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