OpenMS  2.6.0
MRMDecoy.h
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31 // $Maintainer: George Rosenberger $
32 // $Authors: George Rosenberger, Hannes Roest $
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34 
35 #pragma once
36 
41 
42 #include <boost/algorithm/string.hpp>
43 #include <boost/lexical_cast.hpp>
44 #include <boost/assign.hpp>
45 #include <boost/random/mersenne_twister.hpp>
46 #include <boost/random/uniform_int.hpp>
47 #include <boost/random/variate_generator.hpp>
48 #include <boost/unordered_map.hpp>
49 
50 #include <string>
51 #include <vector>
52 #include <map>
53 #include <utility> // for pair
54 
55 // #define DEBUG_MRMDECOY
56 
57 namespace OpenMS
58 {
88  class OPENMS_DLLAPI MRMDecoy :
89  public DefaultParamHandler,
90  public ProgressLogger
91  {
92 
93 public:
94 
95  typedef std::vector<size_t> IndexType;
96 
97  MRMDecoy();
98 
121  void generateDecoys(const OpenMS::TargetedExperiment& exp,
123  const String& method,
124  const double aim_decoy_fraction,
125  const bool switchKR,
126  const String& decoy_tag,
127  const int max_attempts,
128  const double identity_threshold,
129  const double precursor_mz_shift,
130  const double product_mz_shift,
131  const double product_mz_threshold,
132  const std::vector<String>& fragment_types,
133  const std::vector<size_t>& fragment_charges,
134  const bool enable_specific_losses,
135  const bool enable_unspecific_losses,
136  const int round_decPow = -4) const;
137 
138  typedef std::vector<OpenMS::TargetedExperiment::Protein> ProteinVectorType;
139  typedef std::vector<OpenMS::TargetedExperiment::Peptide> PeptideVectorType;
140  typedef std::vector<OpenMS::ReactionMonitoringTransition> TransitionVectorType;
141 
142  typedef std::map<String, std::vector<const ReactionMonitoringTransition*> > PeptideTransitionMapType;
143 
148  float AASequenceIdentity(const String& sequence, const String& decoy) const;
149 
159  const double identity_threshold,
160  int seed = -1,
161  const int max_attempts = 100) const;
162 
171  static OpenMS::TargetedExperiment::Peptide reversePeptide(
173  const bool keepN,
174  const bool keepC,
175  const String& const_pattern = String());
176 
185  static IndexType findFixedResidues(const std::string& sequence,
186  bool keepN, bool keepC, const OpenMS::String& keep_const_pattern);
187 
188 protected:
189 
193  bool hasCNterminalMods_(const OpenMS::TargetedExperiment::Peptide& peptide, bool checkCterminalAA) const;
194 
200  IndexType findFixedResidues_(const std::string& sequence) const;
201 
207  IndexType findFixedAndTermResidues_(const std::string& sequence) const;
208 
215  OpenMS::TargetedExperiment::Peptide pseudoreversePeptide_(
216  const OpenMS::TargetedExperiment::Peptide& peptide) const;
217 
223  OpenMS::TargetedExperiment::Peptide reversePeptide_(
224  const OpenMS::TargetedExperiment::Peptide& peptide) const;
225 
227  void updateMembers_() override;
228 
230  bool keepN_;
231  bool keepC_;
232  };
233 }
234 
DefaultParamHandler.h
TargetedExperiment.h
OpenMS::MRMDecoy::keep_const_pattern_
String keep_const_pattern_
Definition: MRMDecoy.h:229
OpenMS::MRMDecoy::IndexType
std::vector< size_t > IndexType
Definition: MRMDecoy.h:95
OpenMS::TargetedExperimentHelper::Peptide
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
OpenMS::MRMDecoy::ProteinVectorType
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMDecoy.h:138
OpenMS::String
A more convenient string class.
Definition: String.h:59
OpenMS::MRMDecoy
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.
Definition: MRMDecoy.h:88
OpenMS::MRMDecoy::TransitionVectorType
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMDecoy.h:140
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
ProgressLogger.h
MRMIonSeries.h
OpenMS::MRMDecoy::keepC_
bool keepC_
Definition: MRMDecoy.h:231
OpenMS::MRMDecoy::PeptideTransitionMapType
std::map< String, std::vector< const ReactionMonitoringTransition * > > PeptideTransitionMapType
Definition: MRMDecoy.h:142
OpenMS::MRMDecoy::keepN_
bool keepN_
Definition: MRMDecoy.h:230
OpenMS::TargetedExperiment
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
OpenMS::MRMDecoy::PeptideVectorType
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMDecoy.h:139