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OpenMS
2.4.0
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82 virtual void getIdentifications(std::vector<PeptideIdentification> & ids,
const PeakMap & exp) = 0;
91 void updateMembers_()
override;
94 void filterPermuts_(std::set<String> & permut);
100 void filterDecomps_(std::vector<MassDecomposition> & decomps);
103 void getDecompositions_(std::vector<MassDecomposition> & decomps,
double mass,
bool no_caching =
false);
106 void permute_(
String prefix,
String s, std::set<String> & permutations);
108 Size countMissedCleavagesTryptic_(
const String & peptide)
const;
111 void getCIDSpectrumLight_(
PeakSpectrum & spec,
const String & sequence,
double prefix,
double suffix);
114 void getCIDSpectrum_(
PeakSpectrum & spec,
const String & sequence,
Size charge,
double prefix = 0.0,
double suffix = 0.0);
117 void initIsotopeDistributions_();
120 double estimatePrecursorWeight_(
const PeakSpectrum & ETD_spec,
Size & charge);
196 Permut(
const std::set<String>::const_iterator & permut,
double s) :
203 permut_(rhs.permut_),
222 const std::set<String>::const_iterator &
getPermut()
const
227 void setPermut(
const std::set<String>::const_iterator & it)
Size max_subscore_number_
Definition: CompNovoIdentificationBase.h:170
Size max_number_aa_per_decomp_
Definition: CompNovoIdentificationBase.h:154
bool PermutScoreComparator(const CompNovoIdentificationBase::Permut &p1, const CompNovoIdentificationBase::Permut &p2)
Map< Size, std::vector< double > > isotope_distributions_
Definition: CompNovoIdentificationBase.h:141
double score_
Definition: CompNovoIdentificationBase.h:245
Map< double, std::vector< MassDecomposition > > decomp_cache_
Definition: CompNovoIdentificationBase.h:174
MassDecompositionAlgorithm mass_decomp_algorithm_
Definition: CompNovoIdentificationBase.h:146
A more convenient string class.
Definition: String.h:57
Map< char, const Residue * > name_to_residue_
mapping for the internal representation character to the actual residue
Definition: CompNovoIdentificationBase.h:135
Similarity score of Zhang.
Definition: ZhangSimilarityScore.h:54
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
double max_mz_
Definition: CompNovoIdentificationBase.h:164
std::set< String >::const_iterator permut_
Definition: CompNovoIdentificationBase.h:244
double getScore() const
Definition: CompNovoIdentificationBase.h:232
Simple class to store permutations and a score.
Definition: CompNovoIdentificationBase.h:185
Permut(const Permut &rhs)
Definition: CompNovoIdentificationBase.h:202
Mass decomposition algorithm, given a mass it suggests possible compositions.
Definition: MassDecompositionAlgorithm.h:68
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
Map< Size, Map< Size, std::set< String > > > subspec_to_sequences_
Definition: CompNovoIdentificationBase.h:152
bool tryptic_only_
Definition: CompNovoIdentificationBase.h:156
Definition: CompNovoIonScoringBase.h:66
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
const std::set< String >::const_iterator & getPermut() const
Definition: CompNovoIdentificationBase.h:222
virtual ~Permut()
Definition: CompNovoIdentificationBase.h:208
Map< const Residue *, char > residue_to_name_
mapping of the actual residue to the internal representing character
Definition: CompNovoIdentificationBase.h:138
double max_decomp_weight_
Definition: CompNovoIdentificationBase.h:168
Permut & operator=(const Permut &rhs)
Definition: CompNovoIdentificationBase.h:212
double decomp_weights_precision_
Definition: CompNovoIdentificationBase.h:162
Map< String, std::set< String > > permute_cache_
Definition: CompNovoIdentificationBase.h:176
double fragment_mass_tolerance_
Definition: CompNovoIdentificationBase.h:158
Size max_number_pivot_
Definition: CompNovoIdentificationBase.h:160
double min_mz_
Definition: CompNovoIdentificationBase.h:166
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:57
double min_aa_weight_
Definition: CompNovoIdentificationBase.h:148
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentificationBase.h:86
void setPermut(const std::set< String >::const_iterator &it)
Definition: CompNovoIdentificationBase.h:227
ZhangSimilarityScore zhang_
Definition: CompNovoIdentificationBase.h:150
Permut(const std::set< String >::const_iterator &permut, double s)
Definition: CompNovoIdentificationBase.h:196
Representation of a peptide/protein sequence.
Definition: AASequence.h:107
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:50
Size max_isotope_
Definition: CompNovoIdentificationBase.h:172
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
Permut()
Definition: CompNovoIdentificationBase.h:189
Map< char, double > aa_to_weight_
masses of the amino acids
Definition: CompNovoIdentificationBase.h:144
void setScore(double score)
Definition: CompNovoIdentificationBase.h:237