OpenMS  3.0.0
SpectrumLookup.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
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34 
35 #pragma once
36 
39 
40 #include <boost/regex.hpp>
41 
42 namespace OpenMS
43 {
67  class OPENMS_DLLAPI SpectrumLookup
68  {
69  public:
70 
72  static const String& default_scan_regexp;
73 
75  std::vector<boost::regex> reference_formats;
76 
78  double rt_tolerance;
79 
82 
84  virtual ~SpectrumLookup();
85 
87  bool empty() const;
88 
102  template <typename SpectrumContainer>
103  void readSpectra(const SpectrumContainer& spectra,
104  const String& scan_regexp = default_scan_regexp)
105  {
106  rts_.clear();
107  ids_.clear();
108  scans_.clear();
109  n_spectra_ = spectra.size();
110  setScanRegExp_(scan_regexp);
111  for (Size i = 0; i < n_spectra_; ++i)
112  {
113  const MSSpectrum& spectrum = spectra[i];
114  const String& native_id = spectrum.getNativeID();
115  Int scan_no = -1;
116  if (!scan_regexp.empty())
117  {
118  scan_no = extractScanNumber(native_id, scan_regexp_, true);
119  if (scan_no < 0)
120  {
121  OPENMS_LOG_WARN << "Warning: Could not extract scan number from spectrum native ID '" + native_id + "' using regular expression '" + scan_regexp + "'. Look-up by scan number may not work properly." << std::endl;
122  }
123  }
124  addEntry_(i, spectrum.getRT(), scan_no, native_id);
125  }
126  }
127 
139  Size findByRT(double rt) const;
140 
150  Size findByNativeID(const String& native_id) const;
151 
162  Size findByIndex(Size index, bool count_from_one = false) const;
163 
173  Size findByScanNumber(Size scan_number) const;
174 
187  Size findByReference(const String& spectrum_ref) const;
188 
198  void addReferenceFormat(const String& regexp);
199 
211  static Int extractScanNumber(const String& native_id,
212  const boost::regex& scan_regexp,
213  bool no_error = false);
214 
215  static Int extractScanNumber(const String& native_id,
216  const String& native_id_type_accession);
222  static std::string getRegExFromNativeID(const String& id);
223 
227  static bool isNativeID(const String& id);
228 
229  protected:
230 
232  static const String& regexp_names_;
233 
235 
236  boost::regex scan_regexp_;
237 
238  std::vector<String> regexp_name_list_;
239 
240  std::map<double, Size> rts_;
241  std::map<String, Size> ids_;
242  std::map<Size, Size> scans_;
243 
252  void addEntry_(Size index, double rt, Int scan_number,
253  const String& native_id);
254 
266  Size findByRegExpMatch_(const String& spectrum_ref, const String& regexp,
267  const boost::smatch& match) const;
268 
274  void setScanRegExp_(const String& scan_regexp);
275 
276  private:
277 
280 
282  SpectrumLookup& operator=(const SpectrumLookup&);
283 
284  };
285 
286 } //namespace OpenMS
287 
LogStream.h
OpenMS::SpectrumLookup::ids_
std::map< String, Size > ids_
Mapping: native ID -> spectrum index.
Definition: SpectrumLookup.h:241
OpenMS::SpectrumLookup::scan_regexp_
boost::regex scan_regexp_
Regular expression to extract scan numbers.
Definition: SpectrumLookup.h:236
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::SpectrumLookup::rts_
std::map< double, Size > rts_
Mapping: RT -> spectrum index.
Definition: SpectrumLookup.h:240
OpenMS::SpectrumLookup::n_spectra_
Size n_spectra_
Number of spectra.
Definition: SpectrumLookup.h:234
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::MSSpectrum::getRT
double getRT() const
OpenMS::SpectrumLookup::default_scan_regexp
static const String & default_scan_regexp
Default regular expression for extracting scan numbers from spectrum native IDs.
Definition: SpectrumLookup.h:72
OPENMS_LOG_WARN
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged.
Definition: LogStream.h:460
OpenMS::SpectrumLookup::regexp_name_list_
std::vector< String > regexp_name_list_
Named groups in vector format.
Definition: SpectrumLookup.h:238
OpenMS::SpectrumLookup::regexp_names_
static const String & regexp_names_
Named groups recognized in regular expression.
Definition: SpectrumLookup.h:232
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::SpectrumLookup::scans_
std::map< Size, Size > scans_
Mapping: scan number -> spectrum index.
Definition: SpectrumLookup.h:242
OpenMS::SpectrumLookup::rt_tolerance
double rt_tolerance
Tolerance for look-up by retention time.
Definition: SpectrumLookup.h:78
OpenMS::SpectrumLookup
Helper class for looking up spectra based on different attributes.
Definition: SpectrumLookup.h:67
OpenMS::SpectrumLookup::readSpectra
void readSpectra(const SpectrumContainer &spectra, const String &scan_regexp=default_scan_regexp)
Read and index spectra for later look-up.
Definition: SpectrumLookup.h:103
OpenMS::SpectrumLookup::reference_formats
std::vector< boost::regex > reference_formats
Possible formats of spectrum references, defined as regular expressions.
Definition: SpectrumLookup.h:75
OpenMS::SpectrumSettings::getNativeID
const String & getNativeID() const
returns the native identifier for the spectrum, used by the acquisition software.
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
MSSpectrum.h