| OpenMS 2.5.0

SeedListGenerator.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: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/StandardTypes.h>
38 #include <OpenMS/DATASTRUCTURES/DPosition.h>
39 #include <OpenMS/DATASTRUCTURES/Map.h>
40 #include <OpenMS/KERNEL/MSExperiment.h>
41 #include <OpenMS/KERNEL/ConsensusMap.h>
42 #include <OpenMS/KERNEL/FeatureMap.h>
43 #include <OpenMS/METADATA/PeptideIdentification.h>
44
45 #include <vector>
46
47 namespace OpenMS
48 {
56 class OPENMS_DLLAPI SeedListGenerator
57 {
58 public:
59
61 typedef std::vector<DPosition<2> > SeedList;
62
63
65 SeedListGenerator();
66
67
73 void generateSeedList(const PeakMap & experiment, SeedList & seeds);
74
75
83 void generateSeedList(std::vector<PeptideIdentification> & peptides,
84 SeedList & seeds, bool use_peptide_mass = false);
85
86
95 void generateSeedLists(const ConsensusMap & consensus,
96 Map<UInt64, SeedList> & seed_lists);
97
98
100 void convertSeedList(const SeedList & seeds, FeatureMap & features);
101
102
104 void convertSeedList(const FeatureMap & features, SeedList & seeds);
105
106 };
107
108 }
109
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
StandardTypes.h
ConsensusMap.h
FeatureMap.h
OpenMS::SeedListGenerator
Generate seed lists for feature detection.
Definition: SeedListGenerator.h:56
OpenMS::Map
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
DPosition.h
PeptideIdentification.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
Map.h
OpenMS::SeedListGenerator::SeedList
std::vector< DPosition< 2 > > SeedList
List of seed positions.
Definition: SeedListGenerator.h:61
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79