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