OpenMS
SeedListGenerator.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Hendrik Weisser $
6 // $Authors: Hendrik Weisser $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
17 
18 #include <vector>
19 
20 namespace OpenMS
21 {
29  class OPENMS_DLLAPI SeedListGenerator
30  {
31 public:
32 
34  typedef std::vector<DPosition<2> > SeedList;
35 
36 
39 
40 
46  void generateSeedList(const PeakMap & experiment, SeedList & seeds);
47 
48 
56  void generateSeedList(std::vector<PeptideIdentification> & peptides,
57  SeedList & seeds, bool use_peptide_mass = false);
58 
59 
68  void generateSeedLists(const ConsensusMap & consensus,
69  std::map<UInt64, SeedList> & seed_lists);
70 
71 
73  void convertSeedList(const SeedList & seeds, FeatureMap & features);
74 
75 
77  void convertSeedList(const FeatureMap & features, SeedList & seeds);
78 
79  };
80 
81 }
82 
A container for consensus elements.
Definition: ConsensusMap.h:66
A container for features.
Definition: FeatureMap.h:80
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
Generate seed lists for feature detection.
Definition: SeedListGenerator.h:30
std::vector< DPosition< 2 > > SeedList
List of seed positions.
Definition: SeedListGenerator.h:34
void convertSeedList(const SeedList &seeds, FeatureMap &features)
Convert a list of seed positions to a feature map (expected format for FeatureFinder)
void generateSeedList(std::vector< PeptideIdentification > &peptides, SeedList &seeds, bool use_peptide_mass=false)
Generate a seed list based on a list of peptide identifications.
void generateSeedLists(const ConsensusMap &consensus, std::map< UInt64, SeedList > &seed_lists)
Generate seed lists based on a consensus map.
void convertSeedList(const FeatureMap &features, SeedList &seeds)
Convert a feature map with seed positions back to a simple list.
SeedListGenerator()
Default constructor.
void generateSeedList(const PeakMap &experiment, SeedList &seeds)
Generate a seed list based on an MS experiment.
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19