35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMDECOY_H 
   36 #define OPENMS_ANALYSIS_OPENSWATH_MRMDECOY_H 
   41 #include <boost/algorithm/string.hpp> 
   42 #include <boost/lexical_cast.hpp> 
   43 #include <boost/assign.hpp> 
   44 #include <boost/random/mersenne_twister.hpp> 
   45 #include <boost/random/uniform_int.hpp> 
   46 #include <boost/random/variate_generator.hpp> 
  110                         double identity_threshold, 
int max_attempts, 
double mz_threshold, 
 
  111                         bool theoretical, 
double mz_shift, 
bool exclude_similar, 
 
  112                         double similarity_threshold, 
bool remove_CNterm_mods, 
double precursor_mass_shift);
 
  122                              int max_transitions);
 
  128     typedef std::map<String, std::map<String, double> > 
IonSeries;
 
  136     std::pair<String, DoubleReal> getDecoyIon(
String ionid,
 
  137                                               std::map<
String, std::map<String, DoubleReal> >& decoy_ionseries);
 
  142     std::pair<String, double> getTargetIon(
double ProductMZ, 
double mz_threshold,
 
  143                                            std::map<
String, std::map<String, double> > target_ionseries);
 
  160     std::map<String, std::map<String, double> > getIonSeries(
 
  161       AASequence sequence, 
int precursor_charge, 
int max_isotopes = 2);
 
  166     std::vector<std::pair<std::string::size_type, std::string> > find_all_tryptic(
 
  167       std::string sequence);
 
  172     float AASequenceIdentity(
const String& sequence, 
const String& decoy);
 
  193       int max_attempts = 10);
 
A more convenient string class. 
Definition: String.h:56
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMDecoy.h:126
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMDecoy.h:125
Representation of a peptide/protein sequence. 
Definition: AASequence.h:84
MRMDecoy()
Definition: MRMDecoy.h:91
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMDecoy.h:124
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object...
Definition: MRMDecoy.h:87
std::map< String, std::vector< const ReactionMonitoringTransition * > > PeptideTransitionMapType
Definition: MRMDecoy.h:131
Base class for all classes that want to report their progess. 
Definition: ProgressLogger.h:56
This class stores an prediction of an SRM/MRM transition. 
Definition: TargetedExperiment.h:53
std::map< String, IonSeries > IonSeriesMapType
Definition: MRMDecoy.h:129
std::map< String, std::map< String, double > > IonSeries
Definition: MRMDecoy.h:128
Definition: TargetedExperimentHelper.h:211