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MRMFeatureFinderScoring.h
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34 
35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H
36 #define OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H
37 
38 #define USE_SP_INTERFACE
39 
40 // Actual scoring
42 
45 
46 // Kernel classes
54 
55 #include <boost/shared_ptr.hpp>
56 #include <boost/make_shared.hpp>
57 
58 #ifdef _OPENMP
59 #include <omp.h>
60 #endif
61 
62 bool SortDoubleDoublePairFirst(const std::pair<double, double>& left, const std::pair<double, double>& right);
63 
64 namespace OpenMS
65 {
66 
89  class OPENMS_DLLAPI MRMFeatureFinderScoring :
90  public DefaultParamHandler,
91  public ProgressLogger
92  {
93 
94 public:
96 
97 
98  // All the filters expect MSSpectrum<PeakT>, thus we give it an "MSSpectrum"
99  // but filled with Chromatogram Peaks.
100 
101  // this is the type in which we store the chromatograms for this analysis
108  // a transition group holds the MSSpectra with the Chromatogram peaks from above
110  typedef std::map<String, MRMTransitionGroupType> TransitionGroupMapType;
112 
115 
118 
120 
121 
134  void pickExperiment(MSExperiment<Peak1D> & chromatograms, FeatureMap& output, TargetedExperiment& transition_exp,
136 
151  void pickExperiment(OpenSwath::SpectrumAccessPtr input, FeatureMap& output, OpenSwath::LightTargetedExperiment& transition_exp,
152  TransformationDescription trafo, OpenSwath::SpectrumAccessPtr swath_map, TransitionGroupMapType& transition_group_map);
153 
161  void prepareProteinPeptideMaps_(OpenSwath::LightTargetedExperiment& transition_exp);
163 
180  void scorePeakgroups(MRMTransitionGroupType& transition_group, TransformationDescription & trafo,
181  OpenSwath::SpectrumAccessPtr swath_map, FeatureMap& output);
182 
185  void setStrictFlag(bool f)
186  {
187  strict_ = f;
188  }
189 
200  {
201  ms1_map_ = ms1_map;
202  }
203 
219  void mapExperimentToTransitionList(OpenSwath::SpectrumAccessPtr input, OpenSwath::LightTargetedExperiment& transition_exp,
220  TransitionGroupMapType& transition_group_map, TransformationDescription trafo, double rt_extraction_window);
221 private:
222 
224  void updateMembers_();
225 
226  // parameters
231  bool strict_;
232 
233  // scoring parameters
237 
238  // members
239  std::map<OpenMS::String, const PeptideType*> PeptideRefMap_;
243 
244  // data
246 
247  };
248 }
249 
250 #undef run_identifier
251 #endif // OPENMS_ANALYSIS_OPENSWATH_MRMFEATUREFINDERSCORING_H
252 
double spacing_for_spectra_resampling_
Definition: MRMFeatureFinderScoring.h:236
OpenSwath::LightPeptide PeptideType
Definition: MRMFeatureFinderScoring.h:105
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/ANALYSIS/OPENSWATH/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:90
Scoring of an elution peak using an exponentially modified gaussian distribution model.
Definition: EmgScoring.h:60
MRMTransitionGroup< MSSpectrum< ChromatogramPeak >, TransitionType > MRMTransitionGroupType
Definition: MRMFeatureFinderScoring.h:109
OpenMS::DIAScoring diascoring_
Definition: MRMFeatureFinderScoring.h:241
A container for features.
Definition: FeatureMap.h:93
OpenSwath::LightTransition TransitionType
Definition: MRMFeatureFinderScoring.h:103
The MRMFeatureFinder finds and scores peaks of transitions that co-elute.
Definition: MRMFeatureFinderScoring.h:89
bool write_convex_hull_
Definition: MRMFeatureFinderScoring.h:230
int add_up_spectra_
Definition: MRMFeatureFinderScoring.h:235
std::map< String, MRMTransitionGroupType > TransitionGroupMapType
Definition: MRMFeatureFinderScoring.h:110
double rt_extraction_window_
Definition: MRMFeatureFinderScoring.h:227
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
void setMS1Map(OpenSwath::SpectrumAccessPtr ms1_map)
Add an MS1 map containing spectra.
Definition: MRMFeatureFinderScoring.h:199
OpenMS::EmgScoring emgscoring_
Definition: MRMFeatureFinderScoring.h:242
The representation of a transition group that has information about the individual chromatograms as w...
Definition: MRMTransitionGroup.h:56
int stop_report_after_feature_
Definition: MRMFeatureFinderScoring.h:229
OpenSwath::LightProtein ProteinType
Definition: MRMFeatureFinderScoring.h:106
Definition: TransitionExperiment.h:155
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenSwath::SpectrumAccessPtr ms1_map_
Definition: MRMFeatureFinderScoring.h:245
Scoring of an spectrum at the peak apex of an chromatographic elution peak.
Definition: DIAScoring.h:82
double quantification_cutoff_
Definition: MRMFeatureFinderScoring.h:228
std::map< OpenMS::String, const PeptideType * > PeptideRefMap_
Definition: MRMFeatureFinderScoring.h:239
void setStrictFlag(bool f)
Set the flag for strict mapping.
Definition: MRMFeatureFinderScoring.h:185
Definition: TransitionExperiment.h:47
A structure to store which scores should be used by the Algorithm.
Definition: OpenSwathScoring.h:57
OpenSwath::LightTargetedExperiment TargetedExpType
Definition: MRMFeatureFinderScoring.h:104
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
bool SortDoubleDoublePairFirst(const std::pair< double, double > &left, const std::pair< double, double > &right)
OpenSwath::LightModification ModificationType
Definition: MRMFeatureFinderScoring.h:107
double rt_normalization_factor_
Definition: MRMFeatureFinderScoring.h:234
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:58
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Definition: TransitionExperiment.h:173
Definition: TransitionExperiment.h:179
OpenSwath_Scores_Usage su_
Definition: MRMFeatureFinderScoring.h:240
MSSpectrum< ChromatogramPeak > RichPeakChromatogram
Type definitions.
Definition: MRMFeatureFinderScoring.h:102
bool strict_
Definition: MRMFeatureFinderScoring.h:231
Definition: TransitionExperiment.h:149

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:49 using doxygen 1.8.9.1