| 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 | |