OpenMS  2.4.0
InternalCalibration.h
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31 // $Maintainer: Chris Bielow $
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34 
35 #pragma once
36 
43 
44 #include <vector>
45 
46 namespace OpenMS
47 {
48 
49  class FeatureMap;
50 
61  class OPENMS_DLLAPI InternalCalibration
62  : public ProgressLogger
63  {
64  public:
65 
68 
71 
73  struct LockMass
74  {
75  double mz;
76  unsigned int ms_level;
77  int charge;
78 
79  LockMass(double mz_, int lvl_, int charge_)
80  : mz(mz_),
81  ms_level(lvl_),
82  charge(charge_)
83  {}
84  };
85 
86 
87 
110  Size fillCalibrants(const PeakMap exp,
111  const std::vector<InternalCalibration::LockMass>& ref_masses,
112  double tol_ppm,
113  bool lock_require_mono,
114  bool lock_require_iso,
115  CalibrationData& failed_lock_masses,
116  bool verbose = true);
117 
139  Size fillCalibrants(const FeatureMap& fm, double tol_ppm);
140 
156  Size fillCalibrants(const std::vector<PeptideIdentification>& pep_ids, double tol_ppm);
157 
166  const CalibrationData& getCalibrationPoints() const;
167 
192  bool calibrate(PeakMap& exp,
193  const IntList& target_mslvl,
194  MZTrafoModel::MODELTYPE model_type,
195  double rt_chunk,
196  bool use_RANSAC,
197  double post_ppm_median,
198  double post_ppm_MAD,
199  const String& file_models = "",
200  const String& file_models_plot = "",
201  const String& file_residuals = "",
202  const String& file_residuals_plot = "",
203  const String& rscript_executable = "Rscript");
204 
205  /*
206  @brief Transform a precursor's m/z
207 
208  Calibrate m/z of precursors.
209 
210  @param pcs Uncalibrated Precursors
211  @param trafo The calibration function to apply
212  */
213  static void applyTransformation(std::vector<Precursor>& pcs, const MZTrafoModel& trafo);
214 
215  /*
216  @brief Transform a spectrum (data+precursor)
217 
218  See applyTransformation(MSExperiment, ...) for details.
219 
220  @param spec Uncalibrated MSSpectrum
221  @param target_mslvl List (can be unsorted) of MS levels to calibrate
222  @param trafo The calibration function to apply
223  */
224  static void applyTransformation(PeakMap::SpectrumType& spec, const IntList& target_mslvl, const MZTrafoModel& trafo);
225 
226  /*
227  @brief Transform spectra from a whole map (data+precursor)
228 
229  All data peaks and precursor information (if present) are calibrated in m/z.
230 
231  Only spectra whose MS-level is contained in 'target_mslvl' are calibrated.
232  In addition, if a fragmentation spectrum's precursor information originates from an MS level in 'target_mslvl',
233  the precursor (not the spectrum itself) is also subjected to calibration.
234  E.g., If we only have MS and MS/MS spectra: for 'target_mslvl' = {1} then all MS1 spectra and MS2 precursors are calibrated.
235  If 'target_mslvl' = {2}, only MS2 spectra (not their precursors) are calibrated.
236  If 'target_mslvl' = {1,2} all spectra and precursors are calibrated.
237 
238 
239  @param exp Uncalibrated peak map
240  @param target_mslvl List (can be unsorted) of MS levels to calibrate
241  @param trafo The calibration function to apply
242  */
243  static void applyTransformation(PeakMap& exp, const IntList& target_mslvl, const MZTrafoModel& trafo);
244 
245  protected:
261  void fillIDs_( const std::vector<PeptideIdentification>& pep_ids, double tol_ppm );
262 
263  /*
264  @brief Calibrate m/z of a spectrum, ignoring precursors!
265 
266  This method is not exposed as public, because its easy to be misused on spectra while forgetting about the precursors of high-level spectra.
267  */
268  static void applyTransformation_(PeakMap::SpectrumType& spec, const MZTrafoModel& trafo);
269 
270  private:
272 
273 
274  }; // class InternalCalibration
275 
276 } // namespace OpenMS
277 
OpenMS::FileTypes::IDXML
@ IDXML
OpenMS identification format (.idXML)
Definition: FileTypes.h:66
OpenMS::TOPPBase
Base class for TOPP applications.
Definition: TOPPBase.h:150
OpenMS::MZTrafoModel::setRANSACParams
static void setRANSACParams(const Math::RANSACParam &p)
Set the global (program wide) parameters for RANSAC.
OpenMS::TextFile::end
ConstIterator end() const
Gives access to the underlying text buffer.
OpenMS::MSExperiment::set2DData
void set2DData(const Container &container)
Assignment of a data container with RT and MZ to an MSExperiment.
Definition: MSExperiment.h:240
FileHandler.h
FileTypes.h
TextFile.h
OpenMS::MzMLFile::store
void store(const String &filename, const PeakMap &map) const
Stores a map in an MzML file.
OpenMS::MZTrafoModel::setCoefficientLimits
static void setCoefficientLimits(double offset, double scale, double power)
Set coefficient boundaries for which the model coefficient must not exceed to be considered a valid m...
OpenMS::MZTrafoModel::MODELTYPE
MODELTYPE
Definition: MZTrafoModel.h:98
InternalCalibration.h
OpenMS::Math::RANSACParam
A simple struct to carry all the parameters required for a RANSAC run.
Definition: RANSAC.h:58
OpenMS::MzMLFile
File adapter for MzML files.
Definition: MzMLFile.h:55
OpenMS::String
A more convenient string class.
Definition: String.h:57
MzMLFile.h
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FileHandler::getTypeByContent
static FileTypes::Type getTypeByContent(const String &filename)
Determines the file type of a file by parsing the first few lines.
OpenMS::TextFile
This class provides some basic file handling methods for text files.
Definition: TextFile.h:46
LOG_ERROR
#define LOG_ERROR
Macro to be used if non-fatal error are reported (processing continues)
Definition: LogStream.h:446
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
IdXMLFile.h
FeatureXMLFile.h
LOG_INFO
#define LOG_INFO
Macro if a information, e.g. a status should be reported.
Definition: LogStream.h:454
OpenMS::InternalCalibration::LockMass
helper class, describing a lock mass
Definition: InternalCalibration.h:73
OpenMS::InternalCalibration::LockMass::charge
int charge
charge of the ion (to find isotopes)
Definition: InternalCalibration.h:77
OpenMS::InternalCalibration::LockMass::mz
double mz
m/z of the lock mass (incl. adducts)
Definition: InternalCalibration.h:75
OpenMS::IntList
std::vector< Int > IntList
Vector of signed integers.
Definition: ListUtils.h:58
OpenMS::InternalCalibration
A mass recalibration method using linear/quadratic interpolation (robust/weighted) of given reference...
Definition: InternalCalibration.h:61
MZTrafoModel.h
OpenMS::String::hasSubstring
bool hasSubstring(const String &string) const
true if String contains the string, false otherwise
ListUtils.h
OpenMS::CalibrationData::getMetaValues
static StringList getMetaValues()
List of meta-values which are used internally (for conversion to PeakMap).
OpenMS::IdXMLFile::load
void load(const String &filename, std::vector< ProteinIdentification > &protein_ids, std::vector< PeptideIdentification > &peptide_ids)
Loads the identifications of an idXML file without identifier.
OpenMS::MZTrafoModel::enumToName
static const std::string & enumToName(MODELTYPE mt)
Convert enum to string.
OpenMS::InternalCalibration::calibrate
bool calibrate(PeakMap &exp, const IntList &target_mslvl, MZTrafoModel::MODELTYPE model_type, double rt_chunk, bool use_RANSAC, double post_ppm_median, double post_ppm_MAD, const String &file_models="", const String &file_models_plot="", const String &file_residuals="", const String &file_residuals_plot="", const String &rscript_executable="Rscript")
Apply calibration to data.
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::FileTypes::FEATUREXML
@ FEATUREXML
OpenMS feature file (.featureXML)
Definition: FileTypes.h:65
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
ProgressLogger.h
OpenMS::MzMLFile::load
void load(const String &filename, PeakMap &map)
Loads a map from a MzML file. Spectra and chromatograms are sorted by default (this can be disabled u...
TransformationXMLFile.h
OpenMS::InternalCalibration::LockMass::LockMass
LockMass(double mz_, int lvl_, int charge_)
Definition: InternalCalibration.h:79
OpenMS::FileHandler
Facilitates file handling by file type recognition.
Definition: FileHandler.h:62
OpenMS::FeatureXMLFile::load
void load(const String &filename, FeatureMap &feature_map)
loads the file with name filename into map and calls updateRanges().
OpenMS::FileTypes::Type
Type
Actual file types enum.
Definition: FileTypes.h:58
OpenMS::MZTrafoModel::LINEAR_WEIGHTED
@ LINEAR_WEIGHTED
Definition: MZTrafoModel.h:98
OpenMS::DataProcessing::CALIBRATION
@ CALIBRATION
Calibration of m/z positions.
Definition: DataProcessing.h:69
OpenMS::CalibrationData::empty
bool empty() const
Do we have any calibration points.
main
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
OpenMS::InternalCalibration::cal_data_
CalibrationData cal_data_
Definition: InternalCalibration.h:271
MSExperiment.h
OpenMS::TextFile::begin
ConstIterator begin() const
Gives access to the underlying text buffer.
OpenMS::Internal::ClassTest::verbose
int verbose
Verbosity level ( "-v" is 1 and "-V" is 2 )
OpenMS::MZTrafoModel::SIZE_OF_MODELTYPE
@ SIZE_OF_MODELTYPE
Definition: MZTrafoModel.h:98
OpenMS::InternalCalibration::fillCalibrants
Size fillCalibrants(const PeakMap exp, const std::vector< InternalCalibration::LockMass > &ref_masses, double tol_ppm, bool lock_require_mono, bool lock_require_iso, CalibrationData &failed_lock_masses, bool verbose=true)
Extract calibrants from Raw data (mzML)
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:93
OpenMS::InternalCalibration::~InternalCalibration
~InternalCalibration()
Destructor.
Definition: InternalCalibration.h:70
OpenMS::MZTrafoModel
Create and apply models of a mass recalibration function.
Definition: MZTrafoModel.h:66
OpenMS::FeatureXMLFile
This class provides Input/Output functionality for feature maps.
Definition: FeatureXMLFile.h:68
OpenMS::InternalCalibration::LockMass::ms_level
unsigned int ms_level
MS level where it occurs.
Definition: InternalCalibration.h:76
OpenMS::MZTrafoModel::nameToEnum
static MODELTYPE nameToEnum(const std::string &name)
Convert string to enum.
CalibrationData.h
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:195
OpenMS::MSSpectrum
The representation of a 1D spectrum.
Definition: MSSpectrum.h:66
OpenMS::CalibrationData
A helper class, holding all calibration points.
Definition: CalibrationData.h:64
OpenMS::TextFile::ConstIterator
std::vector< String >::const_iterator ConstIterator
Non-mutable iterator.
Definition: TextFile.h:56
OpenMS::MZTrafoModel::names_of_modeltype
static const std::string names_of_modeltype[]
strings corresponding to enum MODELTYPE
Definition: MZTrafoModel.h:99
OpenMS::TextFile::load
void load(const String &filename, bool trim_lines=false, Int first_n=-1, bool skip_empty_lines=false)
Loads data from a text file.
StandardTypes.h
OpenMS::ProgressLogger::setLogType
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!
TOPPBase.h
OpenMS::InternalCalibration::getCalibrationPoints
const CalibrationData & getCalibrationPoints() const
Get container of calibration points.
OpenMS::IdXMLFile
Used to load and store idXML files.
Definition: IdXMLFile.h:63