35 #ifndef OPENMS_ANALYSIS_ID_ACCURATEMASSSEARCHENGINE_H 
   36 #define OPENMS_ANALYSIS_ID_ACCURATEMASSSEARCHENGINE_H 
   99         std::vector<DoubleReal> getIndividualIntensities();
 
  101         std::vector<DoubleReal> getIndividualIntensities() 
const;
 
  103         void setIndividualIntensities(
const std::vector<DoubleReal>&);
 
  105         Size getMatchingIndex();
 
  107         void setMatchingIndex(
const Size&);
 
  109         Size getSourceFeatureIndex();
 
  111         void setSourceFeatureIndex(
const Size&);
 
  115         String getFoundAdduct() 
const;
 
  117         void setFoundAdduct(
const String&);
 
  119         String getFormulaString();
 
  121         String getFormulaString() 
const;
 
  123         void setEmpiricalFormula(
const String&);
 
  125         std::vector<String> getMatchingHMDBids();
 
  127         std::vector<String> getMatchingHMDBids() 
const;
 
  129         void setMatchingHMDBids(
const std::vector<String>&);
 
  139         void outputResults() 
const;
 
  177     void queryByFeature(
const Feature&, 
const Size&, std::vector<AccurateMassSearchResult>&);
 
  178     void queryByConsensusFeature(
const ConsensusFeature&, 
const Size&, 
const Size&, std::vector<AccurateMassSearchResult>&);
 
  186     virtual void updateMembers_();
 
  190     void parseMappingFile_(
const String&);
 
  191     void parseStructMappingFile_(
const String&);
 
  192     void parseAdductsFile_(
const String&);
 
  193     void searchMass_(
const DoubleReal&, std::vector<Size>& hit_indices);
 
  195     void parseAdductString_(
const String&, std::vector<String>&);
 
  198     DoubleReal computeCosineSim_(
const std::vector<DoubleReal>& x, 
const std::vector<DoubleReal>& y);
 
  199     DoubleReal computeEuclideanDist_(
const std::vector<DoubleReal>& x, 
const std::vector<DoubleReal>& y);
 
  234 #endif // OPENMS_ANALYSIS_ID_ACCURATEMASSSEARCHENGINE_H 
String ion_mode_
Definition: AccurateMassSearchEngine.h:218
String mass_error_unit_
Definition: AccurateMassSearchEngine.h:217
std::vector< DoubleReal > individual_intensities_
Definition: AccurateMassSearchEngine.h:150
A more convenient string class. 
Definition: String.h:56
bool iso_similarity_
Definition: AccurateMassSearchEngine.h:219
DoubleReal query_mass_
Definition: AccurateMassSearchEngine.h:144
String empirical_formula_
Definition: AccurateMassSearchEngine.h:155
std::vector< std::vector< String > > MassIDMapping
private member variables 
Definition: AccurateMassSearchEngine.h:207
StringList pos_adducts_
Definition: AccurateMassSearchEngine.h:224
MassIDMapping mass_id_mapping_
Definition: AccurateMassSearchEngine.h:211
A container for consensus elements. 
Definition: ConsensusMap.h:60
std::vector< String > matching_hmdb_ids_
Definition: AccurateMassSearchEngine.h:156
String found_adduct_
Definition: AccurateMassSearchEngine.h:154
DoubleReal observed_rt_
Definition: AccurateMassSearchEngine.h:148
Definition: AccurateMassSearchEngine.h:53
HMDBPropsMapping hmdb_properties_mapping_
Definition: AccurateMassSearchEngine.h:212
DoubleReal mass_error_value_
parameter stuff 
Definition: AccurateMassSearchEngine.h:216
String pos_adducts_fname_
Definition: AccurateMassSearchEngine.h:221
std::map< String, std::vector< String > > HMDBPropsMapping
Definition: AccurateMassSearchEngine.h:208
std::vector< std::vector< AccurateMassSearchResult > > QueryResultsTable
Definition: AccurateMassSearchEngine.h:202
An LC-MS feature. 
Definition: Feature.h:66
StringList neg_adducts_
Definition: AccurateMassSearchEngine.h:225
String list. 
Definition: StringList.h:56
size_t Size
Size type e.g. used as variable which can hold result of size() 
Definition: Types.h:144
Base class for all classes that want to report their progess. 
Definition: ProgressLogger.h:56
DoubleReal error_ppm_
Definition: AccurateMassSearchEngine.h:147
std::vector< String > mass_formula_mapping_
Definition: AccurateMassSearchEngine.h:213
A base class for all classes handling default parameters. 
Definition: DefaultParamHandler.h:90
Size source_feature_index_
Definition: AccurateMassSearchEngine.h:152
Size matching_index_
Definition: AccurateMassSearchEngine.h:151
DoubleReal adduct_mass_
Stored information/results of DB query. 
Definition: AccurateMassSearchEngine.h:143
String neg_adducts_fname_
Definition: AccurateMassSearchEngine.h:222
DoubleReal isotopes_sim_score_
Definition: AccurateMassSearchEngine.h:158
std::vector< DoubleReal > masskey_table_
Definition: AccurateMassSearchEngine.h:210
DoubleReal found_mass_
Definition: AccurateMassSearchEngine.h:145
DoubleReal observed_intensity_
Definition: AccurateMassSearchEngine.h:149
A 2-dimensional consensus feature. 
Definition: ConsensusFeature.h:59
DoubleReal charge_
Definition: AccurateMassSearchEngine.h:146
Data model of MzTab files. Please see the official MzTab specification at https://code.google.com/p/mztab/. 
Definition: MzTab.h:1355
Definition: AccurateMassSearchEngine.h:162