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,
DoubleReal mass,
bool no_caching =
false);
107 void permute_(
String prefix,
String s, std::set<String> & permutations);
109 Size countMissedCleavagesTryptic_(
const String & peptide)
const;
118 void initIsotopeDistributions_();
204 permut_(rhs.permut_),
223 const std::set<String>::const_iterator &
getPermut()
const
228 void setPermut(
const std::set<String>::const_iterator & it)
DoubleReal getScore() const
Definition: CompNovoIdentificationBase.h:233
A more convenient string class.
Definition: String.h:56
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
Permut(const Permut &rhs)
Definition: CompNovoIdentificationBase.h:203
const std::set< String >::const_iterator & getPermut() const
Definition: CompNovoIdentificationBase.h:223
Representation of a peptide/protein sequence.
Definition: AASequence.h:84
DoubleReal max_mz_
Definition: CompNovoIdentificationBase.h:165
Size max_isotope_
Definition: CompNovoIdentificationBase.h:173
DoubleReal decomp_weights_precision_
Definition: CompNovoIdentificationBase.h:163
DoubleReal score_
Definition: CompNovoIdentificationBase.h:246
CompNovoIonScoringBase::IonScore IonScore
Definition: CompNovoIdentificationBase.h:87
DoubleReal max_decomp_weight_
Definition: CompNovoIdentificationBase.h:169
Similarity score of Zhang.
Definition: ZhangSimilarityScore.h:55
ZhangSimilarityScore zhang_
Definition: CompNovoIdentificationBase.h:151
bool PermutScoreComparator(const CompNovoIdentificationBase::Permut &p1, const CompNovoIdentificationBase::Permut &p2)
DoubleReal min_mz_
Definition: CompNovoIdentificationBase.h:167
virtual ~Permut()
Definition: CompNovoIdentificationBase.h:209
Permut(const std::set< String >::const_iterator &permut, DoubleReal s)
Definition: CompNovoIdentificationBase.h:197
Map< char, DoubleReal > aa_to_weight_
masses of the amino acids
Definition: CompNovoIdentificationBase.h:145
Map< Size, std::vector< DoubleReal > > isotope_distributions_
Definition: CompNovoIdentificationBase.h:142
Size max_number_aa_per_decomp_
Definition: CompNovoIdentificationBase.h:155
Permut & operator=(const Permut &rhs)
Definition: CompNovoIdentificationBase.h:213
Size max_number_pivot_
Definition: CompNovoIdentificationBase.h:161
void setPermut(const std::set< String >::const_iterator &it)
Definition: CompNovoIdentificationBase.h:228
run with CompNovoIdentificationBase
Definition: CompNovoIdentificationBase.h:58
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:144
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:90
Map< DoubleReal, std::vector< MassDecomposition > > decomp_cache_
Definition: CompNovoIdentificationBase.h:175
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:66
Map class based on the STL map (containing serveral convenience functions)
Definition: Map.h:50
void setScore(DoubleReal score)
Definition: CompNovoIdentificationBase.h:238
bool tryptic_only_
Definition: CompNovoIdentificationBase.h:157
Permut()
Definition: CompNovoIdentificationBase.h:190
DoubleReal fragment_mass_tolerance_
Definition: CompNovoIdentificationBase.h:159
DoubleReal min_aa_weight_
Definition: CompNovoIdentificationBase.h:149