OpenMS  2.8.0
CompNovoIdentificationCID.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Andreas Bertsch $
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34 
35 
36 #pragma once
37 
38 // OpenMS includes
40 
41 // stl includes
42 #include <vector>
43 
44 namespace OpenMS
45 {
53  class OPENMS_DLLAPI CompNovoIdentificationCID :
55  {
56 
57 public:
58 
64 
67 
71 
74 
79  void getIdentifications(std::vector<PeptideIdentification> & ids, const PeakMap & exp) override;
80 
84 
85 
89 
90 protected:
91 
93  void getDecompositionsDAC_(std::set<String> & sequences, Size left, Size right, double peptide_weight, const PeakSpectrum & CID_orig_spec, Map<double, IonScore> & CID_nodes);
94 
96  void reducePermuts_(std::set<String> & permuts, const PeakSpectrum & CID_orig_spec, double prefix, double suffix);
97 
98  void updateMembers_() override;
99 
101  };
102 }
103 
Simple class to store permutations and a score.
Definition: CompNovoIdentificationBase.h:187
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:59
run with CompNovoIdentificationCID
Definition: CompNovoIdentificationCID.h:55
CompNovoIdentificationCID()
default constructor
void getDecompositionsDAC_(std::set< String > &sequences, Size left, Size right, double peptide_weight, const PeakSpectrum &CID_orig_spec, Map< double, IonScore > &CID_nodes)
call the DAC algorithm for the subspectrum defined via left and right peaks and fill the set with can...
CompNovoIdentificationCID(const CompNovoIdentificationCID &source)
copy constructor
void getIdentification(PeptideIdentification &id, const PeakSpectrum &CID_spec)
performs an ProteinIdentification run on a PeakSpectrum
CompNovoIdentificationBase::Permut Permut
Definition: CompNovoIdentificationCID.h:88
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentificationCID.h:87
double precursor_mass_tolerance_
Definition: CompNovoIdentificationCID.h:100
void updateMembers_() override
update members method from DefaultParamHandler to update the members
CompNovoIonScoringBase::IsotopeType IsotopeType
Definition: CompNovoIdentificationCID.h:86
void getIdentifications(std::vector< PeptideIdentification > &ids, const PeakMap &exp) override
performs an ProteinIdentification run on a PeakMap
void reducePermuts_(std::set< String > &permuts, const PeakSpectrum &CID_orig_spec, double prefix, double suffix)
reduces the given number of permuts by scoring the permutations to the CID and ETD spec
~CompNovoIdentificationCID() override
destructor
CompNovoIdentificationCID & operator=(const CompNovoIdentificationCID &source)
IsotopeType
Definition: CompNovoIonScoringBase.h:60
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:73
The representation of a 1D spectrum.
Definition: MSSpectrum.h:70
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:52
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:65
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
static String suffix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:156
static String prefix(const String &this_s, size_t length)
Definition: StringUtilsSimple.h:147
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Definition: CompNovoIonScoringBase.h:67