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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)
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double | getRT () const |
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void | setRT (double 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 variable
- Access to meta info arrays is faster than to a MetaInfoInterface
- Meta info arrays are stored when using mzML format for storing
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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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double | getMinInt () const |
| Returns the minimum intensity. More...
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double | 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 name if it exists. More...
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void | removeMetaValue (UInt index) |
| Removes the DataValue corresponding to index if 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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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!