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OpenMS
2.5.0
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Go to the documentation of this file.
78 double getObservedPrecursorMass()
const;
79 void setObservedPrecursorMass(
const double&);
81 double getObservedPrecursorRT()
const;
82 void setObservedPrecursorRT(
const double&);
84 double getFoundPrecursorMass()
const;
85 void setFoundPrecursorMass(
const double&);
87 Int getFoundPrecursorCharge()
const;
88 void setFoundPrecursorCharge(
const Int&);
90 double getMatchingScore()
const;
91 void setMatchingScore(
const double&);
93 Size getObservedSpectrumIndex()
const;
94 void setObservedSpectrumIndex(
const Size&);
96 Size getMatchingSpectrumIndex()
const;
97 void setMatchingSpectrumIndex(
const Size&);
99 String getPrimaryIdentifier()
const;
100 void setPrimaryIdentifier(
const String&);
102 String getSecondaryIdentifier()
const;
103 void setSecondaryIdentifier(
const String&);
105 String getCommonName()
const;
106 void setCommonName(
const String&);
108 String getSumFormula()
const;
109 void setSumFormula(
const String&);
111 String getInchiString()
const;
112 void setInchiString(
const String&);
114 String getSMILESString()
const;
115 void setSMILESString(
const String&);
117 String getPrecursorAdduct()
const;
118 void setPrecursorAdduct(
const String&);
162 static double computeHyperScore(
163 double fragment_mass_error,
164 bool fragment_mass_tolerance_unit_ppm,
167 double mz_lower_bound = 0.0);
170 static double computeHyperScore(
171 double fragment_mass_error,
172 bool fragment_mass_tolerance_unit_ppm,
175 std::vector<PeptideHit::PeakAnnotation>& annotations,
176 double mz_lower_bound = 0.0);
182 void updateMembers_()
override;
186 static double computeHyperScore_(
187 double fragment_mass_error,
188 bool fragment_mass_tolerance_unit_ppm,
191 std::vector<PeptideHit::PeakAnnotation>* annotations = 0,
192 double mz_lower_bound = 0.0);
196 void exportMzTab_(
const std::vector<SpectralMatch>&,
MzTab&);
Base class for TOPP applications.
Definition: TOPPBase.h:144
Param copy(const String &prefix, bool remove_prefix=false) const
Returns a new Param object containing all entries that start with prefix.
Definition: MetaboliteSpectralMatching.h:141
File adapter for MzTab files.
Definition: MzTabFile.h:58
Int found_precursor_charge_
Definition: MetaboliteSpectralMatching.h:125
File adapter for MzML files.
Definition: MzMLFile.h:55
struct OpenMS::PrecursorMassComparator PrecursorMZLess
A more convenient string class.
Definition: String.h:58
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
const std::vector< Precursor > & getPrecursors() const
returns a const reference to the precursors
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Data model of MzTab files. Please see the official MzTab specification at https://code....
Definition: MzTab.h:855
#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
double found_precursor_mass_
Definition: MetaboliteSpectralMatching.h:124
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
static String find(const String &filename, StringList directories=StringList())
Looks up the location of the file filename.
String primary_id_
Definition: MetaboliteSpectralMatching.h:131
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
String inchi_string_
Definition: MetaboliteSpectralMatching.h:135
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
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...
double getMatchingScore() const
Size observed_spectrum_idx_
Definition: MetaboliteSpectralMatching.h:127
double observed_precursor_mass_
Definition: MetaboliteSpectralMatching.h:122
String precursor_adduct_
Definition: MetaboliteSpectralMatching.h:137
void store(const String &filename, const MzTab &mz_tab) const
struct OpenMS::SpectralMatchScoreComparator SpectralMatchScoreGreater
void setParameters(const Param ¶m)
Sets the parameters.
const Param & getDefaults() const
Non-mutable access to the default parameters.
bool empty() const
Definition: MSExperiment.h:137
Definition: MetaboliteSpectralMatching.h:54
String secondary_id_
Definition: MetaboliteSpectralMatching.h:132
int main(int argc, const char **argv)
Definition: INIFileEditor.cpp:73
double matching_score_
Definition: MetaboliteSpectralMatching.h:126
Size matching_spectrum_idx_
Definition: MetaboliteSpectralMatching.h:128
String smiles_string_
Definition: MetaboliteSpectralMatching.h:136
Definition: MetaboliteSpectralMatching.h:63
Management and storage of parameters / INI files.
Definition: Param.h:73
double observed_precursor_rt_
Definition: MetaboliteSpectralMatching.h:123
String common_name_
Definition: MetaboliteSpectralMatching.h:133
void setMSLevels(const std::vector< Int > &levels)
sets the desired MS levels for peaks to load
The representation of a 1D spectrum.
Definition: MSSpectrum.h:67
String sum_formula_
Definition: MetaboliteSpectralMatching.h:134
PeakFileOptions & getOptions()
Mutable access to the options for loading/storing.
void setLogType(LogType type) const
Sets the progress log that should be used. The default type is NONE!