OpenMS  3.0.0
PrecursorIonSelectionPreprocessing.h
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35 
36 #pragma once
37 
42 
43 #include <set>
44 namespace OpenMS
45 {
46 
52  class OPENMS_DLLAPI PrecursorIonSelectionPreprocessing :
53  public DefaultParamHandler
54  {
55 public:
59 
61 
62  const std::map<String, std::vector<double> > & getProtMasses() const;
63 
64  const std::vector<double> & getMasses(String acc) const;
65 
66  const std::map<String, std::vector<double> > & getProteinRTMap() const;
67  const std::map<String, std::vector<double> > & getProteinPTMap() const;
68  const std::map<String, std::vector<String> > & getProteinPeptideSequenceMap() const;
69 
70 
80  void dbPreprocessing(String db_path, bool save = true);
81 
93  void dbPreprocessing(String db_path, String rt_model_path, String dt_model_path, bool save = true);
94 
95 
103  void loadPreprocessing();
104 
106  double getWeight(double mass);
107 
108  double getRT(String prot_id, Size peptide_index);
109 
110  double getPT(String prot_id, Size peptide_index);
111 
112  void setFixedModifications(StringList & modifications);
113  const std::map<char, std::vector<String> > & getFixedModifications()
114  {
115  return fixed_modifications_;
116  }
117 
118  void setGaussianParameters(double mu, double sigma);
119  double getGaussMu() const
120  {
121  return mu_;
122  }
123 
124  double getGaussSigma() const
125  {
126  return sigma_;
127  }
128 
129  double getRTProbability(String prot_id, Size peptide_index, Feature & feature);
130  double getRTProbability(double pred_rt, Feature & feature);
131 
132 protected:
134  void savePreprocessedDB_(String db_path, String path);
135  void savePreprocessedDBWithRT_(String db_path, String path);
137  void loadPreprocessedDB_(String path);
139  void filterTaxonomyIdentifier_(FASTAFile::FASTAEntry & entry);
140  Int getScanNumber_(double rt);
141  double getRTProbability_(double min_obs_rt, double max_obs_rt, double pred_rt);
143  void updateMembers_() override;
144 
146  std::vector<double> masses_;
148  std::set<AASequence> sequences_;
150  std::map<String, std::vector<double> > prot_masses_;
152  std::vector<double> bin_masses_;
154  std::vector<UInt> counter_;
157 
159  std::map<String, std::vector<double> > rt_prot_map_;
160  std::map<String, std::vector<double> > pt_prot_map_;
161  std::map<String, std::vector<String> > prot_peptide_seq_map_;
162  std::map<char, std::vector<String> > fixed_modifications_;
163  double sigma_;
164  double mu_;
165 
166 
167  };
168 }
169 
DefaultParamHandler.h
OpenMS::PrecursorIonSelectionPreprocessing::getFixedModifications
const std::map< char, std::vector< String > > & getFixedModifications()
Definition: PrecursorIonSelectionPreprocessing.h:113
OpenMS::PrecursorIonSelectionPreprocessing::sigma_
double sigma_
Definition: PrecursorIonSelectionPreprocessing.h:163
OpenMS::PrecursorIonSelectionPreprocessing::rt_prot_map_
std::map< String, std::vector< double > > rt_prot_map_
Definition: PrecursorIonSelectionPreprocessing.h:159
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::PrecursorIonSelectionPreprocessing::fixed_mods_
bool fixed_mods_
Definition: PrecursorIonSelectionPreprocessing.h:158
OpenMS::FASTAFile::FASTAEntry
FASTA entry type (identifier, description and sequence) The first String corresponds to the identifie...
Definition: FASTAFile.h:71
OpenMS::PrecursorIonSelectionPreprocessing::sequences_
std::set< AASequence > sequences_
the sequences of the tryptic peptides
Definition: PrecursorIonSelectionPreprocessing.h:148
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::PrecursorIonSelectionPreprocessing::mu_
double mu_
Definition: PrecursorIonSelectionPreprocessing.h:164
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS::PrecursorIonSelectionPreprocessing::counter_
std::vector< UInt > counter_
counter for the bins
Definition: PrecursorIonSelectionPreprocessing.h:154
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
FASTAFile.h
FeatureMap.h
OpenMS::PrecursorIonSelectionPreprocessing::prot_peptide_seq_map_
std::map< String, std::vector< String > > prot_peptide_seq_map_
Definition: PrecursorIonSelectionPreprocessing.h:161
OpenMS::PrecursorIonSelectionPreprocessing::masses_
std::vector< double > masses_
all tryptic masses of the distinct peptides in the database
Definition: PrecursorIonSelectionPreprocessing.h:146
OpenMS::StringList
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
AASequence.h
OpenMS::PrecursorIonSelectionPreprocessing::bin_masses_
std::vector< double > bin_masses_
the masses of the bins used for preprocessing (only used if bins are not equidistant,...
Definition: PrecursorIonSelectionPreprocessing.h:152
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::PrecursorIonSelectionPreprocessing::prot_masses_
std::map< String, std::vector< double > > prot_masses_
stores masses of tryptic peptides for proteins, key is the accession number
Definition: PrecursorIonSelectionPreprocessing.h:150
OpenMS::PrecursorIonSelectionPreprocessing::pt_prot_map_
std::map< String, std::vector< double > > pt_prot_map_
Definition: PrecursorIonSelectionPreprocessing.h:160
OpenMS::PrecursorIonSelectionPreprocessing::f_max_
UInt f_max_
maximal relative frequency of a mass
Definition: PrecursorIonSelectionPreprocessing.h:156
OpenMS::PrecursorIonSelectionPreprocessing
This class implements the database preprocessing needing for precursor ion selection.
Definition: PrecursorIonSelectionPreprocessing.h:52
OpenMS::PrecursorIonSelectionPreprocessing::fixed_modifications_
std::map< char, std::vector< String > > fixed_modifications_
Definition: PrecursorIonSelectionPreprocessing.h:162
OpenMS::PrecursorIonSelectionPreprocessing::getGaussSigma
double getGaussSigma() const
Definition: PrecursorIonSelectionPreprocessing.h:124
OpenMS::PrecursorIonSelectionPreprocessing::getGaussMu
double getGaussMu() const
Definition: PrecursorIonSelectionPreprocessing.h:119