36 #ifndef OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTIONPREPROCESSING_H 
   37 #define OPENMS_ANALYSIS_TARGETED_PRECURSORIONSELECTIONPREPROCESSING_H 
   67     const std::map<String, std::vector<DoubleReal> > & getProtMasses() 
const;
 
   70     const std::vector<DoubleReal> & getMasses(
String acc) 
const;
 
   72     const std::map<String, std::vector<DoubleReal> > & getProteinRTMap() 
const;
 
   73     const std::map<String, std::vector<DoubleReal> > & getProteinPTMap() 
const;
 
   74     const std::map<String, std::vector<String> > & getProteinPeptideSequenceMap() 
const;
 
   86     void dbPreprocessing(
String db_path, 
bool save = 
true);
 
   99     void dbPreprocessing(
String db_path, 
String rt_model_path, 
String dt_model_path, 
bool save = 
true);
 
  109     void loadPreprocessing();
 
  118     void setFixedModifications(
StringList & modifications);
 
  121       return fixed_modifications_;
 
  141     void savePreprocessedDBWithRT_(
String db_path, 
String path);
 
  143     void loadPreprocessedDB_(
String path);
 
  149     void updateMembers_();
 
  176 #endif //#ifndef OPENMS_ANALYSIS_ID_PRECURSORIONSELECTIONPREPROCESSING_H 
std::vector< UInt > counter_
counter for the bins 
Definition: PrecursorIonSelectionPreprocessing.h:160
DoubleReal getGaussSigma()
Definition: PrecursorIonSelectionPreprocessing.h:130
A more convenient string class. 
Definition: String.h:56
std::vector< DoubleReal > bin_masses_
the masses of the bins used for preprocessing (only used if bins are not equidistant, i.e. with ppm) 
Definition: PrecursorIonSelectionPreprocessing.h:158
DoubleReal sigma_
Definition: PrecursorIonSelectionPreprocessing.h:169
std::map< String, std::vector< String > > prot_peptide_seq_map_
Definition: PrecursorIonSelectionPreprocessing.h:167
std::set< AASequence > sequences_
the sequences of the tryptic peptides 
Definition: PrecursorIonSelectionPreprocessing.h:154
DoubleReal mu_
Definition: PrecursorIonSelectionPreprocessing.h:170
DoubleReal getGaussMu()
Definition: PrecursorIonSelectionPreprocessing.h:125
This class implements the database preprocessing needing for precursor ion selection. 
Definition: PrecursorIonSelectionPreprocessing.h:56
An LC-MS feature. 
Definition: Feature.h:66
UInt f_max_
maximal relative frequency of a mass 
Definition: PrecursorIonSelectionPreprocessing.h:162
bool fixed_mods_
Definition: PrecursorIonSelectionPreprocessing.h:164
std::map< char, std::vector< String > > fixed_modifications_
Definition: PrecursorIonSelectionPreprocessing.h:168
std::map< String, std::vector< DoubleReal > > rt_prot_map_
Definition: PrecursorIonSelectionPreprocessing.h:165
std::map< String, std::vector< DoubleReal > > pt_prot_map_
Definition: PrecursorIonSelectionPreprocessing.h:166
String list. 
Definition: StringList.h:56
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
FASTA entry type (identifier, description and sequence) 
Definition: FASTAFile.h:61
A base class for all classes handling default parameters. 
Definition: DefaultParamHandler.h:90
std::vector< DoubleReal > masses_
all tryptic masses of the distinct peptides in the database 
Definition: PrecursorIonSelectionPreprocessing.h:152
int Int
Signed integer type. 
Definition: Types.h:100
const std::map< char, std::vector< String > > & getFixedModifications()
Definition: PrecursorIonSelectionPreprocessing.h:119
std::map< String, std::vector< DoubleReal > > prot_masses_
stores masses of tryptic peptides for proteins, key is the accession number 
Definition: PrecursorIonSelectionPreprocessing.h:156