117 const double aim_decoy_fraction,
120 const int max_attempts,
121 const double identity_threshold,
122 const double precursor_mz_shift,
123 const double product_mz_shift,
124 const double product_mz_threshold,
125 const std::vector<String>& fragment_types,
126 const std::vector<size_t>& fragment_charges,
127 const bool enable_specific_losses,
128 const bool enable_unspecific_losses,
129 const int round_decPow = -4)
const;
152 const double identity_threshold,
154 const int max_attempts = 100)
const;
179 bool keepN,
bool keepC,
const OpenMS::String& keep_const_pattern);
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:93
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.
Definition: MRMDecoy.h:84
std::vector< size_t > IndexType
Definition: MRMDecoy.h:88
IndexType findFixedResidues_(const std::string &sequence) const
Find all K, R, P sites in a sequence to be set as fixed.
bool keepC_
Definition: MRMDecoy.h:224
std::map< String, std::vector< const ReactionMonitoringTransition * > > PeptideTransitionMapType
Definition: MRMDecoy.h:135
static IndexType findFixedResidues(const std::string &sequence, bool keepN, bool keepC, const OpenMS::String &keep_const_pattern)
Find all residues in a sequence that should not be reversed / shuffled.
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMDecoy.h:133
static OpenMS::TargetedExperiment::Peptide reversePeptide(const OpenMS::TargetedExperiment::Peptide &peptide, const bool keepN, const bool keepC, const String &const_pattern=String())
Reverse a peptide sequence (with its modifications)
IndexType findFixedAndTermResidues_(const std::string &sequence) const
Find all K, R, P and C-/N-terminal sites in a sequence to be set as fixed.
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMDecoy.h:132
String keep_const_pattern_
Definition: MRMDecoy.h:222
bool keepN_
Definition: MRMDecoy.h:223
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMDecoy.h:131
void updateMembers_() override
Synchronize members with param class.
bool hasCNterminalMods_(const OpenMS::TargetedExperiment::Peptide &peptide, bool checkCterminalAA) const
Check if a peptide has C or N terminal modifications.
float AASequenceIdentity(const String &sequence, const String &decoy) const
Compute relative identity (relative number of matches of amino acids at the same position) between tw...
OpenMS::TargetedExperiment::Peptide reversePeptide_(const OpenMS::TargetedExperiment::Peptide &peptide) const
Reverse a peptide sequence (with its modifications)
void generateDecoys(const OpenMS::TargetedExperiment &exp, OpenMS::TargetedExperiment &dec, const String &method, const double aim_decoy_fraction, const bool switchKR, const String &decoy_tag, const int max_attempts, const double identity_threshold, const double precursor_mz_shift, const double product_mz_shift, const double product_mz_threshold, const std::vector< String > &fragment_types, const std::vector< size_t > &fragment_charges, const bool enable_specific_losses, const bool enable_unspecific_losses, const int round_decPow=-4) const
Generate decoys from a TargetedExperiment.
OpenMS::TargetedExperiment::Peptide pseudoreversePeptide_(const OpenMS::TargetedExperiment::Peptide &peptide) const
Pseudo-reverse a peptide sequence (with its modifications)
OpenMS::TargetedExperiment::Peptide shufflePeptide(OpenMS::TargetedExperiment::Peptide peptide, const double identity_threshold, int seed=-1, const int max_attempts=100) const
Shuffle a peptide (with its modifications) sequence.
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:360
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:65
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47