OpenMS  3.0.0
SeedListGenerator.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
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34 
35 #pragma once
36 
43 
44 #include <vector>
45 
46 namespace OpenMS
47 {
55  class OPENMS_DLLAPI SeedListGenerator
56  {
57 public:
58 
60  typedef std::vector<DPosition<2> > SeedList;
61 
62 
65 
66 
72  void generateSeedList(const PeakMap & experiment, SeedList & seeds);
73 
74 
82  void generateSeedList(std::vector<PeptideIdentification> & peptides,
83  SeedList & seeds, bool use_peptide_mass = false);
84 
85 
94  void generateSeedLists(const ConsensusMap & consensus,
95  std::map<UInt64, SeedList> & seed_lists);
96 
97 
99  void convertSeedList(const SeedList & seeds, FeatureMap & features);
100 
101 
103  void convertSeedList(const FeatureMap & features, SeedList & seeds);
104 
105  };
106 
107 }
108 
OpenMS::FileTypes::IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:64
ConsensusXMLFile.h
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
FileHandler.h
FileTypes.h
Size
SeedListGenerator.h
DPosition.h
OpenMS::DataProcessing::DATA_PROCESSING
General data processing (if no other term applies)
Definition: DataProcessing.h:60
OpenMS::FileTypes::MZML
MzML file (.mzML)
Definition: FileTypes.h:70
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
ConsensusMap.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::FileTypes::CONSENSUSXML
OpenMS consensus map format (.consensusXML)
Definition: FileTypes.h:65
IdXMLFile.h
FeatureXMLFile.h
OpenMS::SeedListGenerator::convertSeedList
void convertSeedList(const SeedList &seeds, FeatureMap &features)
Convert a list of seed positions to a feature map (expected format for FeatureFinder)
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::SeedListGenerator::generateSeedLists
void generateSeedLists(const ConsensusMap &consensus, std::map< UInt64, SeedList > &seed_lists)
Generate seed lists based on a consensus map.
OpenMS::FileTypes::FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:63
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
FeatureMap.h
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:56
OpenMS::FileHandler::getType
static FileTypes::Type getType(const String &filename)
Tries to determine the file type (by name or content)
OpenMS::SeedListGenerator::generateSeedList
void generateSeedList(const PeakMap &experiment, SeedList &seeds)
Generate a seed list based on an MS experiment.
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
OpenMS::FeatureMap::getUnassignedPeptideIdentifications
const std::vector< PeptideIdentification > & getUnassignedPeptideIdentifications() const
non-mutable access to the unassigned peptide identifications
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::FeatureXMLFile::store
void store(const String &filename, const FeatureMap &feature_map)
stores the map feature_map in file with name filename.
OpenMS::ConsensusXMLFile::load
void load(const String &filename, ConsensusMap &map)
Loads a consensus map from file and calls updateRanges.
SVOutStream.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
OpenMS::ConsensusMap::getColumnHeaders
const ColumnHeaders & getColumnHeaders() const
Non-mutable access to the file descriptions.
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::SeedListGenerator
Generate seed lists for feature detection.
Definition: SeedListGenerator.h:55
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:62
OpenMS::SeedListGenerator::SeedList
std::vector< DPosition< 2 > > SeedList
List of seed positions.
Definition: SeedListGenerator.h:60
OPENMS_LOG_INFO
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:465
PeptideIdentification.h
StandardTypes.h
File.h
TOPPBase.h
OpenMS::ConsensusXMLFile
This class provides Input functionality for ConsensusMaps and Output functionality for alignments and...
Definition: ConsensusXMLFile.h:58
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:68
OpenMS::ConsensusMap::ColumnHeaders
std::map< UInt64, ColumnHeader > ColumnHeaders
Definition: ConsensusMap.h:164