OpenMS  3.0.0
CompNovoIdentificationBase.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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34 
35 
36 #pragma once
37 
38 // OpenMS includes
45 
46 // stl includes
47 #include <vector>
48 #include <map>
49 
50 namespace OpenMS
51 {
57  class OPENMS_DLLAPI CompNovoIdentificationBase :
58  public DefaultParamHandler
59  {
60 
61 public:
62 
68 
71 
73  ~CompNovoIdentificationBase() override;
75 
77  CompNovoIdentificationBase & operator=(const CompNovoIdentificationBase & source);
78 
82  virtual void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp) = 0;
85 
87 
88 protected:
89 
91  void updateMembers_() override;
92 
94  void filterPermuts_(std::set<String> & permut) const;
95 
97  void selectPivotIons_(std::vector<Size> & pivots, Size left, Size right, std::map<double, IonScore> & CID_nodes, const PeakSpectrum & CID_orig_spec, double precursor_weight, bool full_range = false);
98 
100  void filterDecomps_(std::vector<MassDecomposition> & decomps);
101 
103  void getDecompositions_(std::vector<MassDecomposition> & decomps, double mass, bool no_caching = false);
104 
106  static void permute_(const String& prefix, String s, std::set<String> & permutations);
107 
108  Size countMissedCleavagesTryptic_(const String & peptide) const;
109 
111  void getCIDSpectrumLight_(PeakSpectrum & spec, const String & sequence, double prefix, double suffix);
112 
114  void getCIDSpectrum_(PeakSpectrum & spec, const String & sequence, Size charge, double prefix = 0.0, double suffix = 0.0);
115 
117  void getETDSpectrum_(PeakSpectrum & spec, const String &sequence, Size /* charge */, double prefix = 0.0, double suffix = 0.0);
118 
120  void initIsotopeDistributions_();
121 
123  void windowMower_(PeakSpectrum & spec, double windowsize, Size no_peaks);
124 
126  double compareSpectra_(const PeakSpectrum & s1, const PeakSpectrum & s2) const;
127 
129  AASequence getModifiedAASequence_(const String & sequence);
130 
132  String getModifiedStringFromAASequence_(const AASequence & sequence);
133 
135  std::map<char, const Residue *> name_to_residue_;
136 
138  std::map<const Residue *, char> residue_to_name_;
139 
141  std::map<char, double> aa_to_weight_;
142 
144 
145  double min_aa_weight_{};
146 
148 
149  std::map<Size, std::map<Size, std::set<String> > > subspec_to_sequences_;
150 
152 
154 
156 
158 
160 
161  double max_mz_;
162 
163  double min_mz_;
164 
166 
168 
170 
171  std::map<double, std::vector<MassDecomposition> > decomp_cache_;
172 
173  std::map<String, std::set<String> > permute_cache_;
174 
175  private:
177  std::map<Size, std::vector<double> > isotope_distributions_;
178 
179 public:
180 
186  class Permut
187  {
188 private:
189 
190  Permut() :
191  score_(0)
192  {
193  }
194 
195 public:
196 
197  Permut(const std::set<String>::const_iterator & permut, double s) :
198  permut_(permut),
199  score_(s)
200  {
201  }
202 
203  Permut(const Permut & rhs) = default;
204  virtual ~Permut() = default;
205 
206  Permut & operator=(const Permut & rhs)
207  {
208  if (&rhs != this)
209  {
210  permut_ = rhs.permut_;
211  score_ = rhs.score_;
212  }
213  return *this;
214  }
215 
216  const std::set<String>::const_iterator & getPermut() const
217  {
218  return permut_;
219  }
220 
221  void setPermut(const std::set<String>::const_iterator & it)
222  {
223  permut_ = it;
224  }
225 
226  double getScore() const
227  {
228  return score_;
229  }
230 
231  void setScore(double score)
232  {
233  score_ = score;
234  }
235 
236 protected:
237 
238  std::set<String>::const_iterator permut_;
239  double score_;
240  };
241 
242  };
243 
244  namespace Internal
245  {
247  }
248 }
249 
OpenMS::CompNovoIdentificationBase::max_subscore_number_
Size max_subscore_number_
Definition: CompNovoIdentificationBase.h:167
DefaultParamHandler.h
OpenMS::CompNovoIdentificationBase::max_number_aa_per_decomp_
Size max_number_aa_per_decomp_
Definition: CompNovoIdentificationBase.h:151
OpenMS::Internal::PermutScoreComparator
bool PermutScoreComparator(const CompNovoIdentificationBase::Permut &p1, const CompNovoIdentificationBase::Permut &p2)
OpenMS::CompNovoIdentificationBase::aa_to_weight_
std::map< char, double > aa_to_weight_
masses of the amino acids
Definition: CompNovoIdentificationBase.h:141
OpenMS::CompNovoIdentificationBase::name_to_residue_
std::map< char, const Residue * > name_to_residue_
mapping for the internal representation character to the actual residue
Definition: CompNovoIdentificationBase.h:135
OpenMS::CompNovoIdentificationBase::permute_cache_
std::map< String, std::set< String > > permute_cache_
Definition: CompNovoIdentificationBase.h:173
OpenMS::CompNovoIdentificationBase::Permut::score_
double score_
Definition: CompNovoIdentificationBase.h:239
OpenMS::StringUtils::suffix
static String suffix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:156
OpenMS::CompNovoIdentificationBase::mass_decomp_algorithm_
MassDecompositionAlgorithm mass_decomp_algorithm_
Definition: CompNovoIdentificationBase.h:143
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::ZhangSimilarityScore
Similarity score of Zhang.
Definition: ZhangSimilarityScore.h:54
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
ZhangSimilarityScore.h
OpenMS::CompNovoIdentificationBase::max_mz_
double max_mz_
Definition: CompNovoIdentificationBase.h:161
OpenMS::CompNovoIdentificationBase::Permut::permut_
std::set< String >::const_iterator permut_
Definition: CompNovoIdentificationBase.h:238
OpenMS::CompNovoIdentificationBase::Permut::getScore
double getScore() const
Definition: CompNovoIdentificationBase.h:226
MassDecomposition.h
OpenMS::CompNovoIdentificationBase::Permut
Simple class to store permutations and a score.
Definition: CompNovoIdentificationBase.h:186
OpenMS::MassDecompositionAlgorithm
Mass decomposition algorithm, given a mass it suggests possible compositions.
Definition: MassDecompositionAlgorithm.h:68
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::CompNovoIdentificationBase::tryptic_only_
bool tryptic_only_
Definition: CompNovoIdentificationBase.h:153
OpenMS::CompNovoIonScoringBase::IonScore
Definition: CompNovoIonScoringBase.h:67
OpenMS::CompNovoIdentificationBase::isotope_distributions_
std::map< Size, std::vector< double > > isotope_distributions_
Definition: CompNovoIdentificationBase.h:177
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::CompNovoIdentificationBase::Permut::getPermut
const std::set< String >::const_iterator & getPermut() const
Definition: CompNovoIdentificationBase.h:216
OpenMS::CompNovoIdentificationBase::max_decomp_weight_
double max_decomp_weight_
Definition: CompNovoIdentificationBase.h:165
OpenMS::CompNovoIdentificationBase::Permut::operator=
Permut & operator=(const Permut &rhs)
Definition: CompNovoIdentificationBase.h:206
MassDecompositionAlgorithm.h
OpenMS::CompNovoIdentificationBase::decomp_weights_precision_
double decomp_weights_precision_
Definition: CompNovoIdentificationBase.h:159
OpenMS::CompNovoIdentificationBase::decomp_cache_
std::map< double, std::vector< MassDecomposition > > decomp_cache_
Definition: CompNovoIdentificationBase.h:171
OpenMS::CompNovoIdentificationBase::fragment_mass_tolerance_
double fragment_mass_tolerance_
Definition: CompNovoIdentificationBase.h:155
OpenMS::CompNovoIdentificationBase::max_number_pivot_
Size max_number_pivot_
Definition: CompNovoIdentificationBase.h:157
OpenMS::CompNovoIdentificationBase::min_mz_
double min_mz_
Definition: CompNovoIdentificationBase.h:163
OpenMS::CompNovoIdentificationBase
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:57
CompNovoIonScoringBase.h
OpenMS::CompNovoIdentificationBase::IonScore
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentificationBase.h:86
OpenMS::CompNovoIdentificationBase::subspec_to_sequences_
std::map< Size, std::map< Size, std::set< String > > > subspec_to_sequences_
Definition: CompNovoIdentificationBase.h:149
OpenMS::CompNovoIdentificationBase::Permut::setPermut
void setPermut(const std::set< String >::const_iterator &it)
Definition: CompNovoIdentificationBase.h:221
OpenMS::CompNovoIdentificationBase::zhang_
ZhangSimilarityScore zhang_
Definition: CompNovoIdentificationBase.h:147
OpenMS::CompNovoIdentificationBase::residue_to_name_
std::map< const Residue *, char > residue_to_name_
mapping of the actual residue to the internal representing character
Definition: CompNovoIdentificationBase.h:138
OpenMS::CompNovoIdentificationBase::Permut::Permut
Permut(const std::set< String >::const_iterator &permut, double s)
Definition: CompNovoIdentificationBase.h:197
OpenMS::StringUtils::prefix
static String prefix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:147
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::CompNovoIdentificationBase::max_isotope_
Size max_isotope_
Definition: CompNovoIdentificationBase.h:169
PeptideIdentification.h
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::CompNovoIdentificationBase::Permut::Permut
Permut()
Definition: CompNovoIdentificationBase.h:190
OpenMS::CompNovoIdentificationBase::Permut::setScore
void setScore(double score)
Definition: CompNovoIdentificationBase.h:231