#include <OpenMS/ANALYSIS/OPENSWATH/ConfidenceScoring.h>
 
  
 | Public Member Functions | |
| ConfidenceScoring (bool test_mode_=false) | |
| Constructor.  More... | |
| void | initialize (TargetedExperiment library, Size n_decoys, Size n_transitions, TransformationDescription rt_trafo) | 
| void | initializeGlm (double intercept, double rt_coef, double int_coef) | 
| void | scoreMap (FeatureMap<> &features) | 
| Score a feature map -> make sure the class is properly initialized.  More... | |
|  Public Member Functions inherited from ProgressLogger | |
| ProgressLogger () | |
| Constructor.  More... | |
| ~ProgressLogger () | |
| Destructor.  More... | |
| void | setLogType (LogType type) const | 
| Sets the progress log that should be used. The default type is NONE!  More... | |
| LogType | getLogType () const | 
| Returns the type of progress log being used.  More... | |
| void | startProgress (SignedSize begin, SignedSize end, const String &label) const | 
| Initializes the progress display.  More... | |
| void | setProgress (SignedSize value) const | 
| Sets the current progress.  More... | |
| void | endProgress () const | 
| Ends the progress display.  More... | |
| Protected Types | |
| typedef boost::bimap < DoubleReal, boost::bimaps::multiset_of < DoubleReal > > | BimapType | 
| Mapping: Q3 m/z <-> transition intensity (maybe not unique!)  More... | |
| Protected Member Functions | |
| void | chooseDecoys_ () | 
| Randomize the list of decoy indexes.  More... | |
| DoubleReal | manhattanDist_ (DoubleList x, DoubleList y) | 
| Manhattan distance.  More... | |
| DoubleReal | getAssayRT_ (const TargetedExperiment::Peptide &assay, const String &cv_accession="MS:1000896") | 
| Get the retention time of an assay.  More... | |
| void | extractIntensities_ (BimapType &intensity_map, Size n_transitions, DoubleList &intensities) | 
| DoubleReal | scoreAssay_ (const TargetedExperiment::Peptide &assay, DoubleReal feature_rt, DoubleList &feature_intensities, const std::set< String > &transition_ids=std::set< String >()) | 
| void | scoreFeature_ (Feature &feature) | 
| Score a feature.  More... | |
| Protected Attributes | |
| struct { | |
| DoubleReal intercept | |
| DoubleReal rt_coef | |
| DoubleReal int_coef | |
| } | glm_ | 
| Binomial GLM.  More... | |
| struct { | |
| DoubleReal min_rt | |
| DoubleReal max_rt | |
| } | rt_norm_ | 
| Helper for RT normalization (range 0-100)  More... | |
| TargetedExperiment | library_ | 
| IntList | decoy_index_ | 
| Size | n_decoys_ | 
| Map< String, IntList > | transition_map_ | 
| Size | n_transitions_ | 
| TransformationDescription | rt_trafo_ | 
| RT transformation to map measured RTs to assay RTs.  More... | |
| boost::mt19937 | generator_ | 
| boost::variate_generator < boost::mt19937 &, boost::uniform_int<> > | rand_gen_ | 
| Random number generator (must be initialized in init. list of c'tor!)  More... | |
|  Protected Attributes inherited from ProgressLogger | |
| LogType | type_ | 
| SignedSize | begin_ | 
| SignedSize | end_ | 
| SignedSize | value_ | 
| QProgressDialog * | dlg_ | 
| StopWatch | stop_watch_ | 
| time_t | last_invoke_ | 
| Additional Inherited Members | |
|  Public Types inherited from ProgressLogger | |
| enum | LogType { CMD, GUI, NONE } | 
| Possible log types.  More... | |
|  Static Protected Attributes inherited from ProgressLogger | |
| static int | recursion_depth_ | 
| 
 | protected | 
Mapping: Q3 m/z <-> transition intensity (maybe not unique!)
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 | inline | 
Constructor.
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 | protected | 
Randomize the list of decoy indexes.
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 | protected | 
Extract the n_transitions highest intensities from intensity_map, store them in intensities 
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 | protected | 
Get the retention time of an assay.
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 | inline | 
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 | protected | 
Manhattan distance.
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 | protected | 
Score the assay assay against feature data (feature_rt, feature_intensities), optionally using only the specified transitions (transition_ids) 
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 | protected | 
Score a feature.
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 | inline | 
Score a feature map -> make sure the class is properly initialized.
both functions initializeGlm and initialize need to be called first.
The input to the program is
References UniqueIdInterface::getUniqueId(), LOG_DEBUG, and LOG_WARN.
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 | protected | 
| 
 | protected | 
| struct { ... } glm_ | 
Binomial GLM.
| DoubleReal int_coef | 
| DoubleReal intercept | 
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 | protected | 
| DoubleReal max_rt | 
| DoubleReal min_rt | 
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 | protected | 
| 
 | protected | 
| 
 | protected | 
Random number generator (must be initialized in init. list of c'tor!)
| DoubleReal rt_coef | 
| struct { ... } rt_norm_ | 
Helper for RT normalization (range 0-100)
| 
 | protected | 
RT transformation to map measured RTs to assay RTs.
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:26 using doxygen 1.8.5 |