OpenMS
AccurateMassSearchEngine.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Erhan Kenar, Chris Bielow $
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34 
35 #pragma once
36 
38 #include <OpenMS/KERNEL/Feature.h>
42 #include <OpenMS/FORMAT/MzTab.h>
43 #include <OpenMS/FORMAT/MzTabM.h>
48 #include <OpenMS/SYSTEM/File.h>
50 
51 
52 #include <iosfwd>
53 #include <vector>
54 
55 namespace OpenMS
56 {
57  class OPENMS_DLLAPI AccurateMassSearchResult
58  {
59  public:
62 
65 
68 
71 
73  double getObservedMZ() const;
74 
76  void setObservedMZ(const double&);
77 
79  double getCalculatedMZ() const;
80 
82  void setCalculatedMZ(const double&);
83 
85  double getQueryMass() const;
86 
88  void setQueryMass(const double&);
89 
91  double getFoundMass() const;
92 
94  void setFoundMass(const double&);
95 
97  Int getCharge() const;
98 
100  void setCharge(const Int&);
101 
103  double getMZErrorPPM() const;
104 
106  void setMZErrorPPM(const double);
107 
109  double getObservedRT() const;
110 
112  void setObservedRT(const double& rt);
113 
115  double getObservedIntensity() const;
116 
118  void setObservedIntensity(const double&);
119 
121  std::vector<double> getIndividualIntensities() const;
122 
124  void setIndividualIntensities(const std::vector<double>&);
125 
127  void setMatchingIndex(const Size&);
128 
131 
132  const String& getFoundAdduct() const;
133  void setFoundAdduct(const String&);
134 
135  const String& getFormulaString() const;
137 
138  const std::vector<String>& getMatchingHMDBids() const;
139  void setMatchingHMDBids(const std::vector<String>&);
140 
142  const std::vector<double>& getMasstraceIntensities() const;
143  void setMasstraceIntensities(const std::vector<double>&);
144 
145  double getIsotopesSimScore() const;
146  void setIsotopesSimScore(const double&);
147 
148  // debug/output functions
149  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const AccurateMassSearchResult& amsr);
150 
151 private:
153  double observed_mz_;
156  double db_mass_;
159  double observed_rt_;
161  std::vector<double> individual_intensities_;
164 
167  std::vector<String> matching_hmdb_ids_;
168 
169  std::vector<double> mass_trace_intensities_;
171  };
172 
173  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const AccurateMassSearchResult& amsr);
174 
206  class OPENMS_DLLAPI AccurateMassSearchEngine :
207  public DefaultParamHandler,
208  public ProgressLogger
209  {
210 public:
211 
213  static constexpr char search_engine_identifier[] = "AccurateMassSearchEngine";
214 
217 
220 
226  void queryByMZ(const double& observed_mz, const Int& observed_charge, const String& ion_mode, std::vector<AccurateMassSearchResult>& results, const EmpiricalFormula& observed_adduct = EmpiricalFormula()) const;
227  void queryByFeature(const Feature& feature, const Size& feature_index, const String& ion_mode, std::vector<AccurateMassSearchResult>& results) const;
228  void queryByConsensusFeature(const ConsensusFeature& cfeat, const Size& cf_index, const Size& number_of_maps, const String& ion_mode, std::vector<AccurateMassSearchResult>& results) const;
229 
232  void run(FeatureMap&, MzTab&) const;
233 
234  void run(FeatureMap&, MzTabM&) const;
235 
239  void run(ConsensusMap&, MzTab&) const;
240 
242  void init();
243 
244 protected:
245  void updateMembers_() override;
246 
247 private:
249 
252  template <typename MAPTYPE> String resolveAutoMode_(const MAPTYPE& map) const
253  {
254  String ion_mode_internal;
255  String ion_mode_detect_msg = "";
256  if (map.size() > 0)
257  {
258  if (map[0].metaValueExists("scan_polarity"))
259  {
260  StringList pols = ListUtils::create<String>(String(map[0].getMetaValue("scan_polarity")), ';');
261  if (pols.size() == 1 && !pols[0].empty())
262  {
263  pols[0].toLower();
264  if (pols[0] == "positive" || pols[0] == "negative")
265  {
266  ion_mode_internal = pols[0];
267  OPENMS_LOG_INFO << "Setting auto ion-mode to '" << ion_mode_internal << "' for file " << File::basename(map.getLoadedFilePath()) << std::endl;
268  }
269  else ion_mode_detect_msg = String("Meta value 'scan_polarity' does not contain unknown ion mode") + String(map[0].getMetaValue("scan_polarity"));
270  }
271  else
272  {
273  ion_mode_detect_msg = String("ambiguous ion mode: ") + String(map[0].getMetaValue("scan_polarity"));
274  }
275  }
276  else
277  {
278  ion_mode_detect_msg = String("Meta value 'scan_polarity' not found in (Consensus-)Feature map");
279  }
280  }
281  else
282  { // do nothing, since map is
283  OPENMS_LOG_INFO << "Meta value 'scan_polarity' cannot be determined since (Consensus-)Feature map is empty!" << std::endl;
284  }
285 
286  if (!ion_mode_detect_msg.empty())
287  {
288  throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, String("Auto ionization mode could not resolve ion mode of data (") + ion_mode_detect_msg + "!");
289  }
290 
291  return ion_mode_internal;
292  }
293 
296  void parseAdductsFile_(const String& filename, std::vector<AdductInfo>& result);
297  void searchMass_(double neutral_query_mass, double diff_mass, std::pair<Size, Size>& hit_indices) const;
298 
300  void annotate_(const std::vector<AccurateMassSearchResult>&, BaseFeature&) const;
301 
303  std::vector<AccurateMassSearchResult> extractQueryResults_(const Feature& feature, const Size& feature_index, const String& ion_mode_internal, Size& dummy_count) const;
304 
307  IdentificationData& id,
308  const std::vector<AccurateMassSearchResult>& amr,
309  const IdentificationData::InputFileRef& file_ref,
310  const IdentificationData::ScoreTypeRef& mass_error_ppm_score_ref,
311  const IdentificationData::ScoreTypeRef& mass_error_Da_score_ref,
313  BaseFeature& f) const;
314 
317  double computeCosineSim_(const std::vector<double>& x, const std::vector<double>& y) const;
318 
319  double computeIsotopePatternSimilarity_(const Feature& feat, const EmpiricalFormula& form) const;
320 
321  typedef std::vector<std::vector<AccurateMassSearchResult> > QueryResultsTable;
322 
323  void exportMzTab_(const QueryResultsTable& overall_results, const Size number_of_maps, MzTab& mztab_out, const std::vector<String>& file_locations) const;
324 
325  void exportMzTabM_(const FeatureMap& fmap, MzTabM& mztabm_out) const;
326 
328  typedef std::vector<std::vector<String> > MassIDMapping;
329  typedef std::map<String, std::vector<String> > HMDBPropsMapping;
330 
332  {
333  double mass;
334  std::vector<String> massIDs;
336  };
337  std::vector<MappingEntry_> mass_mappings_;
338 
339  struct CompareEntryAndMass_ // defined here to allow for inlining by compiler
340  {
341  double asMass(const MappingEntry_& v) const
342  {
343  return v.mass;
344  }
345 
346  double asMass(double t) const
347  {
348  return t;
349  }
350 
351  template <typename T1, typename T2>
352  bool operator()(T1 const& t1, T2 const& t2) const
353  {
354  return asMass(t1) < asMass(t2);
355  }
356 
357  };
358 
360 
362 
363  bool legacyID_ = true;
364 
370 
373 
376 
377  std::vector<AdductInfo> pos_adducts_;
378  std::vector<AdductInfo> neg_adducts_;
379 
383 
385  };
386 
387 }
#define OPENMS_LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:475
An algorithm to search for exact mass matches from a spectrum against a database (e....
Definition: AccurateMassSearchEngine.h:209
void run(FeatureMap &, MzTabM &) const
void init()
parse database and adduct files
void parseStructMappingFile_(const StringList &)
std::vector< std::vector< String > > MassIDMapping
private member variables
Definition: AccurateMassSearchEngine.h:328
String pos_adducts_fname_
Definition: AccurateMassSearchEngine.h:371
bool keep_unidentified_masses_
Definition: AccurateMassSearchEngine.h:384
double mass
Definition: AccurateMassSearchEngine.h:333
void queryByConsensusFeature(const ConsensusFeature &cfeat, const Size &cf_index, const Size &number_of_maps, const String &ion_mode, std::vector< AccurateMassSearchResult > &results) const
AccurateMassSearchEngine()
Default constructor.
String mass_error_unit_
Definition: AccurateMassSearchEngine.h:367
StringList db_struct_file_
Definition: AccurateMassSearchEngine.h:375
void exportMzTabM_(const FeatureMap &fmap, MzTabM &mztabm_out) const
~AccurateMassSearchEngine() override
Default destructor.
void addMatchesToID_(IdentificationData &id, const std::vector< AccurateMassSearchResult > &amr, const IdentificationData::InputFileRef &file_ref, const IdentificationData::ScoreTypeRef &mass_error_ppm_score_ref, const IdentificationData::ScoreTypeRef &mass_error_Da_score_ref, const IdentificationData::ProcessingStepRef &step_ref, BaseFeature &f) const
Add resulting matches to IdentificationData.
double mass_error_value_
parameter stuff
Definition: AccurateMassSearchEngine.h:366
void run(ConsensusMap &, MzTab &) const
void searchMass_(double neutral_query_mass, double diff_mass, std::pair< Size, Size > &hit_indices) const
void queryByMZ(const double &observed_mz, const Int &observed_charge, const String &ion_mode, std::vector< AccurateMassSearchResult > &results, const EmpiricalFormula &observed_adduct=EmpiricalFormula()) const
search for a specific observed mass by enumerating all possible adducts and search M+X against databa...
std::vector< std::vector< AccurateMassSearchResult > > QueryResultsTable
Definition: AccurateMassSearchEngine.h:321
void annotate_(const std::vector< AccurateMassSearchResult > &, BaseFeature &) const
Add search results to a Consensus/Feature.
bool iso_similarity_
Definition: AccurateMassSearchEngine.h:369
std::vector< AdductInfo > pos_adducts_
Definition: AccurateMassSearchEngine.h:377
String neg_adducts_fname_
Definition: AccurateMassSearchEngine.h:372
HMDBPropsMapping hmdb_properties_mapping_
Definition: AccurateMassSearchEngine.h:359
std::vector< String > massIDs
Definition: AccurateMassSearchEngine.h:334
String ion_mode_
Definition: AccurateMassSearchEngine.h:368
double computeIsotopePatternSimilarity_(const Feature &feat, const EmpiricalFormula &form) const
void parseMappingFile_(const StringList &)
String database_version_
Definition: AccurateMassSearchEngine.h:381
double computeCosineSim_(const std::vector< double > &x, const std::vector< double > &y) const
String database_location_
Definition: AccurateMassSearchEngine.h:382
bool is_initialized_
true if init_() was called without any subsequent param changes
Definition: AccurateMassSearchEngine.h:361
std::vector< AccurateMassSearchResult > extractQueryResults_(const Feature &feature, const Size &feature_index, const String &ion_mode_internal, Size &dummy_count) const
Extract query results from feature.
StringList db_mapping_file_
Definition: AccurateMassSearchEngine.h:374
std::vector< AdductInfo > neg_adducts_
Definition: AccurateMassSearchEngine.h:378
String database_name_
Definition: AccurateMassSearchEngine.h:380
String formula
Definition: AccurateMassSearchEngine.h:335
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
void run(FeatureMap &, MzTab &) const
String resolveAutoMode_(const MAPTYPE &map) const
private member functions
Definition: AccurateMassSearchEngine.h:252
std::map< String, std::vector< String > > HMDBPropsMapping
Definition: AccurateMassSearchEngine.h:329
void exportMzTab_(const QueryResultsTable &overall_results, const Size number_of_maps, MzTab &mztab_out, const std::vector< String > &file_locations) const
void queryByFeature(const Feature &feature, const Size &feature_index, const String &ion_mode, std::vector< AccurateMassSearchResult > &results) const
void parseAdductsFile_(const String &filename, std::vector< AdductInfo > &result)
std::vector< MappingEntry_ > mass_mappings_
Definition: AccurateMassSearchEngine.h:337
Definition: AccurateMassSearchEngine.h:332
Definition: AccurateMassSearchEngine.h:58
const std::vector< String > & getMatchingHMDBids() const
std::vector< double > mass_trace_intensities_
Definition: AccurateMassSearchEngine.h:169
std::vector< double > getIndividualIntensities() const
get the observed intensities
void setMasstraceIntensities(const std::vector< double > &)
std::vector< String > matching_hmdb_ids_
Definition: AccurateMassSearchEngine.h:167
double getObservedMZ() const
get the m/z of the small molecule + adduct
std::vector< double > individual_intensities_
Definition: AccurateMassSearchEngine.h:161
AccurateMassSearchResult & operator=(const AccurateMassSearchResult &)
assignment operator
double getFoundMass() const
get the mass returned by the query (uncharged small molecule)
void setQueryMass(const double &)
set the mass used to query the database (uncharged small molecule)
const String & getFoundAdduct() const
double observed_intensity_
Definition: AccurateMassSearchEngine.h:160
void setIsotopesSimScore(const double &)
void setSourceFeatureIndex(const Size &)
const String & getFormulaString() const
double searched_mass_
Definition: AccurateMassSearchEngine.h:155
void setFoundMass(const double &)
set the mass returned by the query (uncharged small molecule)
double theoretical_mz_
Definition: AccurateMassSearchEngine.h:154
AccurateMassSearchResult()
Default constructor.
double getMZErrorPPM() const
get the error between observed and theoretical m/z in ppm
double observed_rt_
Definition: AccurateMassSearchEngine.h:159
Int getCharge() const
get the charge
double isotopes_sim_score_
Definition: AccurateMassSearchEngine.h:170
~AccurateMassSearchResult()
Default destructor.
String empirical_formula_
Definition: AccurateMassSearchEngine.h:166
void setCharge(const Int &)
set the charge
friend std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
void setFoundAdduct(const String &)
double getQueryMass() const
get the mass used to query the database (uncharged small molecule)
void setObservedMZ(const double &)
set the m/z of the small molecule + adduct
AccurateMassSearchResult(const AccurateMassSearchResult &)
copy constructor
void setEmpiricalFormula(const String &)
void setMZErrorPPM(const double)
set the error between observed and theoretical m/z in ppm
double getObservedRT() const
get the observed rt
double getObservedIntensity() const
get the observed intensity
String found_adduct_
Definition: AccurateMassSearchEngine.h:165
double observed_mz_
Stored information/results of DB query.
Definition: AccurateMassSearchEngine.h:153
double db_mass_
Definition: AccurateMassSearchEngine.h:156
void setMatchingIndex(const Size &)
Size source_feature_index_
Definition: AccurateMassSearchEngine.h:163
Size matching_index_
Definition: AccurateMassSearchEngine.h:162
void setObservedIntensity(const double &)
set the observed intensity
void setMatchingHMDBids(const std::vector< String > &)
double mz_error_ppm_
Definition: AccurateMassSearchEngine.h:158
const std::vector< double > & getMasstraceIntensities() const
return trace intensities of the underlying feature;
void setObservedRT(const double &rt)
set the observed rt
Int charge_
Definition: AccurateMassSearchEngine.h:157
void setCalculatedMZ(const double &)
set the theoretical m/z of the small molecule + adduct
void setIndividualIntensities(const std::vector< double > &)
set the observed intensities
double getCalculatedMZ() const
get the theoretical m/z of the small molecule + adduct
A basic LC-MS feature.
Definition: BaseFeature.h:59
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:71
A container for consensus elements.
Definition: ConsensusMap.h:92
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
Representation of an empirical formula.
Definition: EmpiricalFormula.h:85
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:341
A container for features.
Definition: FeatureMap.h:106
An LC-MS feature.
Definition: Feature.h:72
static String basename(const String &file)
Definition: IdentificationData.h:113
Data model of MzTab-M files Please see the MzTab-M specification at https://github....
Definition: MzTabM.h:234
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:478
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:53
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:70
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
Definition: AccurateMassSearchEngine.h:340
bool operator()(T1 const &t1, T2 const &t2) const
Definition: AccurateMassSearchEngine.h:352
double asMass(double t) const
Definition: AccurateMassSearchEngine.h:346
double asMass(const MappingEntry_ &v) const
Definition: AccurateMassSearchEngine.h:341