQuantitationMethod
,
IsobaricQuantitationMethod
getReferencingHits() :
PeptideIdentification
getRefIntensity() :
IsotopeWaveletTransform< PeakType >::TransSpectrum
getReflectronState() :
MassAnalyzer
getRefSpectrum() :
IsotopeWaveletTransform< PeakType >::TransSpectrum
getRegionEndpoints_() :
TwoDOptimization
getRemovePrecursorNearPeaks() :
SequestInfile
getRequirementLevel() :
CVMappingRule
getResidue() :
AASequence
,
ResidueDB
getResidueDB_() :
AASequence
getResidues() :
ResidueDB
getResidueSets() :
Residue
,
ResidueDB
getResiduesInUpperCase() :
SequestInfile
getResidueTypeName() :
Residue
getResolution() :
IonDetector
,
MassAnalyzer
getResolution_() :
RawMSSignalSimulation
getResolutionMethod() :
MassAnalyzer
getResolutionType() :
MassAnalyzer
getResultMap() :
FeatureGroupingAlgorithmUnlabeled
getResults() :
MascotRemoteQuery
,
ProteinResolver
getRetentionTime() :
CentroidPeak
,
MS2Info
,
Peptide
,
ReactionMonitoringTransition
,
IncludeExcludeTarget
getRetentionTimes_() :
MapAlignmentAlgorithmIdentification
getRevision() :
VersionInfo
getRightEndpoint() :
PeakShape
getRightPaddingIndex() :
ContinuousWaveletTransform
getRightSplitter() :
HistogramWidget
,
HistogramDialog
getROBB760107() :
AAIndex
getRow() :
CsvFile
getRowIndex() :
LPWrapper
getRowLowerBound() :
LPWrapper
getRowName() :
LPWrapper
getRowUpperBound() :
LPWrapper
getRSD() :
LinearRegression
getRSquared() :
LinearRegression
getRT() :
FeatureOpenMS
,
IFeature
,
MockFeature
,
MockMRMFeature
,
PrecursorIonSelectionPreprocessing
,
AreaIterator< ValueT, ReferenceT, PointerT, SpectrumIteratorT, PeakIteratorT >
,
IsotopeWaveletTransform< PeakType >::TransSpectrum
,
MockFeature
,
ChromatogramPeak
,
MSSpectrum< PeakT >
,
Peak2D
,
GridFeature
,
IFeature
,
IMRMFeature
,
FeatureOpenMS
,
MRMFeatureOpenMS
getRTBounds() :
FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >
getRTProbability() :
PrecursorIonSelectionPreprocessing
getRTProbability_() :
PrecursorIonSelectionPreprocessing
getRTProfileIntensity_() :
ITRAQLabeler
getRTRange() :
FeatureFileOptions
,
PeakFileOptions
getRTShift() :
Adduct
,
Compomer
getRunIDs() :
QcMLFile
getRunNames() :
QcMLFile
getSample() :
ExperimentalSettings
getSamples() :
BaseModel< D >
,
InterpolationModel
,
ProductModel< 2 >
,
BaseModel< D >
getSamplingGrid_() :
RawMSSignalSimulation
getSaveFileName() :
TOPPASScene
getScale() :
LinearInterpolation< Key, Value >
,
ContinuousWaveletTransform
,
ProductModel< 2 >
,
ContinuousWaveletTransform
getScale_0() :
BilinearInterpolation< Key, Value >
getScale_1() :
BilinearInterpolation< Key, Value >
getScalingFactor() :
InterpolationModel
getScanDirection() :
MassAnalyzer
getScanLaw() :
MassAnalyzer
getScanMode() :
InstrumentSettings
getScanNumber() :
Deisotoper
getScanNumber_() :
PrecursorIonSelectionPreprocessing
getScanRate() :
MassAnalyzer
getScanTime() :
MassAnalyzer
,
MassTrace
getScanTRIndex() :
SuperHirnParameters
getScanWindows() :
InstrumentSettings
getScene() :
TOPPASWidget
getScopePath() :
CVMappingRule
getScore() :
FeatureHypothesis
,
PILISScoring
,
CompNovoIdentificationBase::Permut
,
PeptideHit
,
MRMFeature
,
DeconvPeak
,
ProteinHit
getScore_() :
PILISScoring
getScores() :
PILISScoring
,
MRMFeature
getScoreType() :
PeptideIdentification
,
ProteinIdentification
getSdIntens_() :
IsotopeWaveletTransform< PeakType >
getSearchEngine() :
ProteinIdentification
getSearchEngineAndVersion() :
InspectOutfile
,
PepNovoOutfile
getSearchEngineVersion() :
ProteinIdentification
getSearchParameters() :
ProteinIdentification
getSearchType() :
MascotInfile
getSectionDescription() :
Param
getSelectedPen() :
Annotations1DContainer
getSeparator() :
BigString
getSeparator_() :
QuantitativeExperimentalDesign
getSequence() :
ProteinHit
,
PeptideHit
,
IMSElement
getSequenceHeaderFilter() :
SequestInfile
getSequences() :
InspectOutfile
,
SequestOutfile
getShortenedNumber_() :
AxisPainter
getShortName() :
Residue
getShortReportFlag() :
Deisotoper
getShowFragmentIons() :
SequestInfile
getSideChainBasicity() :
Residue
getSigma() :
GaussTraceFitter< PeakType >
,
IsotopeWaveletTransform< PeakType >
getSigmaSquare() :
EGHTraceFitter< PeakType >
getSignal() :
ContinuousWaveletTransform
getSignalLength() :
ContinuousWaveletTransform
getSignalToNoise() :
SHFeature
,
LCElutionPeak
,
MSPeak
,
CentroidPeak
,
SignalToNoiseEstimator< Container >
getSignalToNoiseBackground() :
LCElutionPeak
getSignificanceBorders() :
SVMWrapper
getSignificanceThreshold() :
ProteinIdentification
,
PeptideIdentification
getSILAClabels() :
SILACAnalyzer
getSimilarity() :
SpectraMerger::SpectraDistance_
getSimulatedFeatures() :
MSSim
getSingleMass() :
Adduct
getSize() :
MSExperiment< PeakT, ChromatogramPeakT >
,
MassTrace
,
FeatureHypothesis
,
AcqusHandler
,
ContinuousWaveletTransform
getSizeOnly() :
FeatureFileOptions
getSlope() :
LinearRegression
getSmallestScore() :
PosteriorErrorProbabilityModel
getSmallMoleculeOptionalColumnNames() :
MzTab
getSmallMoleculeSectionData() :
MzTab
getSmoothedIntensities() :
MassTrace
getSnapFactor() :
SpectrumCanvas
getSoftware() :
DataProcessing
,
TargetedExperiment
,
Instrument
,
DataProcessing
getSolver() :
PSProteinInference
,
LPWrapper
getSourceClassification() :
ResidueModification
getSourceClassificationName() :
ResidueModification
getSourceFeatureIndex() :
AccurateMassSearchResult
getSourceFile() :
SpectrumSettings
,
ChromatogramSettings
,
SpectrumSettings
getSourceFiles() :
TargetedExperiment
,
ExperimentalSettings
getSourceOutParam() :
TOPPASEdge
getSourceOutParamName() :
TOPPASEdge
getSourceVertex() :
TOPPASEdge
getSpacing() :
ContinuousWaveletTransform
getSpecificity() :
EnzymaticDigestion
getSpecificityByName() :
EnzymaticDigestion
getSpecificityType() :
Modification
getSpecRef() :
MzTabSpectraRef
getSpectra() :
MSExperiment< PeakT, ChromatogramPeakT >
,
InspectInfile
getSpectraByRT() :
SpectrumAccessOpenMSCached
,
ISpectraReader
,
SpectrumAccessOpenMS
,
ISpectrumAccess
getSpectraIdentificationViewWidget() :
TOPPViewBase
getSpectraIndex() :
CachedmzML
getSpectraMetaInfo() :
SpectrumAccessOpenMSCached
,
SpectrumAccessOpenMS
getSpectraScanNumberEnd() :
ClusteredMS2ConsensusSpectrum
getSpectraScanNumberStart() :
ClusteredMS2ConsensusSpectrum
getSpectrum() :
TrypticIterator
,
FastaIterator
,
FastaIteratorIntern
,
EdwardsLippertIterator
,
PILISModel
,
PeakIndex
,
TheoreticalSpectrumGenerator
,
PepIterator
getSpectrum_() :
PILISIdentification
getSpectrumAccessOpenMSPtr() :
SimpleOpenMSSpectraFactory
getSpectrumAlignment() :
SpectrumAlignment
getSpectrumById() :
ISpectraReader
,
SpectrumAccessOpenMSCached
,
ISpectrumAccess
,
SpectrumAccessOpenMS
getSpectrumIdentifications() :
Identification
getSpectrumMetaById() :
SpectrumAccessOpenMS
,
ISpectraReader
,
ISpectrumAccess
,
SpectrumAccessOpenMSCached
getSpectrumParameters() :
TOPPViewBase
getSpectrumWidget() :
SpectrumCanvas
getStandDevRes() :
LinearRegression
getStandErrSlope() :
LinearRegression
getStart() :
PeptideEvidence
getStartPoint() :
Annotation1DDistanceItem
getStartScan() :
MS2ConsensusSpectrum
,
MS2Fragment
getStartTR() :
MS2ConsensusSpectrum
,
MS2Fragment
getState() :
HiddenMarkovModel
,
Sample
,
HiddenMarkovModel
getStatistics() :
PeptideAndProteinQuant
getStats() :
ItraqQuantifier
getStatus() :
TOPPASToolVertex
,
LPWrapper
getStream() :
LogConfigHandler
,
StreamHandler
getStreamTypeByName_() :
LogConfigHandler
getString() :
EmpiricalFormula
,
RNPxlReportRow
,
RNPxlReportRowHeader
getStringDataArrays() :
MSChromatogram< PeakT >
,
MSSpectrum< PeakT >
,
MSChromatogram< PeakT >
getStringList_() :
TOPPBase
getStringOption_() :
TOPPBase
getStringValue() :
DBConnection
getSubordinates() :
Feature
getSubsamples() :
Sample
getSubsection_() :
TOPPBase
getSubsectionDefaults_() :
TOPPBase
getSubsections() :
DefaultParamHandler
getSubsequence() :
AASequence
getSubtreeStatus() :
TOPPASVertex
getSuccessorStates() :
HMMState
getSuffix() :
AASequence
getSummedFeatureIntensity() :
FeatureHypothesis
getSupportedCharges() :
SvmTheoreticalSpectrumGeneratorSet
getSupportedImageFormats() :
IDEvaluationBase
getSurvivalFunction_() :
PILISScoring
getSVCProbabilities() :
SVMWrapper
getSvmModel() :
SvmTheoreticalSpectrumGeneratorSet
getSVRProbability() :
SVMWrapper
getSymbol() :
Element
getSymbols() :
ElementDB
getSymmetricMeasure() :
PeakShape
getSynonyms() :
Residue
,
ResidueModification
getSystemParameterDefaults_() :
File
getSystemParameters() :
File
getSystemTime() :
StopWatch
getTableSteps() :
IsotopeWavelet
getTableWidget() :
SpectraIdentificationViewWidget
getTabWidth() :
FuzzyStringComparator
getTagCount() :
InspectInfile
getTags() :
SuffixArrayTrypticCompressed
,
Param
,
SuffixArraySeqan
,
SuffixArrayPeptideFinder
,
SuffixArray
getTargetCVTerms() :
TargetedExperiment
getTargetInParam() :
TOPPASEdge
getTargetInParamName() :
TOPPASEdge
getTargetIon() :
MRMDecoy
getTargetVertex() :
TOPPASEdge
getTau() :
EGHTraceFitter< PeakType >
getTaxon() :
XTandemInfile
getTaxonomy() :
MascotInfile
getTaxonomyFilename() :
XTandemInfile
getTempDir() :
TOPPASScene
getTempDirectory() :
File
getTemperature() :
HPLC
,
Digestion
getTerm() :
ControlledVocabulary
getTermByName() :
ControlledVocabulary
getTerminalModification() :
ModificationsDB
getTerminalModificationsByDiffMonoMass() :
ModificationsDB
getTermName() :
CVMappingTerm
getTerms() :
ControlledVocabulary
getTermSpecificity() :
ResidueModification
,
ModificationDefinition
getTermSpecificityName() :
ResidueModification
getText() :
Annotation1DItem
getTheoreticalmaxPosition() :
FeatureFinderAlgorithmPickedHelperStructs::MassTraces< PeakType >
getTheta() :
Deisotoper
getThreeLetterCode() :
Residue
getThreshold() :
ClusterHierarchical
getTIC() :
MSExperiment< PeakT, ChromatogramPeakT >
getTime() :
VersionInfo
,
DateTime
getTimeArray() :
Chromatogram
getTimepoints() :
Gradient
getTOFTotalPathLength() :
MassAnalyzer
getTolerance() :
EdwardsLippertIterator
,
SuffixArraySeqan
,
FastaIterator
,
SuffixArrayTrypticCompressed
,
SuffixArrayPeptideFinder
,
TrypticIterator
,
PepIterator
,
FastaIteratorIntern
,
SuffixArray
getToleranceMZ() :
SuperHirnParameters
getTool() :
ToolsDialog
getToolDescriptions() :
ToolDescriptionHandler
getToolNamesFromINI() :
INIUpdater
getToolToolStatus_() :
TOPPASEdge
getToolUserDefaults_() :
TOPPBase
getTopoNr() :
TOPPASVertex
getTOPPToolList() :
ToolHandler
getTR() :
MS2Fragment
,
MS2ConsensusSpectrum
getTrace() :
Param::ParamIterator
getTraceLength() :
MassTrace
getTransform() :
IsotopeWaveletTransform< PeakType >
getTransformHighRes() :
IsotopeWaveletTransform< PeakType >
getTransIntensity() :
IsotopeWaveletTransform< PeakType >::TransSpectrum
getTransition() :
MRMTransitionGroup< SpectrumType, TransitionType >
getTransitionGroupID() :
MRMTransitionGroup< SpectrumType, TransitionType >
getTransitionProbability() :
HiddenMarkovModel
getTransitionProbability_() :
HiddenMarkovModel
getTransitions() :
MRMTransitionGroup< SpectrumType, TransitionType >
,
TargetedExperiment
,
LightTargetedExperiment
getTransitionsMuteable() :
MRMTransitionGroup< SpectrumType, TransitionType >
getTranslationTableRef() :
PeptideEvidence
getTreatment() :
Sample
getTreeWidget() :
SpectraViewWidget
getTrTol() :
SuperHirnParameters
getTSVHeader() :
TransitionTSVReader
getTValue() :
LinearRegression
getType() :
TOPPASToolVertex
,
SampleTreatment
,
SpectrumSettings
,
MassAnalyzer
,
FileHandler
,
IonDetector
getTypeByContent() :
FileHandler
getTypeByFileName() :
FileHandler
getTypes() :
ToolHandler
getUnassignedPeptideIdentifications() :
ConsensusMap
,
FeatureMap< FeatureT >
,
ConsensusMap
getUnchargedMass() :
Precursor
getUniModAccession() :
ResidueModification
getUniqueId() :
UniqueIdGenerator
,
UniqueIdInterface
getUniqueName() :
File
getUnit() :
DataValue
,
CVTerm
,
MetaInfoRegistry
getUnmodifiedAASequence_() :
ICPLLabeler
getUnmodifiedSequence_() :
SILACLabeler
getUpper() :
LinearRegression
getUpperRTBound() :
TraceFitter< PeakType >
,
EGHTraceFitter< PeakType >
,
GaussTraceFitter< PeakType >
getURL() :
TOPPASResource
,
ContactPerson
getUserDirectory() :
File
getUserTime() :
StopWatch
getUseTags() :
SuffixArray
,
SuffixArrayTrypticCompressed
,
SuffixArrayPeptideFinder
,
SuffixArraySeqan
getUseTerm() :
CVMappingTerm
getUseTermName() :
CVMappingTerm
getUtilList() :
ToolHandler
getValue() :
Param
,
MetaInfo
,
DistanceMatrix< Value >
,
MzTabParameter
,
Matrix< Value >
,
DistanceMatrix< Value >
,
CVTerm
,
Matrix< Value >
,
MetaInfo
getValueAtRT() :
ISignalToNoise
,
SignalToNoiseOpenMS< PeakT >
,
MockSignalToNoise
getValueByLambda() :
IsotopeWavelet
getValueByLambdaExact() :
IsotopeWavelet
getValueByLambdaExtrapol() :
IsotopeWavelet
getValueByMass() :
IsotopeWavelet
getVariableModificationNames() :
ModificationDefinitionsSet
getVariableModifications() :
MascotInfile
,
ModificationDefinitionsSet
getVariant() :
Tagging
getVASM830103() :
AAIndex
getVectorWout() :
LocalLinearMap
getVendor() :
Instrument
getVerboseLevel() :
FuzzyStringComparator
getVersion() :
XMLFile
,
VersionInfo
,
Software
getVersionStruct() :
VersionInfo
getVertexAt_() :
TOPPASScene
getVerticalProjection() :
Spectrum2DWidget
getVisibleArea() :
SpectrumCanvas
getVisibleConsensusData() :
SpectrumCanvas
getVisibleFeatureData() :
SpectrumCanvas
getVisibleIdentifications() :
SpectrumCanvas
getVisiblePeakData() :
SpectrumCanvas
getVolume() :
Sample
getWantedRecords() :
InspectOutfile
getWavelet() :
ContinuousWaveletTransform
getWeight() :
WeightWrapper
,
Weights
,
PrecursorIonSelectionPreprocessing
,
AveragePosition< D >
,
WeightWrapper
getWeightMode() :
WeightWrapper
getWhitelist() :
FuzzyStringComparator
getWidth() :
CentroidData
,
BaseFeature
,
FeatureHandle
getWILM950102() :
AAIndex
getWindowId() :
EnhancedTabBarWidgetInterface
,
TOPPASWidget
,
SpectrumWidget
getWorkspace() :
TOPPViewBase
getWriteSupplementalData() :
PeakFileOptions
getX() :
DPosition< D, TCoordinateType >
getXCorrMatrix() :
MRMScoring
getXIC_() :
PSLPFormulation
getXIntercept() :
LinearRegression
getXIonToFull() :
Residue
getXIonToFullAverageWeight() :
Residue
getXIonToFullMonoWeight() :
Residue
getXRefTypeName() :
ControlledVocabulary::CVTerm
getXSize() :
SaveImageDialog
getY() :
DPosition< D, TCoordinateType >
getYIonToFull() :
Residue
getYIonToFullAverageWeight() :
Residue
getYIonToFullMonoWeight() :
Residue
getYSize() :
SaveImageDialog
getZIonMinusOneToFull() :
Residue
getZIonMinusOneToFullAverageWeight() :
Residue
getZIonMinusOneToFullMonoWeight() :
Residue
getZIonPlusOneToFull() :
Residue
getZIonPlusOneToFullAverageWeight() :
Residue
getZIonPlusOneToFullMonoWeight() :
Residue
getZIonPlusTwoToFull() :
Residue
getZIonPlusTwoToFullAverageWeight() :
Residue
getZIonPlusTwoToFullMonoWeight() :
Residue
getZIonToFull() :
Residue
getZIonToFullAverageWeight() :
Residue
getZIonToFullMonoWeight() :
Residue
getZoomScan() :
InstrumentSettings
GlobalExceptionHandler() :
GlobalExceptionHandler
go() :
Deisotoper
goNext_() :
SuffixArraySeqan
goNextSubTree_() :
SuffixArraySeqan
GoodDiffFilter() :
GoodDiffFilter
goToNextAA_() :
TrypticIterator
,
EdwardsLippertIterator
gotRedirect() :
MascotRemoteQuery
gradient() :
MultiGradientSelector
Gradient() :
Gradient
gradient() :
MultiGradientSelector
GradientVisualizer() :
GradientVisualizer
grid_at() :
HashGrid< Cluster >
grid_begin() :
HashGrid< Cluster >
grid_end() :
HashGrid< Cluster >
gridCell_() :
HierarchicalClustering< PointRef >
gridCells5x5_() :
HierarchicalClustering< PointRef >
GridFeature() :
GridFeature
gridLines() :
AxisWidget
gridLinesShown() :
SpectrumCanvas
group() :
FeatureGroupingAlgorithmUnlabeled
,
FeatureGroupingAlgorithm
,
FeatureGroupingAlgorithmIdentification
,
FeatureGroupingAlgorithm
,
FeatureGroupingAlgorithmLabeled
,
FeatureGroupingAlgorithmQT
group_() :
FeatureGroupingAlgorithmQT
GumbelDistributionFitResult() :
GumbelDistributionFitter::GumbelDistributionFitResult
GumbelDistributionFitter() :
GumbelDistributionFitter
gumbelDistributionFitterdf_() :
GumbelDistributionFitter
gumbelDistributionFitterf_() :
GumbelDistributionFitter
gumbelDistributionFitterfdf_() :
GumbelDistributionFitter
GzipIfstream() :
GzipIfstream
GzipInputStream() :
GzipInputStream
OpenMS / TOPP release 1.11.1
Documentation generated on Thu Nov 14 2013 11:20:59 using doxygen 1.8.5