35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMASSAY_H 36 #define OPENMS_ANALYSIS_OPENSWATH_MRMASSAY_H 44 #include <boost/bind.hpp> 45 #include <boost/lexical_cast.hpp> 46 #include <boost/random/mersenne_twister.hpp> 47 #include <boost/random/uniform_int.hpp> 48 #include <boost/random/variate_generator.hpp> 84 typedef boost::unordered_map<size_t, boost::unordered_map<String, std::set<std::string> > >
SequenceMapT;
85 typedef boost::unordered_map<size_t, boost::unordered_map<String, std::vector<std::pair<double, std::string> > > >
IonMapT;
86 typedef std::map<String, std::vector<std::pair<std::string, double> > >
PeptideMapT;
89 typedef boost::unordered_map<String, TargetedExperiment::Peptide>
TargetDecoyMapT;
105 void reannotateTransitions(
OpenMS::TargetedExperiment& exp,
double precursor_mz_threshold,
double product_mz_threshold, std::vector<String> fragment_types, std::vector<size_t> fragment_charges,
bool enable_reannotation,
bool enable_specific_losses,
bool enable_unspecific_losses,
int round_decPow = -4);
117 void restrictTransitions(
OpenMS::TargetedExperiment& exp,
double lower_mz_limit,
double upper_mz_limit, std::vector<std::pair<double, double> > swathes);
145 std::vector<String> fragment_types,
146 std::vector<size_t> fragment_charges,
147 bool enable_specific_losses,
148 bool enable_unspecific_losses,
149 bool enable_ms2_precursors,
151 std::vector<std::pair<double, double> > swathes,
152 int round_decPow = -4,
153 size_t max_num_alternative_localizations = 20,
154 int shuffle_seed = -1);
166 std::vector<std::string> getMatchingPeptidoforms_(
const double fragment_ion,
167 const std::vector<std::pair<double, std::string> >& ions,
168 const double mz_threshold);
178 int getSwath_(
const std::vector<std::pair<double, double> > swathes,
const double precursor_mz);
189 bool isInSwath_(
const std::vector<std::pair<double, double> > swathes,
const double precursor_mz,
const double product_mz);
199 std::string getRandomSequence_(
size_t sequence_size, boost::variate_generator<boost::mt19937&, boost::uniform_int<> > pseudoRNG);
209 std::vector<std::vector<size_t> > nchoosekcombinations_(std::vector<size_t> n,
size_t k);
222 std::vector<OpenMS::AASequence> addModificationsSequences_(std::vector<OpenMS::AASequence> sequences, std::vector<std::vector<size_t> > mods_combs,
OpenMS::String modification);
263 std::vector<String> fragment_types,
264 std::vector<size_t> fragment_charges,
265 bool enable_specific_losses,
266 bool enable_unspecific_losses,
267 bool enable_ms2_precursors,
268 std::vector<std::pair<double, double> > swathes,
270 size_t max_num_alternative_localizations,
271 SequenceMapT& TargetSequenceMap,
272 IonMapT& TargetIonMap,
273 PeptideMapT& TargetPeptideMap);
281 void generateDecoySequences_(boost::unordered_map<
size_t,
282 boost::unordered_map<
String, std::set<std::string> > >& TargetSequenceMap,
283 boost::unordered_map<String, String>& DecoySequenceMap,
293 std::vector<String> fragment_types, std::vector<size_t> fragment_charges,
294 bool enable_specific_losses,
295 bool enable_unspecific_losses,
296 bool enable_ms2_precursors,
297 std::vector<std::pair<double, double> > swathes,
299 TargetDecoyMapT& TargetDecoyMap,
300 PeptideMapT& TargetPeptideMap,
301 boost::unordered_map<String, String>& DecoySequenceMap,
302 IonMapT& DecoyIonMap,
303 PeptideMapT& DecoyPeptideMap);
312 TransitionVectorType& transitions,
double mz_threshold,
313 std::vector<std::pair<double, double> > swathes,
315 PeptideMapT& TargetPeptideMap,
316 IonMapT& TargetIonMap);
327 TransitionVectorType& transitions,
329 std::vector<std::pair<double, double> > swathes,
331 PeptideMapT& DecoyPeptideMap,
332 TargetDecoyMapT& TargetDecoyMap,
334 IonMapT TargetIonMap);
339 #endif // OPENMS_ANALYSIS_OPENSWATH_MRMASSAY_H
boost::unordered_map< size_t, boost::unordered_map< String, std::set< std::string > > > SequenceMapT
Definition: MRMAssay.h:84
Generate assays from a TargetedExperiment.
Definition: MRMAssay.h:67
A more convenient string class.
Definition: String.h:57
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
boost::unordered_map< size_t, boost::unordered_map< String, std::vector< std::pair< double, std::string > > > > IonMapT
Definition: MRMAssay.h:85
std::map< String, std::vector< std::pair< std::string, double > > > PeptideMapT
Definition: MRMAssay.h:86
boost::unordered_map< String, TargetedExperiment::Peptide > TargetDecoyMapT
Definition: MRMAssay.h:89
boost::unordered_map< String, String > SequenceMap_T
Definition: MRMAssay.h:87
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMAssay.h:81
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMAssay.h:80
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:55
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:62
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMAssay.h:82