|
OpenMS
2.5.0
|
Go to the documentation of this file.
42 #include <boost/algorithm/string.hpp>
43 #include <boost/lexical_cast.hpp>
44 #include <boost/assign.hpp>
45 #include <boost/random/mersenne_twister.hpp>
46 #include <boost/random/uniform_int.hpp>
47 #include <boost/random/variate_generator.hpp>
48 #include <boost/unordered_map.hpp>
124 const double aim_decoy_fraction,
127 const int max_attempts,
128 const double identity_threshold,
129 const double precursor_mz_shift,
130 const double product_mz_shift,
131 const double product_mz_threshold,
132 const std::vector<String>& fragment_types,
133 const std::vector<size_t>& fragment_charges,
134 const bool enable_specific_losses,
135 const bool enable_unspecific_losses,
136 const int round_decPow = -4)
const;
148 float AASequenceIdentity(
const String& sequence,
const String& decoy)
const;
159 const double identity_threshold,
161 const int max_attempts = 100)
const;
185 static IndexType findFixedResidues(
const std::string& sequence,
186 bool keepN,
bool keepC,
const OpenMS::String& keep_const_pattern);
200 IndexType findFixedResidues_(
const std::string& sequence)
const;
207 IndexType findFixedAndTermResidues_(
const std::string& sequence)
const;
227 void updateMembers_()
override;
String keep_const_pattern_
Definition: MRMDecoy.h:229
std::vector< size_t > IndexType
Definition: MRMDecoy.h:95
Represents a peptide (amino acid sequence)
Definition: TargetedExperimentHelper.h:370
std::vector< OpenMS::TargetedExperiment::Protein > ProteinVectorType
Definition: MRMDecoy.h:138
A more convenient string class.
Definition: String.h:58
This class generates a TargetedExperiment object with decoys based on a TargetedExperiment object.
Definition: MRMDecoy.h:88
std::vector< OpenMS::ReactionMonitoringTransition > TransitionVectorType
Definition: MRMDecoy.h:140
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
bool keepC_
Definition: MRMDecoy.h:231
std::map< String, std::vector< const ReactionMonitoringTransition * > > PeptideTransitionMapType
Definition: MRMDecoy.h:142
bool keepN_
Definition: MRMDecoy.h:230
A description of a targeted experiment containing precursor and production ions.
Definition: TargetedExperiment.h:64
std::vector< OpenMS::TargetedExperiment::Peptide > PeptideVectorType
Definition: MRMDecoy.h:139