OpenMS
2.4.0
Here is a list of all class members with links to the classes they belong to:
- a -
a_ion_score :
RNPxlSearch::AnnotatedHit
abundance :
SIPIncorporation
accessions :
SIPPeptide
accumulated :
SIPPeptide
ADDITIONAL_ISOTOPES :
TOPPMetaProSIP
addMS2MarkerIons() :
RNPxlSearch::RNPxlFragmentIonGenerator
addPrecursorWithCompleteRNA_() :
RNPxlSearch::RNPxlFragmentIonGenerator
addShiftedImmoniumIons() :
RNPxlSearch::RNPxlFragmentIonGenerator
addSpecialLysImmonumIons() :
RNPxlSearch::RNPxlFragmentIonGenerator
ANNOTATIONS_MARKER_ION_PREFIX :
RNPxlSearch
arch :
OpenMSOSInfo
- b -
best_localization :
RNPxlSearch::AnnotatedHit
best_localization_score :
RNPxlSearch::AnnotatedHit
- c -
calculateCorrelation() :
TOPPMetaProSIP
calculateDecompositionWeightsIsotopicPatterns() :
MetaProSIPDecomposition
calculateGlobalLR() :
TOPPMetaProSIP
calculateIsotopePatternsFor13CRange() :
MetaProSIPDecomposition
calculateIsotopePatternsFor13CRangeOfAveraginePeptide() :
MetaProSIPDecomposition
calculateIsotopePatternsFor15NRange() :
MetaProSIPDecomposition
calculateIsotopePatternsFor15NRangeOfAveraginePeptide() :
MetaProSIPDecomposition
calculateIsotopePatternsFor18ORange() :
MetaProSIPDecomposition
calculateIsotopePatternsFor18ORangeOfAveraginePeptide() :
MetaProSIPDecomposition
calculateIsotopePatternsFor2HRange() :
MetaProSIPDecomposition
calculateIsotopePatternsFor2HRangeOfAveraginePeptide() :
MetaProSIPDecomposition
can_xl_ :
RNPxlSearch
charge :
SIPPeptide
checkRDependencies() :
RIntegration
clusterSIPPeptides() :
MetaProSIPClustering
correlateXICsToMono() :
MetaProSIPXICExtraction
correlation :
SIPIncorporation
correlation_map :
SIPPeptide
correlation_maxima :
SIPPeptide
createBinnedPeptideRIAData_() :
MetaProSIPReporting
createCSVReport() :
MetaProSIPReporting
createPeptideCentricCSVReport() :
MetaProSIPReporting
createQualityReport() :
MetaProSIPReporting
cross_linked_nucleotide :
RNPxlSearch::AnnotatedHit
- d -
decomposition_map :
SIPPeptide
- e -
err :
RNPxlSearch::AnnotatedHit
explained_TIC_fraction :
SIPPeptide
extractIncorporationsAtCorrelationMaxima() :
TOPPMetaProSIP
extractIncorporationsAtHeighestDecompositionWeights() :
TOPPMetaProSIP
extractIsotopicIntensities() :
TOPPMetaProSIP
extractPeakSpectrum() :
TOPPMetaProSIP
extractXICs() :
MetaProSIPXICExtraction
extractXICsOfIsotopeTraces() :
MetaProSIPXICExtraction
- f -
fast_scoring_ :
RNPxlSearch
feasible_adducts :
RNPxlSearch::MS2AdductsOfSinglePrecursorAdduct
feature_mz :
SIPPeptide
feature_rt :
SIPPeptide
FEATURE_STRING :
TOPPMetaProSIP
feature_type :
SIPPeptide
filterIsotopicIntensities() :
TOPPMetaProSIP
findApexRT() :
TOPPMetaProSIP
formula :
RNPxlSearch::FragmentAdductDefinition_
fragment_annotations :
RNPxlSearch::AnnotatedHit
,
SimpleSearchEngine::AnnotatedHit
FragmentAdductDefinition_() :
RNPxlSearch::FragmentAdductDefinition_
- g -
generatePartialLossSpectrum() :
RNPxlSearch::RNPxlFragmentIonGenerator
getAllFeasibleFragmentAdducts() :
RNPxlSearch::RNPxlParameterParsing
getArchAsString() :
OpenMSOSInfo
getBestRateScorePair() :
TOPPMetaProSIP
getFeasibleFragmentAdducts() :
RNPxlSearch::RNPxlParameterParsing
getHighPoints() :
MetaProSIPInterpolation
getModifications() :
RNPxlSearch::RNPxlParameterParsing
getModifications_() :
SimpleSearchEngine
,
TOPPOpenPepXLLF
getNumberOfLabelingElements() :
MetaProSIPDecomposition
getOSAsString() :
OpenMSOSInfo
getRIAClusterCenter() :
MetaProSIPClustering
getTargetNucleotideToFragmentAdducts() :
RNPxlSearch::RNPxlParameterParsing
global_LR :
SIPPeptide
- h -
hasBetterScore() :
RNPxlSearch::AnnotatedHit
,
SimpleSearchEngine::AnnotatedHit
- i -
immonium_score :
RNPxlSearch::AnnotatedHit
incorporations :
SIPPeptide
initializeSpectrumGenerators() :
RNPxlSearch
isotope_error :
RNPxlSearch::AnnotatedHit
isotopicIntensitiesToSpectrum() :
TOPPMetaProSIP
- l -
localization_ :
RNPxlSearch
localization_scores :
RNPxlSearch::AnnotatedHit
- m -
main_() :
RNPxlSearch
,
SimpleSearchEngine
,
TOPPMetaProSIP
,
TOPPOpenPepXL
,
TOPPOpenPepXLLF
mapPrecursorMassesToScans() :
RNPxlSearch
marker_ions :
RNPxlSearch::MS2AdductsOfSinglePrecursorAdduct
marker_ions_score :
RNPxlSearch::AnnotatedHit
mass :
RNPxlSearch::FragmentAdductDefinition_
mass_diff :
SIPPeptide
mass_theo :
SIPPeptide
mergeSpectra() :
TOPPMetaProSIP
MIC :
RNPxlSearch::AnnotatedHit
Morph :
RNPxlSearch::AnnotatedHit
mz_theo :
SIPPeptide
- n -
name :
RNPxlSearch::FragmentAdductDefinition_
non_zero_decomposition_coefficients :
SIPPeptide
normalizeToMax() :
TOPPMetaProSIP
NucleotideToFeasibleFragmentAdducts :
RNPxlSearch
NucleotideToFragmentAdductMap :
RNPxlSearch::RNPxlParameterParsing
- o -
OpenMSOSInfo() :
OpenMSOSInfo
operator()() :
RIALess
,
SequenceLess
,
SizeLess
operator<() :
RNPxlSearch::FragmentAdductDefinition_
operator=() :
RNPxlSearch::FragmentAdductDefinition_
operator==() :
RNPxlSearch::FragmentAdductDefinition_
os :
OpenMSOSInfo
os_version :
OpenMSOSInfo
- p -
partial_loss_score :
RNPxlSearch::AnnotatedHit
patterns :
SIPPeptide
peptide_mod_index :
RNPxlSearch::AnnotatedHit
,
SimpleSearchEngine::AnnotatedHit
pl_err :
RNPxlSearch::AnnotatedHit
pl_MIC :
RNPxlSearch::AnnotatedHit
pl_Morph :
RNPxlSearch::AnnotatedHit
plotFilteredSpectra() :
MetaProSIPReporting
plotHeatMap() :
MetaProSIPReporting
plotScoresAndWeights() :
MetaProSIPReporting
postProcessHits_() :
RNPxlSearch
,
SimpleSearchEngine
postScoreHits_() :
RNPxlSearch
precursor_score :
RNPxlSearch::AnnotatedHit
PrecursorsToMS2Adducts :
RNPxlSearch::RNPxlParameterParsing
preprocessPairs_() :
TOPPOpenPepXL
preprocessSpectra_() :
RNPxlSearch
,
SimpleSearchEngine
- r -
rate :
RateScorePair
,
SIPIncorporation
reconstruction :
SIPPeptide
reconstruction_monoistopic :
SIPPeptide
registerOptionsAndFlags_() :
RNPxlSearch
,
SimpleSearchEngine
,
TOPPMetaProSIP
,
TOPPOpenPepXL
,
TOPPOpenPepXLLF
rna_mod_index :
RNPxlSearch::AnnotatedHit
RNPxlSearch() :
RNPxlSearch
RR :
SIPPeptide
- s -
score :
RateScorePair
,
RNPxlSearch::AnnotatedHit
,
SimpleSearchEngine::AnnotatedHit
,
SIPPeptide
scorePartialLossFragments_() :
RNPxlSearch
scoreTotalLossFragments_() :
RNPxlSearch
sequence :
RNPxlSearch::AnnotatedHit
,
SimpleSearchEngine::AnnotatedHit
,
SIPPeptide
SimpleSearchEngine() :
SimpleSearchEngine
- t -
TOPPMetaProSIP() :
TOPPMetaProSIP
TOPPOpenPepXL() :
TOPPOpenPepXL
TOPPOpenPepXLLF() :
TOPPOpenPepXLLF
total_MIC :
RNPxlSearch::AnnotatedHit
- u -
UNASSIGNED_ID_STRING :
TOPPMetaProSIP
UNIDENTIFIED_STRING :
TOPPMetaProSIP
unique :
SIPPeptide
UNKNOWN_NUCLEOTIDE :
RNPxlSearch::AnnotatedHit
- w -
writeHTML() :
MetaProSIPReporting
writePeakIntensities_() :
TOPPMetaProSIP
Generated on Sat Nov 24 2018 05:42:57 for OpenMS by
1.8.14