allow_missing_peaks | SILACAnalyzer | private |
begin_ | ProgressLogger | mutableprotected |
calculateLabelsAndMassShifts(std::map< String, DoubleReal > label_identifiers) | SILACAnalyzer | |
charge_max | SILACAnalyzer | private |
charge_min | SILACAnalyzer | private |
clusterData(const MSExperiment<> &, const PeakWidthEstimator::Result &, std::vector< Clustering * > &, std::vector< std::vector< SILACPattern > > &data) | SILACAnalyzer | |
Clustering typedef | SILACAnalyzer | private |
CMD enum value | ProgressLogger | |
dlg_ | ProgressLogger | mutableprotected |
end_ | ProgressLogger | mutableprotected |
endProgress() const | ProgressLogger | |
estimatePeakWidth(const MSExperiment< Peak1D > &exp) | SILACAnalyzer | |
filterData(MSExperiment< Peak1D > &exp, const PeakWidthEstimator::Result &peak_width, std::vector< std::vector< SILACPattern > > &data) | SILACAnalyzer | |
generateClusterConsensusByCluster(ConsensusMap &, const Clustering &) const | SILACAnalyzer | |
generateClusterConsensusByPattern(ConsensusMap &, const Clustering &, UInt &cluster_id) const | SILACAnalyzer | |
generateClusterDebug(std::ostream &out, const Clustering &clustering, UInt &cluster_id) const | SILACAnalyzer | |
generateClusterFeatureByCluster(FeatureMap<> &, const Clustering &) const | SILACAnalyzer | |
generateFilterConsensusByPattern(ConsensusMap &, const std::vector< SILACPattern > &) const | SILACAnalyzer | |
generateSingleConsensusByPattern(const SILACPattern &) const | SILACAnalyzer | private |
getLogType() const | ProgressLogger | |
getMassShifts() | SILACAnalyzer | inline |
getSILAClabels() | SILACAnalyzer | inline |
GUI enum value | ProgressLogger | |
in | SILACAnalyzer | private |
in_filters | SILACAnalyzer | private |
initialize(String selected_labels_, UInt charge_min_, UInt charge_max_, Int missed_cleavages_, UInt isotopes_per_peptide_min_, UInt isotopes_per_peptide_max_, DoubleReal rt_threshold_, DoubleReal rt_min_, DoubleReal intensity_cutoff_, DoubleReal intensity_correlation_, DoubleReal model_deviation_, bool allow_missing_peaks_, std::map< String, DoubleReal > label_identifiers) | SILACAnalyzer | inline |
intensity_correlation | SILACAnalyzer | private |
intensity_cutoff | SILACAnalyzer | private |
isotopes_per_peptide_max | SILACAnalyzer | private |
isotopes_per_peptide_min | SILACAnalyzer | private |
last_invoke_ | ProgressLogger | mutableprotected |
LogType enum name | ProgressLogger | |
massShifts | SILACAnalyzer | private |
missed_cleavages | SILACAnalyzer | private |
model_deviation | SILACAnalyzer | private |
msq | SILACAnalyzer | private |
NONE enum value | ProgressLogger | |
out | SILACAnalyzer | private |
out_clusters | SILACAnalyzer | private |
out_debug | SILACAnalyzer | private |
out_features | SILACAnalyzer | private |
out_filters | SILACAnalyzer | private |
out_mzq | SILACAnalyzer | private |
ProgressLogger() | ProgressLogger | |
readConsensus(const String &filename, ConsensusMap &in) const | SILACAnalyzer | inline |
readFilterConsensusByPattern(ConsensusMap &, std::vector< std::vector< SILACPattern > > &) | SILACAnalyzer | |
recursion_depth_ | ProgressLogger | protectedstatic |
rt_min | SILACAnalyzer | private |
rt_threshold | SILACAnalyzer | private |
run_all(MSExperiment< Peak1D > &exp, ConsensusMap &out_map) | SILACAnalyzer | inline |
selectColor(UInt nr) | SILACAnalyzer | static |
selected_labels | SILACAnalyzer | private |
setLogType(LogType type) const | ProgressLogger | |
setProgress(SignedSize value) const | ProgressLogger | |
SILACAnalyzer() | SILACAnalyzer | inline |
SILAClabels | SILACAnalyzer | private |
startProgress(SignedSize begin, SignedSize end, const String &label) const | ProgressLogger | |
stop_watch_ | ProgressLogger | mutableprotected |
type_ | ProgressLogger | mutableprotected |
value_ | ProgressLogger | mutableprotected |
writeConsensus(const String &filename, ConsensusMap &out) const | SILACAnalyzer | inline |
writeFeatures(const String &filename, FeatureMap<> &out) const | SILACAnalyzer | inline |
writeMzQuantML(const String &filename, MSQuantifications &msq) const | SILACAnalyzer | inline |
~ProgressLogger() | ProgressLogger | |