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DIAPrescoring.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Witold Wolski $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <algorithm>
38 #include <iterator>
39 #include <boost/bind.hpp>
40 #include <boost/lexical_cast.hpp>
41
42 #include <OpenMS/OPENSWATHALGO/DATAACCESS/DataFrameWriter.h>
43 #include <OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h>
44 #include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
45
46 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
47
48 namespace OpenMS
49 {
64 class OPENMS_DLLAPI DiaPrescore :
65 public DefaultParamHandler
66 {
67 double dia_extract_window_; //done
68 int nr_isotopes_;
69 int nr_charges_;
70 public:
71
72 DiaPrescore();
73
74 DiaPrescore(double dia_extract_window, int nr_isotopes = 4, int nr_charges = 4);
75
76 void defineDefaults();
77
78 void updateMembers_() override;
79
87 void score(OpenSwath::SpectrumPtr spec,
88 const std::vector<OpenSwath::LightTransition>& lt,
89 double& dotprod,
90 double& manhattan);
91
96 void operator()(OpenSwath::SpectrumAccessPtr swath_ptr,
97 OpenSwath::LightTargetedExperiment& transition_exp_used,
98 OpenSwath::IDataFrameWriter* ivw);
99 };
100
101
102 }
103
DataFrameWriter.h
OpenMS::DiaPrescore::nr_charges_
int nr_charges_
Definition: DIAPrescoring.h:69
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenSwath::SpectrumAccessPtr
boost::shared_ptr< ISpectrumAccess > SpectrumAccessPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:89
OpenMS::DiaPrescore::dia_extract_window_
double dia_extract_window_
Definition: DIAPrescoring.h:67
OpenMS::DiaPrescore
Scoring of an spectrum given library intensities of a transition group.
Definition: DIAPrescoring.h:64
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
DefaultParamHandler.h
OpenSwath::LightTargetedExperiment
Definition: TransitionExperiment.h:207
OpenSwath::SpectrumPtr
boost::shared_ptr< Spectrum > SpectrumPtr
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/DataStructures.h:292
OpenSwath::IDataFrameWriter
Definition: DataFrameWriter.h:45
OpenMS::DiaPrescore::nr_isotopes_
int nr_isotopes_
Definition: DIAPrescoring.h:68
TransitionExperiment.h
ISpectrumAccess.h