| 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 |  |