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typedef CompNovoIonScoringBase::IsotopeType | IsotopeType |
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typedef CompNovoIonScoringBase::IonScore | IonScore |
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typedef CompNovoIdentificationBase::Permut | Permut |
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void | getIdentifications (std::vector< PeptideIdentification > &ids, const PeakMap &exp) override |
| performs an ProteinIdentification run on a PeakMap More...
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void | getIdentification (PeptideIdentification &id, const PeakSpectrum &CID_spec, const PeakSpectrum &ETD_spec) |
| performs an ProteinIdentification run on a PeakSpectrum More...
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void | getDecompositionsDAC_ (std::set< String > &sequences, Size left, Size right, double peptide_weight, const PeakSpectrum &CID_orig_spec, const PeakSpectrum &ETD_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 candidates sequences More...
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void | reducePermuts_ (std::set< String > &permuts, const PeakSpectrum &CID_orig_spec, const PeakSpectrum &ETD_orig_spec, double prefix, double suffix) |
| reduces the given number of permuts by scoring the permutations to the CID and ETD spec More...
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void | getETDSpectrum_ (PeakSpectrum &spec, const String &sequence, Size, double prefix=0.0, double suffix=0.0) |
| fills the spectrum with c and z type ions More...
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double | estimatePrecursorWeight_ (const PeakSpectrum &ETD_spec, Size &charge) |
| estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor is found in the MS/MS spec More...
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typedef CompNovoIonScoringBase::IonScore | IonScore |
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void | updateMembers_ () override |
| update members method from DefaultParamHandler to update the members More...
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void | filterPermuts_ (std::set< String > &permut) |
| filters the permutations More...
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void | selectPivotIons_ (std::vector< Size > &pivots, Size left, Size right, Map< double, IonScore > &CID_nodes, const PeakSpectrum &CID_orig_spec, double precursor_weight, bool full_range=false) |
| selects pivot ion of the given range using the scores given in CID_nodes More...
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void | filterDecomps_ (std::vector< MassDecomposition > &decomps) |
| filters the decomps by the amino acid frequencies More...
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void | getDecompositions_ (std::vector< MassDecomposition > &decomps, double mass, bool no_caching=false) |
| produces mass decompositions using the given mass More...
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void | permute_ (String prefix, String s, std::set< String > &permutations) |
| permuts the String s adds the prefix and stores the results in permutations More...
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Size | countMissedCleavagesTryptic_ (const String &peptide) const |
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void | getCIDSpectrumLight_ (PeakSpectrum &spec, const String &sequence, double prefix, double suffix) |
| fills the spec with b and y ions, no other ion types or doubly charged variants are used More...
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void | getCIDSpectrum_ (PeakSpectrum &spec, const String &sequence, Size charge, double prefix=0.0, double suffix=0.0) |
| fills the spectrum with b,y ions, multiple charged variants; if prefix and suffix weights are given, the sequence is treated as tag More...
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void | initIsotopeDistributions_ () |
| initializes the score distribution pre-calculated for the use in spectrum generation More...
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double | estimatePrecursorWeight_ (const PeakSpectrum &ETD_spec, Size &charge) |
| estimates an exact precursor weight of the ETD spectrum, because in most of the cases the precursor is found in the MS/MS spec More...
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void | windowMower_ (PeakSpectrum &spec, double windowsize, Size no_peaks) |
| keep for each window of size windowsize in the m/z range of the spectrum exactly no_peaks More...
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double | compareSpectra_ (const PeakSpectrum &s1, const PeakSpectrum &s2) |
| compares two spectra More...
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AASequence | getModifiedAASequence_ (const String &sequence) |
| returns a modified AASequence from a given internal representation More...
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String | getModifiedStringFromAASequence_ (const AASequence &sequence) |
| returns the internal representation of a given AASequence More...
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Protected Member Functions inherited from DefaultParamHandler |
void | defaultsToParam_ () |
| Updates the parameters after the defaults have been set in the constructor. More...
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Map< char, const Residue * > | name_to_residue_ |
| mapping for the internal representation character to the actual residue More...
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Map< const Residue *, char > | residue_to_name_ |
| mapping of the actual residue to the internal representing character More...
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Map< Size, std::vector< double > > | isotope_distributions_ |
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Map< char, double > | aa_to_weight_ |
| masses of the amino acids More...
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MassDecompositionAlgorithm | mass_decomp_algorithm_ |
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double | min_aa_weight_ |
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ZhangSimilarityScore | zhang_ |
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Map< Size, Map< Size, std::set< String > > > | subspec_to_sequences_ |
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Size | max_number_aa_per_decomp_ |
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bool | tryptic_only_ |
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double | fragment_mass_tolerance_ |
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Size | max_number_pivot_ |
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double | decomp_weights_precision_ |
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double | max_mz_ |
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double | min_mz_ |
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double | max_decomp_weight_ |
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Size | max_subscore_number_ |
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Size | max_isotope_ |
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Map< double, std::vector< MassDecomposition > > | decomp_cache_ |
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Map< String, std::set< String > > | permute_cache_ |
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Protected Attributes inherited from DefaultParamHandler |
Param | param_ |
| Container for current parameters. More...
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Param | defaults_ |
| Container for default parameters. This member should be filled in the constructor of derived classes! More...
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std::vector< String > | subsections_ |
| Container for registered subsections. This member should be filled in the constructor of derived classes! More...
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String | error_name_ |
| Name that is displayed in error messages during the parameter checking. More...
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bool | check_defaults_ |
| If this member is set to false no checking if parameters in done;. More...
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bool | warn_empty_defaults_ |
| If this member is set to false no warning is emitted when defaults are empty;. More...
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