| OpenMS 2.5.0

SONARScoring.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
38 #include <OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h>
39 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ITransition.h>
40 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
41
42 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
43
44 #include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScoring.h>
45
46 namespace OpenMS
47 {
54 class OPENMS_DLLAPI SONARScoring :
55 public DefaultParamHandler
56 {
57 public:
58
60
61 SONARScoring();
63
65 ~SONARScoring() override {}
67 //
68
69 void computeSonarScores(OpenSwath::IMRMFeature* imrmfeature,
70 const std::vector<OpenSwath::LightTransition> & transitions,
71 const std::vector<OpenSwath::SwathMap>& swath_maps,
72 OpenSwath_Scores & scores);
73
74 private:
75
76 void computeXCorr_(std::vector<std::vector<double> >& sonar_profiles,
77 double& xcorr_coelution_score, double& xcorr_shape_score);
78
80 SONARScoring(const SONARScoring& rhs);
81
83 SONARScoring& operator=(const SONARScoring& rhs);
84
86 void updateMembers_() override;
87
88 double dia_extract_window_;
89 bool dia_centroided_;
90 bool dia_extraction_ppm_;
91
92 };
93 }
94
95
DataStructures.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenSwath::IMRMFeature
Definition: ITransition.h:56
OpenMS::SONARScoring
Scoring of an spectrum using SONAR data.
Definition: SONARScoring.h:54
OpenMS::SONARScoring::~SONARScoring
~SONARScoring() override
Destructor.
Definition: SONARScoring.h:65
OpenMS::SONARScoring::dia_extraction_ppm_
bool dia_extraction_ppm_
Definition: SONARScoring.h:90
OpenMS::SONARScoring::dia_extract_window_
double dia_extract_window_
Definition: SONARScoring.h:88
OpenSwathScoring.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::SONARScoring::dia_centroided_
bool dia_centroided_
Definition: SONARScoring.h:89
DefaultParamHandler.h
OpenMS::OpenSwath_Scores
A structure to hold the different scores computed by OpenSWATH.
Definition: OpenSwathScores.h:80
TransitionExperiment.h
ISpectrumAccess.h
ITransition.h