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|  | MSSpectrum () | 
|  | Constructor.  More... 
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|  | MSSpectrum (const MSSpectrum &source) | 
|  | Copy constructor.  More... 
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|  | ~MSSpectrum () | 
|  | Destructor.  More... 
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| MSSpectrum & | operator= (const MSSpectrum &source) | 
|  | Assignment operator.  More... 
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| bool | operator== (const MSSpectrum &rhs) const | 
|  | Equality operator.  More... 
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| bool | operator!= (const MSSpectrum &rhs) const | 
|  | Equality operator.  More... 
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| virtual void | updateRanges () | 
|  | Updates minimum and maximum position/intensity.  More... 
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| void | clear (bool clear_meta_data) | 
|  | Clears all data and meta data.  More... 
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| Returns the absolute retention time (is seconds)  | 
| DoubleReal | getRT () const | 
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| void | setRT (DoubleReal rt) | 
|  | Sets the absolute retention time (is seconds)  More... 
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| UInt | getMSLevel () const | 
|  | Returns the MS level.  More... 
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| void | setMSLevel (UInt ms_level) | 
|  | Sets the MS level.  More... 
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| const String & | getName () const | 
|  | Returns the name.  More... 
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| void | setName (const String &name) | 
|  | Sets the name.  More... 
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| These methods are used to annotate each peak in a spectrum with meta information. It is an intermediate way between storing the information in the peak's MetaInfoInterface and deriving a new peak type with members for this information. These statements should help you chose which approach to use 
Access to meta info arrays is slower than to a member variableAccess to meta info arrays is faster than to a MetaInfoInterfaceMeta info arrays are stored when using mzML format for storing  | 
| const FloatDataArrays & | getFloatDataArrays () const | 
|  | Returns a const reference to the float meta data arrays.  More... 
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| FloatDataArrays & | getFloatDataArrays () | 
|  | Returns a mutable reference to the float meta data arrays.  More... 
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| const StringDataArrays & | getStringDataArrays () const | 
|  | Returns a const reference to the string meta data arrays.  More... 
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| StringDataArrays & | getStringDataArrays () | 
|  | Returns a mutable reference to the string meta data arrays.  More... 
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| const IntegerDataArrays & | getIntegerDataArrays () const | 
|  | Returns a const reference to the integer meta data arrays.  More... 
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| IntegerDataArrays & | getIntegerDataArrays () | 
|  | Returns a mutable reference to the integer meta data arrays.  More... 
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| void | sortByIntensity (bool reverse=false) | 
|  | Lexicographically sorts the peaks by their intensity.  More... 
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| void | sortByPosition () | 
|  | Lexicographically sorts the peaks by their position.  More... 
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| bool | isSorted () const | 
|  | Checks if all peaks are sorted with respect to ascending m/z.  More... 
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| Size | findNearest (CoordinateType mz) const | 
|  | Binary search for the peak nearest to a specific m/z.  More... 
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| Iterator | MZBegin (CoordinateType mz) | 
|  | Binary search for peak range begin.  More... 
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| Iterator | MZBegin (Iterator begin, CoordinateType mz, Iterator end) | 
|  | Binary search for peak range begin.  More... 
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| Iterator | MZEnd (CoordinateType mz) | 
|  | Binary search for peak range end (returns the past-the-end iterator)  More... 
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| Iterator | MZEnd (Iterator begin, CoordinateType mz, Iterator end) | 
|  | Binary search for peak range end (returns the past-the-end iterator)  More... 
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| ConstIterator | MZBegin (CoordinateType mz) const | 
|  | Binary search for peak range begin.  More... 
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| ConstIterator | MZBegin (ConstIterator begin, CoordinateType mz, ConstIterator end) const | 
|  | Binary search for peak range begin.  More... 
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| ConstIterator | MZEnd (CoordinateType mz) const | 
|  | Binary search for peak range end (returns the past-the-end iterator)  More... 
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| ConstIterator | MZEnd (ConstIterator begin, CoordinateType mz, ConstIterator end) const | 
|  | Binary search for peak range end (returns the past-the-end iterator)  More... 
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|  | RangeManager () | 
|  | Default constructor.  More... 
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|  | RangeManager (const RangeManager &rhs) | 
|  | Copy constructor.  More... 
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| virtual | ~RangeManager () | 
|  | Destructor.  More... 
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| RangeManager & | operator= (const RangeManager &rhs) | 
|  | Assignment operator.  More... 
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| bool | operator== (const RangeManager &rhs) const | 
|  | Equality operator.  More... 
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| bool | operator!= (const RangeManager &rhs) const | 
|  | Equality operator.  More... 
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| const PositionType & | getMin () const | 
|  | Returns the minimum position.  More... 
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| const PositionType & | getMax () const | 
|  | Returns the maximum position.  More... 
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| DoubleReal | getMinInt () const | 
|  | Returns the minimum intensity.  More... 
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| DoubleReal | getMaxInt () const | 
|  | Returns the maximum intensity.  More... 
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| void | clearRanges () | 
|  | Resets the ranges.  More... 
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|  | SpectrumSettings () | 
|  | Constructor.  More... 
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|  | SpectrumSettings (const SpectrumSettings &source) | 
|  | Copy constructor.  More... 
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|  | ~SpectrumSettings () | 
|  | Destructor.  More... 
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| SpectrumSettings & | operator= (const SpectrumSettings &source) | 
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| bool | operator== (const SpectrumSettings &rhs) const | 
|  | Equality operator.  More... 
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| bool | operator!= (const SpectrumSettings &rhs) const | 
|  | Equality operator.  More... 
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| void | unify (const SpectrumSettings &rhs) | 
|  | merge another spectrum setting into this one (data is usually appended, except for spectrum type which needs to be unambiguous to be kept)  More... 
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| SpectrumType | getType () const | 
|  | returns the spectrum type  More... 
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| void | setType (SpectrumType type) | 
|  | sets the spectrum type  More... 
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| const String & | getNativeID () const | 
|  | returns the native identifier for the spectrum, used by the acquisition software.  More... 
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| void | setNativeID (const String &native_id) | 
|  | sets the native identifier for the spectrum, used by the acquisition software.  More... 
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| const String & | getComment () const | 
|  | returns the free-text comment  More... 
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| void | setComment (const String &comment) | 
|  | sets the free-text comment  More... 
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| const InstrumentSettings & | getInstrumentSettings () const | 
|  | returns a const reference to the instrument settings of the current spectrum  More... 
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| InstrumentSettings & | getInstrumentSettings () | 
|  | returns a mutable reference to the instrument settings of the current spectrum  More... 
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| void | setInstrumentSettings (const InstrumentSettings &instrument_settings) | 
|  | sets the instrument settings of the current spectrum  More... 
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| const AcquisitionInfo & | getAcquisitionInfo () const | 
|  | returns a const reference to the acquisition info  More... 
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| AcquisitionInfo & | getAcquisitionInfo () | 
|  | returns a mutable reference to the acquisition info  More... 
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| void | setAcquisitionInfo (const AcquisitionInfo &acquisition_info) | 
|  | sets the acquisition info  More... 
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| const SourceFile & | getSourceFile () const | 
|  | returns a const reference to the source file  More... 
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| SourceFile & | getSourceFile () | 
|  | returns a mutable reference to the source file  More... 
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| void | setSourceFile (const SourceFile &source_file) | 
|  | sets the source file  More... 
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| const std::vector< Precursor > & | getPrecursors () const | 
|  | returns a const reference to the precursors  More... 
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| std::vector< Precursor > & | getPrecursors () | 
|  | returns a mutable reference to the precursors  More... 
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| void | setPrecursors (const std::vector< Precursor > &precursors) | 
|  | sets the precursors  More... 
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| const std::vector< Product > & | getProducts () const | 
|  | returns a const reference to the products  More... 
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| std::vector< Product > & | getProducts () | 
|  | returns a mutable reference to the products  More... 
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| void | setProducts (const std::vector< Product > &products) | 
|  | sets the products  More... 
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| const std::vector < PeptideIdentification > &
 | getPeptideIdentifications () const | 
|  | returns a const reference to the PeptideIdentification vector  More... 
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| std::vector < PeptideIdentification > &
 | getPeptideIdentifications () | 
|  | returns a mutable reference to the PeptideIdentification vector  More... 
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| void | setPeptideIdentifications (const std::vector< PeptideIdentification > &identifications) | 
|  | sets the PeptideIdentification vector  More... 
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| const std::vector < DataProcessing > &
 | getDataProcessing () const | 
|  | returns a const reference to the description of the applied processing  More... 
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| std::vector< DataProcessing > & | getDataProcessing () | 
|  | returns a mutable reference to the description of the applied processing  More... 
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| void | setDataProcessing (const std::vector< DataProcessing > &data_processing) | 
|  | sets the description of the applied processing  More... 
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|  | MetaInfoInterface () | 
|  | constructor  More... 
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|  | MetaInfoInterface (const MetaInfoInterface &rhs) | 
|  | copy constructor  More... 
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|  | ~MetaInfoInterface () | 
|  | destructor  More... 
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| MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) | 
|  | assignment operator  More... 
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| bool | operator== (const MetaInfoInterface &rhs) const | 
|  | Equality operator.  More... 
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| bool | operator!= (const MetaInfoInterface &rhs) const | 
|  | Equality operator.  More... 
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| const DataValue & | getMetaValue (const String &name) const | 
|  | returns the value corresponding to a string  More... 
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| const DataValue & | getMetaValue (UInt index) const | 
|  | returns the value corresponding to an index  More... 
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| bool | metaValueExists (const String &name) const | 
|  | returns if this MetaInfo is set  More... 
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| bool | metaValueExists (UInt index) const | 
|  | returns if this MetaInfo is set  More... 
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| void | setMetaValue (const String &name, const DataValue &value) | 
|  | sets the DataValue corresponding to a name  More... 
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| void | setMetaValue (UInt index, const DataValue &value) | 
|  | sets the DataValue corresponding to an index  More... 
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| void | removeMetaValue (const String &name) | 
|  | Removes the DataValue corresponding to nameif it exists.  More...
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| void | removeMetaValue (UInt index) | 
|  | Removes the DataValue corresponding to indexif it exists.  More...
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| void | getKeys (std::vector< String > &keys) const | 
|  | fills the given vector with a list of all keys for which a value is set  More... 
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| void | getKeys (std::vector< UInt > &keys) const | 
|  | fills the given vector with a list of all keys for which a value is set  More... 
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| bool | isMetaEmpty () const | 
|  | returns if the MetaInfo is empty  More... 
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| void | clearMetaInfo () | 
|  | removes all meta values  More... 
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|  | PersistentObject () | 
|  | Default constructor.  More... 
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| virtual | ~PersistentObject () | 
|  | Destructor.  More... 
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| PersistentObject & | operator= (const PersistentObject &rhs) | 
|  | Assignment operator.  More... 
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| const UID & | getPersistenceId () const | 
|  | Returns the persistence id.  More... 
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| void | setPersistenceId (const UID &persistence_id) | 
|  | Sets the persistence id.  More... 
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| void | clearId (bool deep=true) | 
|  | Clears the persistence id.  More... 
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template<typename PeakT = Peak1D>
class OpenMS::MSSpectrum< PeakT >
The representation of a 1D spectrum. 
It contains peak data and metadata about specific instrument settings, acquisition settings, description of the meta values used in the peaks and precursor info (SpectrumSettings).
Several MSSpectrum instances are contained in a peak map (MSExperiment), which is essentially a vector of spectra with additional information about the experiment.
Precursor info from SpectrumSettings should only be used if this spectrum is a tandem-MS spectrum. The precursor spectrum is the first spectrum in MSExperiment, that has a lower MS-level than the current spectrum.
- Note
- For range operations, see RangeUtils module!