| OpenMS 2.5.0

PeakIntensityPredictor.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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30 // --------------------------------------------------------------------------
31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: $
33 // --------------------------------------------------------------------------
34 //
35
36 #pragma once
37
38 #include <OpenMS/CHEMISTRY/AASequence.h>
39 #include <OpenMS/ANALYSIS/PIP/LocalLinearMap.h>
40
41 namespace OpenMS
42 {
43
64 class OPENMS_DLLAPI PeakIntensityPredictor
65 {
66
67 public:
68
70
71 PeakIntensityPredictor();
74 virtual ~PeakIntensityPredictor();
76
78 double predict(const AASequence & sequence);
79
88 double predict(const AASequence & sequence, std::vector<double> & add_info);
89
91 std::vector<double> predict(const std::vector<AASequence> & sequences);
92
102 std::vector<double> predict(const std::vector<AASequence> & sequences, std::vector<std::vector<double> > & add_info);
103
104 private:
105
107 double map_(const std::vector<double> & data);
109 Size findWinner_(const std::vector<double> & data);
111 std::vector<double> calculateAddInfo_(const std::vector<double> & data);
112
138 std::vector<double> getPropertyVector_(const AASequence & sequence);
139
141 LocalLinearMap llm_;
142
144 PeakIntensityPredictor(const PeakIntensityPredictor & llmModel);
146 PeakIntensityPredictor & operator=(const PeakIntensityPredictor & peakIntensityPredictor);
147
148 };
149
150 } // namespace OpenMS
151
AASequence.h
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::LocalLinearMap
Trained Local Linear Map (LLM) model for peak intensity prediction.
Definition: LocalLinearMap.h:56
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::PeakIntensityPredictor
Predict peak heights of peptides based on Local Linear Map model.
Definition: PeakIntensityPredictor.h:64
OpenMS::PeakIntensityPredictor::llm_
LocalLinearMap llm_
Local Linear Map model.
Definition: PeakIntensityPredictor.h:141
LocalLinearMap.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127