OpenMS
SearchEngineBase.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Chris Bielow $
6 // $Authors: Chris Bielow $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
13 
14 
15 namespace OpenMS
16 {
17 
28  class OPENMS_DLLAPI SearchEngineBase : public TOPPBase
29  {
30  public:
32  SearchEngineBase() = delete;
33 
36 
49  SearchEngineBase(const String& name, const String& description, bool official = true, const std::vector<Citation>& citations = {}, bool toolhandler_test = true);
50 
52  ~SearchEngineBase() override;
53 
68  String getRawfileName(int ms_level = 2) const;
69 
70 
79  String getDBFilename(const String& db = "") const;
80 
81 
87  virtual void registerPeptideIndexingParameter_(Param peptide_indexing_parameter);
88 
93  std::vector<ProteinIdentification>& protein_identifications,
94  std::vector<PeptideIdentification>& peptide_identifications) const;
95  }; // end SearchEngineBase
96 
97 } // end NS OpenMS
Management and storage of parameters / INI files.
Definition: Param.h:44
Base class for Search Engine Adapters.
Definition: SearchEngineBase.h:29
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:34
Base class for TOPP applications.
Definition: TOPPBase.h:122
ExitCodes
Exit codes.
Definition: TOPPBase.h:127
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22