OpenMS  3.0.0
DeNovoAlgorithm.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Sandro Andreotti, Andreas Bertsch$
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34 
35 #pragma once
36 
39 
40 namespace OpenMS
41 {
42  class PeptideIdentification;
43 
51  class OPENMS_DLLAPI DeNovoAlgorithm :
52  public DefaultParamHandler
53  {
54 public:
55 
61 
63  ~DeNovoAlgorithm() override;
64 
66  DeNovoAlgorithm(const DeNovoAlgorithm & rhs);
68 
70  DeNovoAlgorithm & operator=(const DeNovoAlgorithm & rhs);
71 
72  virtual void generateCandidates(std::vector<PeptideIdentification> & candidates, const std::vector<std::vector<DeNovoIonScoring::IonScore> > & ion_scores, const PeakMap & exp) = 0;
73 
74  virtual void generateCandidates(PeptideIdentification & candidates, std::vector<DeNovoIonScoring::IonScore> & ion_scores, const PeakSpectrum & spec) = 0;
75 
76  };
77 
78 } // namespace OpenMS
79 
DefaultParamHandler.h
OpenMS::ProgressLogger::setProgress
void setProgress(SignedSize value) const
Sets the current progress.
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:147
Size
double
OpenMS::MSExperiment::sortSpectra
void sortSpectra(bool sort_mz=true)
Sorts the data points by retention time.
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:57
OpenMS::String
A more convenient string class.
Definition: String.h:58
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::DeNovoAlgorithm
Base class for ion scoring implementation for de novo algorithms.
Definition: DeNovoAlgorithm.h:51
OpenMS::ProgressLogger::startProgress
void startProgress(SignedSize begin, SignedSize end, const String &label) const
Initializes the progress display.
OpenMS::ProgressLogger::endProgress
void endProgress() const
Ends the progress display.
OpenMS::MSExperiment::size
Size size() const
Definition: MSExperiment.h:120
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
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...
DeNovoIonScoring.h
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:71
MSExperiment.h
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:63
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h