OpenMS
SearchEngineBase.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
39 
40 
41 namespace OpenMS
42 {
43 
54  class OPENMS_DLLAPI SearchEngineBase : public TOPPBase
55  {
56  public:
58  SearchEngineBase() = delete;
59 
62 
75  SearchEngineBase(const String& name, const String& description, bool official = true, const std::vector<Citation>& citations = {}, bool toolhandler_test = true);
76 
78  ~SearchEngineBase() override;
79 
94  String getRawfileName(int ms_level = 2) const;
95 
96 
105  String getDBFilename(const String& db = "") const;
106 
107 
113  virtual void registerPeptideIndexingParameter_(Param peptide_indexing_parameter);
114 
119  std::vector<ProteinIdentification>& protein_identifications,
120  std::vector<PeptideIdentification>& peptide_identifications) const;
121  }; // end SearchEngineBase
122 
123 } // end NS OpenMS
Management and storage of parameters / INI files.
Definition: Param.h:70
Base class for Search Engine Adapters.
Definition: SearchEngineBase.h:55
String getDBFilename(const String &db="") const
Reads the '-database' argument from internal parameters (or from db) and tries to find the db in sear...
String getRawfileName(int ms_level=2) const
Reads the '-in' argument from internal parameters (usually an mzML file) and checks if MS2 spectra ar...
SearchEngineBase(const SearchEngineBase &)=delete
No default copy constructor.
SearchEngineBase(const String &name, const String &description, bool official=true, const std::vector< Citation > &citations={}, bool toolhandler_test=true)
Constructor.
virtual SearchEngineBase::ExitCodes reindex_(std::vector< ProteinIdentification > &protein_identifications, std::vector< PeptideIdentification > &peptide_identifications) const
Reindex peptide to protein association.
~SearchEngineBase() override
Destructor.
virtual void registerPeptideIndexingParameter_(Param peptide_indexing_parameter)
Adds option to reassociate peptides with proteins (and annotate target/decoy information)
SearchEngineBase()=delete
No default constructor.
A more convenient string class.
Definition: String.h:60
Base class for TOPP applications.
Definition: TOPPBase.h:148
ExitCodes
Exit codes.
Definition: TOPPBase.h:153
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48