35 #ifndef OPENMS_ANALYSIS_OPENSWATH_MRMASSAY_H 36 #define OPENMS_ANALYSIS_OPENSWATH_MRMASSAY_H 45 #include <boost/bind.hpp> 98 void reannotateTransitions(
OpenMS::TargetedExperiment& exp,
double mz_threshold, std::vector<String> fragment_types, std::vector<size_t> fragment_charges,
bool enable_alternative_localizations,
bool enable_reannotation,
bool enable_losses,
int round_decPow = -4);
110 void restrictTransitions(
OpenMS::TargetedExperiment& exp,
double lower_mz_limit,
double upper_mz_limit, std::vector<std::pair<double, double> > swathes);
137 void uisTransitions(
OpenMS::TargetedExperiment& exp, std::vector<String> fragment_types, std::vector<size_t> fragment_charges,
bool enable_losses,
bool enable_uis_scoring,
bool enable_site_scoring,
double mz_threshold, std::vector<std::pair<double, double> > swathes);
150 void insilicoTransitions(
OpenMS::TargetedExperiment& exp, std::vector<String> fragment_types, std::vector<size_t> fragment_charges,
bool enable_losses,
int round_decPow = -4);
160 bool isUIS_(
const double fragment_ion, std::vector<double> ions,
const double mz_threshold);
176 int getSwath_(
const std::vector<std::pair<double, double> > swathes,
const double precursor_mz);
185 bool isInSwath_(
const std::vector<std::pair<double, double> > swathes,
const double precursor_mz,
const double product_mz);
195 std::vector<std::vector<size_t> > nchoosekcombinations_(std::vector<size_t> n,
size_t k);
213 std::vector<OpenMS::AASequence> addModificationsSequences_(std::vector<OpenMS::AASequence> sequences, std::vector<std::vector<size_t> > mods_combs,
OpenMS::String modification);
224 void addModification_(std::vector<TargetedExperiment::Peptide::Modification>& mods,
int location,
ResidueModification& rmod,
const String& name);
Generate assays from a TargetedExperiment.
Definition: MRMAssay.h:65
A more convenient string class.
Definition: String.h:57
Representation of a modification.
Definition: ResidueModification.h:65
Representation of a peptide/protein sequence.
Definition: AASequence.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMAssay.h:79
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMAssay.h:78
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
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMAssay.h:80
This class stores a SRM/MRM transition.
Definition: ReactionMonitoringTransition.h:55