|
| | MSSpectrum () |
| | Constructor. More...
|
| |
| | MSSpectrum (const MSSpectrum &source) |
| | Copy constructor. More...
|
| |
| | ~MSSpectrum () |
| | Destructor. More...
|
| |
| MSSpectrum & | operator= (const MSSpectrum &source) |
| | Assignment operator. More...
|
| |
| bool | operator== (const MSSpectrum &rhs) const |
| | Equality operator. More...
|
| |
| bool | operator!= (const MSSpectrum &rhs) const |
| | Equality operator. More...
|
| |
| virtual void | updateRanges () |
| | Updates minimum and maximum position/intensity. More...
|
| |
| void | clear (bool clear_meta_data) |
| | Clears all data and meta data. More...
|
| |
|
Returns the absolute retention time (is seconds)
|
| DoubleReal | getRT () const |
| |
| void | setRT (DoubleReal rt) |
| | Sets the absolute retention time (is seconds) More...
|
| |
| UInt | getMSLevel () const |
| | Returns the MS level. More...
|
| |
| void | setMSLevel (UInt ms_level) |
| | Sets the MS level. More...
|
| |
| const String & | getName () const |
| | Returns the name. More...
|
| |
| void | setName (const String &name) |
| | Sets the name. More...
|
| |
|
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
|
| const FloatDataArrays & | getFloatDataArrays () const |
| | Returns a const reference to the float meta data arrays. More...
|
| |
| FloatDataArrays & | getFloatDataArrays () |
| | Returns a mutable reference to the float meta data arrays. More...
|
| |
| const StringDataArrays & | getStringDataArrays () const |
| | Returns a const reference to the string meta data arrays. More...
|
| |
| StringDataArrays & | getStringDataArrays () |
| | Returns a mutable reference to the string meta data arrays. More...
|
| |
| const IntegerDataArrays & | getIntegerDataArrays () const |
| | Returns a const reference to the integer meta data arrays. More...
|
| |
| IntegerDataArrays & | getIntegerDataArrays () |
| | Returns a mutable reference to the integer meta data arrays. More...
|
| |
|
| void | sortByIntensity (bool reverse=false) |
| | Lexicographically sorts the peaks by their intensity. More...
|
| |
| void | sortByPosition () |
| | Lexicographically sorts the peaks by their position. More...
|
| |
| bool | isSorted () const |
| | Checks if all peaks are sorted with respect to ascending m/z. More...
|
| |
|
| Size | findNearest (CoordinateType mz) const |
| | Binary search for the peak nearest to a specific m/z. More...
|
| |
| Iterator | MZBegin (CoordinateType mz) |
| | Binary search for peak range begin. More...
|
| |
| Iterator | MZBegin (Iterator begin, CoordinateType mz, Iterator end) |
| | Binary search for peak range begin. More...
|
| |
| Iterator | MZEnd (CoordinateType mz) |
| | Binary search for peak range end (returns the past-the-end iterator) More...
|
| |
| Iterator | MZEnd (Iterator begin, CoordinateType mz, Iterator end) |
| | Binary search for peak range end (returns the past-the-end iterator) More...
|
| |
| ConstIterator | MZBegin (CoordinateType mz) const |
| | Binary search for peak range begin. More...
|
| |
| ConstIterator | MZBegin (ConstIterator begin, CoordinateType mz, ConstIterator end) const |
| | Binary search for peak range begin. More...
|
| |
| ConstIterator | MZEnd (CoordinateType mz) const |
| | Binary search for peak range end (returns the past-the-end iterator) More...
|
| |
| ConstIterator | MZEnd (ConstIterator begin, CoordinateType mz, ConstIterator end) const |
| | Binary search for peak range end (returns the past-the-end iterator) More...
|
| |
| | RangeManager () |
| | Default constructor. More...
|
| |
| | RangeManager (const RangeManager &rhs) |
| | Copy constructor. More...
|
| |
| virtual | ~RangeManager () |
| | Destructor. More...
|
| |
| RangeManager & | operator= (const RangeManager &rhs) |
| | Assignment operator. More...
|
| |
| bool | operator== (const RangeManager &rhs) const |
| | Equality operator. More...
|
| |
| bool | operator!= (const RangeManager &rhs) const |
| | Equality operator. More...
|
| |
| const PositionType & | getMin () const |
| | Returns the minimum position. More...
|
| |
| const PositionType & | getMax () const |
| | Returns the maximum position. More...
|
| |
| DoubleReal | getMinInt () const |
| | Returns the minimum intensity. More...
|
| |
| DoubleReal | getMaxInt () const |
| | Returns the maximum intensity. More...
|
| |
| void | clearRanges () |
| | Resets the ranges. More...
|
| |
| | SpectrumSettings () |
| | Constructor. More...
|
| |
| | SpectrumSettings (const SpectrumSettings &source) |
| | Copy constructor. More...
|
| |
| | ~SpectrumSettings () |
| | Destructor. More...
|
| |
| SpectrumSettings & | operator= (const SpectrumSettings &source) |
| |
| bool | operator== (const SpectrumSettings &rhs) const |
| | Equality operator. More...
|
| |
| bool | operator!= (const SpectrumSettings &rhs) const |
| | Equality operator. More...
|
| |
| 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...
|
| |
| SpectrumType | getType () const |
| | returns the spectrum type More...
|
| |
| void | setType (SpectrumType type) |
| | sets the spectrum type More...
|
| |
| const String & | getNativeID () const |
| | returns the native identifier for the spectrum, used by the acquisition software. More...
|
| |
| void | setNativeID (const String &native_id) |
| | sets the native identifier for the spectrum, used by the acquisition software. More...
|
| |
| const String & | getComment () const |
| | returns the free-text comment More...
|
| |
| void | setComment (const String &comment) |
| | sets the free-text comment More...
|
| |
| const InstrumentSettings & | getInstrumentSettings () const |
| | returns a const reference to the instrument settings of the current spectrum More...
|
| |
| InstrumentSettings & | getInstrumentSettings () |
| | returns a mutable reference to the instrument settings of the current spectrum More...
|
| |
| void | setInstrumentSettings (const InstrumentSettings &instrument_settings) |
| | sets the instrument settings of the current spectrum More...
|
| |
| const AcquisitionInfo & | getAcquisitionInfo () const |
| | returns a const reference to the acquisition info More...
|
| |
| AcquisitionInfo & | getAcquisitionInfo () |
| | returns a mutable reference to the acquisition info More...
|
| |
| void | setAcquisitionInfo (const AcquisitionInfo &acquisition_info) |
| | sets the acquisition info More...
|
| |
| const SourceFile & | getSourceFile () const |
| | returns a const reference to the source file More...
|
| |
| SourceFile & | getSourceFile () |
| | returns a mutable reference to the source file More...
|
| |
| void | setSourceFile (const SourceFile &source_file) |
| | sets the source file More...
|
| |
| const std::vector< Precursor > & | getPrecursors () const |
| | returns a const reference to the precursors More...
|
| |
| std::vector< Precursor > & | getPrecursors () |
| | returns a mutable reference to the precursors More...
|
| |
| void | setPrecursors (const std::vector< Precursor > &precursors) |
| | sets the precursors More...
|
| |
| const std::vector< Product > & | getProducts () const |
| | returns a const reference to the products More...
|
| |
| std::vector< Product > & | getProducts () |
| | returns a mutable reference to the products More...
|
| |
| void | setProducts (const std::vector< Product > &products) |
| | sets the products More...
|
| |
const std::vector
< PeptideIdentification > & | getPeptideIdentifications () const |
| | returns a const reference to the PeptideIdentification vector More...
|
| |
std::vector
< PeptideIdentification > & | getPeptideIdentifications () |
| | returns a mutable reference to the PeptideIdentification vector More...
|
| |
| void | setPeptideIdentifications (const std::vector< PeptideIdentification > &identifications) |
| | sets the PeptideIdentification vector More...
|
| |
const std::vector
< DataProcessing > & | getDataProcessing () const |
| | returns a const reference to the description of the applied processing More...
|
| |
| std::vector< DataProcessing > & | getDataProcessing () |
| | returns a mutable reference to the description of the applied processing More...
|
| |
| void | setDataProcessing (const std::vector< DataProcessing > &data_processing) |
| | sets the description of the applied processing More...
|
| |
| | MetaInfoInterface () |
| | constructor More...
|
| |
| | MetaInfoInterface (const MetaInfoInterface &rhs) |
| | copy constructor More...
|
| |
| | ~MetaInfoInterface () |
| | destructor More...
|
| |
| MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) |
| | assignment operator More...
|
| |
| bool | operator== (const MetaInfoInterface &rhs) const |
| | Equality operator. More...
|
| |
| bool | operator!= (const MetaInfoInterface &rhs) const |
| | Equality operator. More...
|
| |
| const DataValue & | getMetaValue (const String &name) const |
| | returns the value corresponding to a string More...
|
| |
| const DataValue & | getMetaValue (UInt index) const |
| | returns the value corresponding to an index More...
|
| |
| bool | metaValueExists (const String &name) const |
| | returns if this MetaInfo is set More...
|
| |
| bool | metaValueExists (UInt index) const |
| | returns if this MetaInfo is set More...
|
| |
| void | setMetaValue (const String &name, const DataValue &value) |
| | sets the DataValue corresponding to a name More...
|
| |
| void | setMetaValue (UInt index, const DataValue &value) |
| | sets the DataValue corresponding to an index More...
|
| |
| void | removeMetaValue (const String &name) |
| | Removes the DataValue corresponding to name if it exists. More...
|
| |
| void | removeMetaValue (UInt index) |
| | Removes the DataValue corresponding to index if it exists. More...
|
| |
| void | getKeys (std::vector< String > &keys) const |
| | fills the given vector with a list of all keys for which a value is set More...
|
| |
| void | getKeys (std::vector< UInt > &keys) const |
| | fills the given vector with a list of all keys for which a value is set More...
|
| |
| bool | isMetaEmpty () const |
| | returns if the MetaInfo is empty More...
|
| |
| void | clearMetaInfo () |
| | removes all meta values More...
|
| |
| | PersistentObject () |
| | Default constructor. More...
|
| |
| virtual | ~PersistentObject () |
| | Destructor. More...
|
| |
| PersistentObject & | operator= (const PersistentObject &rhs) |
| | Assignment operator. More...
|
| |
| const UID & | getPersistenceId () const |
| | Returns the persistence id. More...
|
| |
| void | setPersistenceId (const UID &persistence_id) |
| | Sets the persistence id. More...
|
| |
| void | clearId (bool deep=true) |
| | Clears the persistence id. More...
|
| |
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!