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| BinnedSpectrum () |
| default constructor More...
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| BinnedSpectrum (Real size, UInt spread, PeakSpectrum ps) |
| detailed constructor More...
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| BinnedSpectrum (const BinnedSpectrum &source) |
| copy constructor More...
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virtual | ~BinnedSpectrum () |
| destructor More...
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BinnedSpectrum & | operator= (const BinnedSpectrum &source) |
| assignment operator More...
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BinnedSpectrum & | operator= (const PeakSpectrum &source) |
| assignment operator for PeakSpectra More...
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bool | operator== (const BinnedSpectrum &rhs) const |
| equality operator More...
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bool | operator!= (const BinnedSpectrum &rhs) const |
| inequality operator More...
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bool | operator== (const PeakSpectrum &rhs) const |
| equality operator for PeakSpectra More...
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bool | operator!= (const PeakSpectrum &rhs) const |
| inequality operator for PeakSpectra More...
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double | getBinSize () const |
| get the BinSize More...
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UInt | getBinSpread () const |
| get the BinSpread More...
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UInt | getBinNumber () const |
| get the BinNumber, number of Bins More...
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UInt | getFilledBinNumber () const |
| get the FilledBinNumber, number of filled Bins More...
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const SparseVector< Real > & | getBins () const |
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SparseVector< Real > & | getBins () |
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const_bin_iterator | begin () const |
| returns the const begin iterator of the container More...
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const_bin_iterator | end () const |
| returns the const end iterator of the container More...
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bin_iterator | begin () |
| returns the begin iterator of the container More...
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bin_iterator | end () |
| returns the end iterator of the container More...
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void | setBinSize (double s) |
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void | setBinSpread (UInt s) |
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void | setBinning () |
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bool | checkCompliance (const BinnedSpectrum &bs) const |
| function to check comparability of two BinnedSpectrum objects, i.e. if they have equal bin size and spread More...
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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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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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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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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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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 | 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 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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| 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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This is a binned representation of a PeakSpectrum.
- Parameters
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sz | the size of the bins and |
sp | number of neighboring bins to both sides affected by a peak contribution |
ps | the peakspectrum, that shall be represented |
sz denotes the size of a bin in Th
, thereby deciding the number of bins(all of size sz) the spectrum is discretized to. Each bin will represent a certain Th
range and the peaks will be put in the respective bins and sum up inside. sp denotes the number of neighboring bins to the left and the number of neighboring bins to the right a peak is also added to. E.g. a BinnedSpectrum with binsize of 0.5 Th
will have a peak at 100 Th
in bin no. 200, a peak at 100.1 Th
will be in bin no. 201. If the binspread is 1, the peak at 100 Th will be added to bin no. 199, 200 and 201. If the binspread is 2, the peak at 100 Th
will also be added to bin no. 198 and 202, and so on.