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