70 String getEnzymeName()
const;
73 void setEnzyme(
const String name);
76 void digest(
const AASequence& protein, std::vector<AASequence>& output)
const;
82 double getLogThreshold()
const;
86 void setLogThreshold(
double threshold);
120 p_cleave(0), p_miss(0) {}
122 p_cleave(p_c), p_miss(p_m) {}
const DigestionEnzyme * enzyme_
Used enzyme.
Definition: EnzymaticDigestionLogModel.h:132
A more convenient string class.
Definition: String.h:57
Definition: EnzymaticDigestionLogModel.h:90
double p_cleave
Definition: EnzymaticDigestionLogModel.h:116
Size< TNeedle >::Type position(const PatternAuxData< TNeedle > &dh)
Definition: AhoCorasickAmbiguous.h:561
Abstract base class for digestion enzymes.
Definition: DigestionEnzyme.h:52
BindingSite_()
Definition: EnzymaticDigestionLogModel.h:95
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
double p_miss
Definition: EnzymaticDigestionLogModel.h:117
bool operator<(const BindingSite_ &rhs) const
Definition: EnzymaticDigestionLogModel.h:101
double log_model_threshold_
Threshold to decide if position is cleaved or missed (only for the model)
Definition: EnzymaticDigestionLogModel.h:135
CleavageModel_(const double &p_c, const double &p_m)
Definition: EnzymaticDigestionLogModel.h:121
ConstIterator for AASequence.
Definition: AASequence.h:117
bool operator==(const BindingSite_ &rhs) const
Definition: EnzymaticDigestionLogModel.h:106
BindingSite_(const Size &p, const String &name)
Definition: EnzymaticDigestionLogModel.h:98
CleavageModel_()
Definition: EnzymaticDigestionLogModel.h:119
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Map< BindingSite_, CleavageModel_ > model_data_
Holds the cleavage model.
Definition: EnzymaticDigestionLogModel.h:137
String AAname
Definition: EnzymaticDigestionLogModel.h:93
Class for the Log L model of enzymatic digestion of proteins.
Definition: EnzymaticDigestionLogModel.h:57
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
Size position
Definition: EnzymaticDigestionLogModel.h:92
Definition: EnzymaticDigestionLogModel.h:114