36 #ifndef OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATIONBASE_H 37 #define OPENMS_ANALYSIS_DENOVO_COMPNOVOIDENTIFICATIONBASE_H 83 virtual void getIdentifications(std::vector<PeptideIdentification> & ids,
const PeakMap & exp) = 0;
92 void updateMembers_();
95 void filterPermuts_(std::set<String> & permut);
101 void filterDecomps_(std::vector<MassDecomposition> & decomps);
104 void getDecompositions_(std::vector<MassDecomposition> & decomps,
double mass,
bool no_caching =
false);
107 void permute_(
String prefix,
String s, std::set<String> & permutations);
109 Size countMissedCleavagesTryptic_(
const String & peptide)
const;
112 void getCIDSpectrumLight_(
PeakSpectrum & spec,
const String & sequence,
double prefix,
double suffix);
115 void getCIDSpectrum_(
PeakSpectrum & spec,
const String & sequence,
Size charge,
double prefix = 0.0,
double suffix = 0.0);
118 void initIsotopeDistributions_();
121 double estimatePrecursorWeight_(
const PeakSpectrum & ETD_spec,
Size & charge);
197 Permut(
const std::set<String>::const_iterator & permut,
double s) :
204 permut_(rhs.permut_),
223 const std::set<String>::const_iterator &
getPermut()
const 228 void setPermut(
const std::set<String>::const_iterator & it)
void setScore(double score)
Definition: CompNovoIdentificationBase.h:238
A more convenient string class.
Definition: String.h:57
std::set< String >::const_iterator permut_
Definition: CompNovoIdentificationBase.h:245
Map< char, const Residue * > name_to_residue_
mapping for the internal representation character to the actual residue
Definition: CompNovoIdentificationBase.h:136
Map< const Residue *, char > residue_to_name_
mapping of the actual residue to the internal representing character
Definition: CompNovoIdentificationBase.h:139
double score_
Definition: CompNovoIdentificationBase.h:246
Permut(const Permut &rhs)
Definition: CompNovoIdentificationBase.h:203
double fragment_mass_tolerance_
Definition: CompNovoIdentificationBase.h:159
Map< Size, std::vector< double > > isotope_distributions_
Definition: CompNovoIdentificationBase.h:142
Representation of a peptide/protein sequence.
Definition: AASequence.h:108
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Size max_isotope_
Definition: CompNovoIdentificationBase.h:173
double getScore() const
Definition: CompNovoIdentificationBase.h:233
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentificationBase.h:87
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
Similarity score of Zhang.
Definition: ZhangSimilarityScore.h:55
ZhangSimilarityScore zhang_
Definition: CompNovoIdentificationBase.h:151
double min_aa_weight_
Definition: CompNovoIdentificationBase.h:149
bool PermutScoreComparator(const CompNovoIdentificationBase::Permut &p1, const CompNovoIdentificationBase::Permut &p2)
virtual ~Permut()
Definition: CompNovoIdentificationBase.h:209
const std::set< String >::const_iterator & getPermut() const
Definition: CompNovoIdentificationBase.h:223
Map< double, std::vector< MassDecomposition > > decomp_cache_
Definition: CompNovoIdentificationBase.h:175
double max_decomp_weight_
Definition: CompNovoIdentificationBase.h:169
double decomp_weights_precision_
Definition: CompNovoIdentificationBase.h:163
Size max_number_aa_per_decomp_
Definition: CompNovoIdentificationBase.h:155
Permut & operator=(const Permut &rhs)
Definition: CompNovoIdentificationBase.h:213
double max_mz_
Definition: CompNovoIdentificationBase.h:165
Size max_number_pivot_
Definition: CompNovoIdentificationBase.h:161
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:82
void setPermut(const std::set< String >::const_iterator &it)
Definition: CompNovoIdentificationBase.h:228
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:58
Permut(const std::set< String >::const_iterator &permut, double s)
Definition: CompNovoIdentificationBase.h:197
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:128
Map< Size, Map< Size, std::set< String > > > subspec_to_sequences_
Definition: CompNovoIdentificationBase.h:153
Map< String, std::set< String > > permute_cache_
Definition: CompNovoIdentificationBase.h:177
MassDecompositionAlgorithm mass_decomp_algorithm_
Definition: CompNovoIdentificationBase.h:147
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Map< char, double > aa_to_weight_
masses of the amino acids
Definition: CompNovoIdentificationBase.h:145
Mass decomposition algorithm, given a mass it suggests possible compositions.
Definition: MassDecompositionAlgorithm.h:69
Size max_subscore_number_
Definition: CompNovoIdentificationBase.h:171
Simple class to store permutations and a score.
Definition: CompNovoIdentificationBase.h:186
Definition: CompNovoIonScoringBase.h:67
Map class based on the STL map (containing several convenience functions)
Definition: Map.h:51
double min_mz_
Definition: CompNovoIdentificationBase.h:167
bool tryptic_only_
Definition: CompNovoIdentificationBase.h:157
Permut()
Definition: CompNovoIdentificationBase.h:190