OpenMS
PepNovoInfile.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: Timo Sachsenberg $
6 // $Authors: $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
13 #include <OpenMS/FORMAT/TextFile.h>
14 
15 #include <map>
16 
17 
18 namespace OpenMS
19 {
27  class OPENMS_DLLAPI PepNovoInfile
28  {
29 public:
32 
34  PepNovoInfile(const PepNovoInfile & pepnovo_infile);
35 
37  virtual ~PepNovoInfile();
38 
40  PepNovoInfile & operator=(const PepNovoInfile & pepnovo_infile);
41 
43  bool operator==(const PepNovoInfile & pepnovo_infile) const;
44 
50  void store(const String & filename);
51 
57  void setModifications(const StringList & fixed_mods, const StringList & variable_mods);
58 
65  void getModifications(std::map<String, String> & modification_key_map) const;
66 
67 private:
69  std::map<String, String> mods_and_keys_;
71 
72 
78  String handlePTMs_(const String & modification, const bool variable);
79  };
80 
81 } // namespace OpenMS
82 
Representation of a set of modification definitions.
Definition: ModificationDefinitionsSet.h:33
PepNovo input file adapter.
Definition: PepNovoInfile.h:28
PepNovoInfile & operator=(const PepNovoInfile &pepnovo_infile)
assignment operator
PepNovoInfile(const PepNovoInfile &pepnovo_infile)
copy constructor
ModificationDefinitionsSet mods_
Definition: PepNovoInfile.h:68
void getModifications(std::map< String, String > &modification_key_map) const
return the modifications.
TextFile ptm_file_
Definition: PepNovoInfile.h:70
void store(const String &filename)
PepNovoInfile()
default constructor
void setModifications(const StringList &fixed_mods, const StringList &variable_mods)
generates the PepNovo Infile for given fixed and variable modifications *
String handlePTMs_(const String &modification, const bool variable)
virtual ~PepNovoInfile()
destructor
bool operator==(const PepNovoInfile &pepnovo_infile) const
equality operator
std::map< String, String > mods_and_keys_
Definition: PepNovoInfile.h:69
A more convenient string class.
Definition: String.h:34
This class provides some basic file handling methods for text files.
Definition: TextFile.h:21
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22