OpenMS
DecoyGenerator.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Timo Sachsenberg $
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34 
35 #pragma once
36 
37 #include <OpenMS/CONCEPT/Types.h>
39 
40 namespace OpenMS
41 {
42  class AASequence;
43  class DigestionEnzymeProtein;
44 
48  class OPENMS_DLLAPI DecoyGenerator
49  {
50  public:
51  // initializes random generator
53 
54  // destructor
55  ~DecoyGenerator() = default;
56 
57  // random seed for shuffling
58  void setSeed(UInt64 seed);
59 
60  /*
61  @brief reverses the protein sequence.
62  note: modifications are discarded
63  */
64  AASequence reverseProtein(const AASequence& protein) const;
65 
66  /*
67  @brief reverses the protein's peptide sequences between enzymatic cutting positions.
68  note: modifications are discarded
69  */
70  AASequence reversePeptides(const AASequence& protein, const String& protease) const;
71 
72  /*
73  @brief shuffle the protein's peptide sequences between enzymatic cutting positions.
74  each peptide is shuffled @param max_attempts times to minimize sequence identity.
75  note: modifications are discarded
76  */
78  const AASequence& aas,
79  const String& protease,
80  const int max_attempts = 100
81  );
82 
83  private:
84  // sequence identity by matching AAs
85  static double SequenceIdentity_(const String& decoy, const String& target);
86 
87  // portable shuffle
89  };
90 }
91 
Representation of a peptide/protein sequence.
Definition: AASequence.h:112
Methods to generate isobaric decoy sequences for DDA target-decoy searches.
Definition: DecoyGenerator.h:49
void setSeed(UInt64 seed)
static double SequenceIdentity_(const String &decoy, const String &target)
AASequence shufflePeptides(const AASequence &aas, const String &protease, const int max_attempts=100)
Math::RandomShuffler shuffler_
Definition: DecoyGenerator.h:88
AASequence reverseProtein(const AASequence &protein) const
AASequence reversePeptides(const AASequence &protein, const String &protease) const
Definition: MathFunctions.h:408
A more convenient string class.
Definition: String.h:60
OPENMS_UINT64_TYPE UInt64
Unsigned integer type (64bit)
Definition: Types.h:77
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48