#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_ |
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Mapping: Q3 m/z <-> transition intensity (maybe not unique!)
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Constructor.
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Randomize the list of decoy indexes.
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Extract the n_transitions highest intensities from intensity_map, store them in intensities
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Get the retention time of an assay.
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Manhattan distance.
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Score the assay assay against feature data (feature_rt, feature_intensities), optionally using only the specified transitions (transition_ids)
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Score a feature.
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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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| struct { ... } glm_ |
Binomial GLM.
| DoubleReal int_coef |
| DoubleReal intercept |
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| DoubleReal max_rt |
| DoubleReal min_rt |
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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)
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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 |