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>
47 #include <boost/unordered_map.hpp>
111 double identity_threshold,
int max_attempts,
double mz_threshold,
112 bool theoretical,
double mz_shift,
bool exclude_similar,
113 double similarity_threshold,
bool remove_CNterm_mods,
114 double precursor_mass_shift,
bool enable_losses,
bool remove_unannotated);
123 int max_transitions);
129 typedef boost::unordered_map<String, boost::unordered_map<String, double> >
IonSeries;
137 std::pair<String, double> getDecoyIon(
String ionid,
138 boost::unordered_map<
String, boost::unordered_map<String, double> >& decoy_ionseries);
143 std::pair<String, double> getTargetIon(
double ProductMZ,
double mz_threshold,
144 boost::unordered_map<
String, boost::unordered_map<String, double> > target_ionseries,
161 boost::unordered_map<String, boost::unordered_map<String, double> > getIonSeries(
167 std::vector<std::pair<std::string::size_type, std::string> > find_all_tryptic(
168 std::string sequence);
173 float AASequenceIdentity(
const String& sequence,
const String& decoy);
194 int max_attempts = 10);
A more convenient string class.
Definition: String.h:57
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMDecoy.h:127
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMDecoy.h:126
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
MRMDecoy()
Definition: MRMDecoy.h:92
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMDecoy.h:125
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object...
Definition: MRMDecoy.h:88
boost::unordered_map< String, IonSeries > IonSeriesMapType
Definition: MRMDecoy.h:130
std::map< String, std::vector< const ReactionMonitoringTransition * > > PeptideTransitionMapType
Definition: MRMDecoy.h:132
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
This class stores an prediction of an SRM/MRM transition.
Definition: TargetedExperiment.h:53
boost::unordered_map< String, boost::unordered_map< String, double > > IonSeries
Definition: MRMDecoy.h:129
Definition: TargetedExperimentHelper.h:211