| OpenMS 2.5.0

Classes | Public Member Functions | Protected Attributes | List of all members
MSSpectrum Class Reference
Kernel

The representation of a 1D spectrum. More...

`#include <OpenMS/KERNEL/MSSpectrum.h>`

Inheritance diagram for MSSpectrum:

## Classes

struct | RTLess
| Comparator for the retention time. More...

## Public Types

Base type definitions
typedef OpenMS::Peak1D | PeakType
| Peak type. More...
typedef PeakType::CoordinateType | CoordinateType
| Coordinate (m/z) type. More...
typedef std::vector< PeakType > | ContainerType
| Spectrum base type. More...
typedef OpenMS::DataArrays::FloatDataArray | FloatDataArray
| Float data array vector type. More...
typedef std::vector< FloatDataArray > | FloatDataArrays
typedef OpenMS::DataArrays::StringDataArray | StringDataArray
| String data array vector type. More...
typedef std::vector< StringDataArray > | StringDataArrays
typedef OpenMS::DataArrays::IntegerDataArray | IntegerDataArray
| Integer data array vector type. More...
typedef std::vector< IntegerDataArray > | IntegerDataArrays
Peak container iterator type definitions
typedef ContainerType::iterator | Iterator
| Mutable iterator. More...
typedef ContainerType::const_iterator | ConstIterator
| Non-mutable iterator. More...
typedef ContainerType::reverse_iterator | ReverseIterator
| Mutable reverse iterator. More...
typedef ContainerType::const_reverse_iterator | ConstReverseIterator
| Non-mutable reverse iterator. More...
Export methods from std::vector<Peak1D>
typedef Precursor::DriftTimeUnit | DriftTimeUnit
Public Types inherited from RangeManager< 1 >
enum |
| Dimension of the position range. More...
typedef DRange< D > | PositionRangeType
| Position range type. More...
typedef DPosition< D > | PositionType
| Position Type. More...
typedef DRange< 1 > | IntensityRangeType
| Intensity range type. More...
Public Types inherited from SpectrumSettings
enum | SpectrumType { UNKNOWN, CENTROID, PROFILE, SIZE_OF_SPECTRUMTYPE }
| Spectrum peak type. More...

## Public Member Functions

| MSSpectrum ()
| Constructor. More...
| MSSpectrum (const MSSpectrum &source)
| Copy constructor. More...
| MSSpectrum (MSSpectrum &&)=default
| Move constructor. More...
| ~MSSpectrum () override
| Destructor. More...
MSSpectrum & | operator= (const MSSpectrum &source)
| Assignment operator. More...
MSSpectrum & | operator= (MSSpectrum &&) &=default
| Move assignment operator. More...
MSSpectrum & | operator= (const SpectrumSettings &source)
| Assignment operator. More...
bool | operator== (const MSSpectrum &rhs) const
| Equality operator. More...
bool | operator!= (const MSSpectrum &rhs) const
| Equality operator. More...
void | updateRanges () override
| Updates minimum and maximum position/intensity. More...
void | clear (bool clear_meta_data)
| Clears all data and meta data. More...
MSSpectrum & | select (const std::vector< Size > &indices)
SpectrumSettings::SpectrumType | getType (const bool query_data) const
| Determine if spectrum is profile or centroided using up to three layers of information. More...
ConstIterator | getBasePeak () const
Iterator | getBasePeak ()
PeakType::IntensityType | getTIC () const
| compute the total ion count (sum of all peak intensities) More...
SpectrumType | getType () const
| returns the spectrum type (centroided (PEAKS) or profile data (RAW)) More...
Accessors for meta information
Returns the absolute retention time (in seconds)
double | getRT () const
void | setRT (double rt)
| Sets the absolute retention time (in seconds) More...
double | getDriftTime () const
| Returns the ion mobility drift time (-1 means it is not set) More...
void | setDriftTime (double dt)
| Sets the ion mobility drift time. More...
DriftTimeUnit | getDriftTimeUnit () const
| Returns the ion mobility drift time unit. More...
void | setDriftTimeUnit (DriftTimeUnit dt)
| Sets the ion mobility drift time unit. 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...
Peak data array methods
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...
void | setFloatDataArrays (const FloatDataArrays &fda)
| Sets 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...
void | setStringDataArrays (const StringDataArrays &sda)
| Sets 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 | setIntegerDataArrays (const IntegerDataArrays &ida)
| Sets the integer meta data arrays. More...
Sorting peaks
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...
Searching a peak or peak range
Size | findNearest (CoordinateType mz) const
| Binary search for the peak nearest to a specific m/z. More...
Int | findNearest (CoordinateType mz, CoordinateType tolerance) const
| Binary search for the peak nearest to a specific m/z given a +/- tolerance windows in Th. More...
Int | findNearest (CoordinateType mz, CoordinateType tolerance_left, CoordinateType tolerance_right) const
| Search for the peak nearest to a specific m/z given two +/- tolerance windows in Th. 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...
Iterator | PosBegin (CoordinateType mz)
| Binary search for peak range begin. More...
Iterator | PosBegin (Iterator begin, CoordinateType mz, Iterator end)
| Binary search for peak range begin. More...
ConstIterator | PosBegin (CoordinateType mz) const
| Binary search for peak range begin. More...
ConstIterator | PosBegin (ConstIterator begin, CoordinateType mz, ConstIterator end) const
| Binary search for peak range begin. More...
Iterator | PosEnd (CoordinateType mz)
| Binary search for peak range end (returns the past-the-end iterator) More...
Iterator | PosEnd (Iterator begin, CoordinateType mz, Iterator end)
| Binary search for peak range end (returns the past-the-end iterator) More...
ConstIterator | PosEnd (CoordinateType mz) const
| Binary search for peak range end (returns the past-the-end iterator) More...
ConstIterator | PosEnd (ConstIterator begin, CoordinateType mz, ConstIterator end) const
| Binary search for peak range end (returns the past-the-end iterator) More...
Public Member Functions inherited from RangeManager< 1 >
| RangeManager ()
| Default constructor. More...
| RangeManager (const RangeManager &rhs)
| Copy constructor. More...
| RangeManager (RangeManager &&) noexcept=default
| Move 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...
double | getMinInt () const
| Returns the minimum intensity. More...
double | getMaxInt () const
| Returns the maximum intensity. More...
void | clearRanges ()
| Resets the ranges. More...
Public Member Functions inherited from SpectrumSettings
| SpectrumSettings ()
| Constructor. More...
| SpectrumSettings (const SpectrumSettings &)=default
| Copy constructor. More...
| SpectrumSettings (SpectrumSettings &&)=default
| Move constructor. More...
| ~SpectrumSettings ()
| Destructor. More...
SpectrumSettings & | operator= (const SpectrumSettings &)=default
SpectrumSettings & | operator= (SpectrumSettings &&) &=default
| Move assignment operator. More...
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 (centroided (PEAKS) or profile data (RAW)) 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...
void | setDataProcessing (const std::vector< DataProcessingPtr > &data_processing)
| sets the description of the applied processing More...
std::vector< DataProcessingPtr > & | getDataProcessing ()
| returns a mutable reference to the description of the applied processing More...
const std::vector< boost::shared_ptr< const DataProcessing > > | getDataProcessing () const
| returns a const reference to the description of the applied processing More...
Public Member Functions inherited from MetaInfoInterface
| MetaInfoInterface ()
| Constructor. More...
| MetaInfoInterface (const MetaInfoInterface &rhs)
| Copy constructor. More...
| MetaInfoInterface (MetaInfoInterface &&) noexcept
| Move constructor. More...
| ~MetaInfoInterface ()
| Destructor. More...
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs)
| Assignment operator. More...
MetaInfoInterface & | operator= (MetaInfoInterface &&) noexcept
| Move 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 DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
const DataValue & | getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
| Returns the value corresponding to an index, or a default value (default: DataValue::EMPTY) if not found. More...
bool | metaValueExists (const String &name) const
| Returns whether an entry with the given name exists. More...
bool | metaValueExists (UInt index) const
| Returns whether an entry with the given index exists. 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...

## Protected Attributes

double | retention_time_
| Retention time. More...
double | drift_time_
| Drift time. More...
DriftTimeUnit | drift_time_unit_
| Drift time unit. More...
UInt | ms_level_
| MS level. More...
String | name_
| Name. More...
FloatDataArrays | float_data_arrays_
| Float data arrays. More...
StringDataArrays | string_data_arrays_
| String data arrays. More...
IntegerDataArrays | integer_data_arrays_
| Integer data arrays. More...
Protected Attributes inherited from RangeManager< 1 >
IntensityRangeType | int_range_
| Intensity range (1-dimensional) More...
PositionRangeType | pos_range_
| Position range (D-dimensional) More...
Protected Attributes inherited from SpectrumSettings
SpectrumType | type_
String | native_id_
String | comment_
InstrumentSettings | instrument_settings_
SourceFile | source_file_
AcquisitionInfo | acquisition_info_
std::vector< Precursor > | precursors_
std::vector< Product > | products_
std::vector< PeptideIdentification > | identification_
std::vector< DataProcessingPtr > | data_processing_
Protected Attributes inherited from MetaInfoInterface
MetaInfo * | meta_
| Pointer to the MetaInfo object (0 by default) More...

## Additional Inherited Members

Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry & | metaRegistry ()
| Returns a reference to the MetaInfoRegistry. More...
Static Public Attributes inherited from SpectrumSettings
static const std::string | NamesOfSpectrumType [SIZE_OF_SPECTRUMTYPE]
| Names of spectrum types. More...
Protected Member Functions inherited from RangeManager< 1 >
void | updateRanges_ (const PeakIteratorType &begin, const PeakIteratorType &end)
| Updates the range using data points in the iterator range. More...
Protected Member Functions inherited from MetaInfoInterface
void | createIfNotExists_ ()
| Creates the MetaInfo object if it does not exist. More...

## Detailed Description

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!

## Member Typedef Documentation

## ◆ ConstIterator

typedef ContainerType::const_iterator ConstIterator

Non-mutable iterator.

## ◆ ConstReverseIterator

typedef ContainerType::const_reverse_iterator ConstReverseIterator

Non-mutable reverse iterator.

## ◆ ContainerType

typedef std::vector<PeakType> ContainerType

Spectrum base type.

## ◆ CoordinateType

typedef PeakType::CoordinateType CoordinateType

Coordinate (m/z) type.

## ◆ DriftTimeUnit

typedef Precursor::DriftTimeUnit DriftTimeUnit

## ◆ FloatDataArray

typedef OpenMS::DataArrays::FloatDataArray FloatDataArray

Float data array vector type.

## ◆ FloatDataArrays

typedef std::vector<FloatDataArray> FloatDataArrays

## ◆ IntegerDataArray

typedef OpenMS::DataArrays::IntegerDataArray IntegerDataArray

Integer data array vector type.

## ◆ IntegerDataArrays

typedef std::vector<IntegerDataArray> IntegerDataArrays

## ◆ Iterator

typedef ContainerType::iterator Iterator

Mutable iterator.

## ◆ PeakType

typedef OpenMS::Peak1D PeakType

Peak type.

## ◆ ReverseIterator

typedef ContainerType::reverse_iterator ReverseIterator

Mutable reverse iterator.

## ◆ StringDataArray

typedef OpenMS::DataArrays::StringDataArray StringDataArray

String data array vector type.

## ◆ StringDataArrays

typedef std::vector<StringDataArray> StringDataArrays

## Constructor & Destructor Documentation

## ◆ MSSpectrum() [1/3]

MSSpectrum | ( |  | ) |

Constructor.

## ◆ MSSpectrum() [2/3]

MSSpectrum | ( | const MSSpectrum & | source | ) |

Copy constructor.

## ◆ MSSpectrum() [3/3]

MSSpectrum | ( | MSSpectrum && |  | ) |

default

Move constructor.

## ◆ ~MSSpectrum()

~MSSpectrum | ( |  | ) |

inline override

Destructor.

## Member Function Documentation

## ◆ clear()

void clear | ( | bool | clear_meta_data | ) |

Clears all data and meta data.

Parameters

  clear_meta_data | If true, all meta data is cleared in addition to the data.

Referenced by SpectraMerger::averageCentroidSpectra_(), SpectraMerger::averageProfileSpectra_(), MzMLSwathFileConsumer::consumeSwathSpectrum_(), ChromatogramTools::convertSpectraToChromatograms(), NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_(), OpenMS::expandIMSpectrum(), WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), MS2File::load(), DTAFile::load(), XMassFile::load(), DTA2DFile::load(), PeakPickerIterative::pick(), and OpenMS::processDriftTimeStack().

## ◆ findNearest() [1/3]

Size findNearest | ( | CoordinateType | mz | ) | const

Binary search for the peak nearest to a specific m/z.

Parameters

  mz | The searched for mass-to-charge ratio searched

Returns
  Returns the index of the peak.

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

Exceptions

  Exception::Precondition | is thrown if the spectrum is empty (not only in debug mode)

Referenced by NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_().

## ◆ findNearest() [2/3]

Int findNearest | ( | CoordinateType | mz,
|  | CoordinateType | tolerance
| ) |  | const

Binary search for the peak nearest to a specific m/z given a +/- tolerance windows in Th.

Parameters

  mz | The searched for mass-to-charge ratio searched
  tolerance | The non-negative tolerance applied to both sides of mz

Returns
  Returns the index of the peak or -1 if no peak present in tolerance window or if spectrum is empty

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.
  Peaks exactly on borders are considered in tolerance window.

## ◆ findNearest() [3/3]

Int findNearest | ( | CoordinateType | mz,
|  | CoordinateType | tolerance_left,
|  | CoordinateType | tolerance_right
| ) |  | const

Search for the peak nearest to a specific m/z given two +/- tolerance windows in Th.

Parameters

  mz | The searched for mass-to-charge ratio searched
  tolerance_left | The non-negative tolerance applied left of mz
  tolerance_right | The non-negative tolerance applied right of mz

Returns
  Returns the index of the peak or -1 if no peak present in tolerance window or if spectrum is empty

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.
  Peaks exactly on borders are considered in tolerance window.
  Search for the left border is done using a binary search followed by a linear scan

## ◆ getBasePeak() [1/2]

ConstIterator getBasePeak | ( |  | ) | const

return the peak with the highest intensity. If the peak is not unique, the first peak in the container is returned. The function works correctly, even if the spectrum is unsorted.

## ◆ getBasePeak() [2/2]

Iterator getBasePeak | ( |  | ) |

return the peak with the highest intensity. If the peak is not unique, the first peak in the container is returned. The function works correctly, even if the spectrum is unsorted.

## ◆ getDriftTime()

double getDriftTime | ( |  | ) | const

Returns the ion mobility drift time (-1 means it is not set)

Note
  Drift times may be stored directly as an attribute of the spectrum (if they relate to the spectrum as a whole). In case of ion mobility spectra, the drift time of the spectrum will always be set here while the drift times attribute in the Precursor class may often be unpopulated.

## ◆ getDriftTimeUnit()

DriftTimeUnit getDriftTimeUnit | ( |  | ) | const

Returns the ion mobility drift time unit.

Referenced by OpenMS::processDriftTimeStack().

## ◆ getFloatDataArrays() [1/2]

const FloatDataArrays& getFloatDataArrays | ( |  | ) | const

Returns a const reference to the float meta data arrays.

Referenced by MetaDataBrowser::add(), MSExperiment::ContainerAdd_< ContainerValueType, false >::addData_(), TOPPViewBase::containsIMData(), OpenMS::expandIMSpectrum(), TwoDOptimization::optimizeRegionsScanwise_(), DataFilters::passes(), PeakPickerIterative::pick(), and TOPPViewBase::showCurrentPeaksAsIonMobility().

## ◆ getFloatDataArrays() [2/2]

FloatDataArrays& getFloatDataArrays | ( |  | ) |

inline

Returns a mutable reference to the float meta data arrays.

## ◆ getIntegerDataArrays() [1/2]

const IntegerDataArrays& getIntegerDataArrays | ( |  | ) | const

Returns a const reference to the integer meta data arrays.

Referenced by MetaDataBrowser::add(), and DataFilters::passes().

## ◆ getIntegerDataArrays() [2/2]

IntegerDataArrays& getIntegerDataArrays | ( |  | ) |

Returns a mutable reference to the integer meta data arrays.

## ◆ getMSLevel()

UInt getMSLevel | ( |  | ) | const

Returns the MS level.

For survey scans this is 1, for MS/MS scans 2, ...

Referenced by FullSwathFileConsumer::consumeSpectrum(), ParentPeakMower::filterSpectrum(), InMSLevelRange< SpectrumType >::operator()(), IsInCollisionEnergyRange< SpectrumType >::operator()(), IsInIsolationWindowSizeRange< SpectrumType >::operator()(), IsInIsolationWindow< SpectrumType >::operator()(), and PeakPickerIterative::pick().

## ◆ getName()

const String& getName | ( |  | ) | const

Returns the name.

Referenced by OpenMS::expandIMSpectrum(), and PeakPickerIterative::pick().

## ◆ getRT()

double getRT | ( |  | ) | const

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), GaussFilter::filter(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getRT(), IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), DTA2DFile::load(), IDMapper::mapPrecursorsToIdentifications(), SpectraMerger::mergeSpectra_(), InRTRange< SpectrumType >::operator()(), PeakPickerIterative::pick(), NucleicAcidSearchEngine::postProcessHits_(), and SpectrumLookup::readSpectra().

## ◆ getStringDataArrays() [1/2]

const StringDataArrays& getStringDataArrays | ( |  | ) | const

Returns a const reference to the string meta data arrays.

Referenced by MetaDataBrowser::add().

## ◆ getStringDataArrays() [2/2]

StringDataArrays& getStringDataArrays | ( |  | ) |

Returns a mutable reference to the string meta data arrays.

## ◆ getTIC()

PeakType::IntensityType getTIC | ( |  | ) | const

compute the total ion count (sum of all peak intensities)

## ◆ getType() [1/2]

SpectrumSettings::SpectrumType getType | ( | const bool | query_data | ) | const

Determine if spectrum is profile or centroided using up to three layers of information.

First, the SpectrumSettings are inquired and the type is returned unless it is unknown. Second, all data processing entries are searched for a centroiding step. If that is unsuccessful as well and `query_data` is true, the data is fed into PeakTypeEstimator().

Parameters

  [query_data] | If SpectrumSettings and DataProcessing information are not sufficient, should the data be queried? (potentially expensive)

Returns
  The spectrum type (centroided, profile or unknown)

## ◆ getType() [2/2]

SpectrumType getType

returns the spectrum type (centroided (PEAKS) or profile data (RAW))

## ◆ isSorted()

bool isSorted | ( |  | ) | const

Checks if all peaks are sorted with respect to ascending m/z.

## ◆ MZBegin() [1/4]

Iterator MZBegin | ( | CoordinateType | mz | ) |

Binary search for peak range begin.

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), IsotopeWaveletTransform< PeakType >::checkPPMTheoModel_(), IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), IsotopeWaveletTransform< PeakType >::TransSpectrum::MZBegin(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

## ◆ MZBegin() [2/4]

Iterator MZBegin | ( | Iterator | begin,
|  | CoordinateType | mz,
|  | Iterator | end
| ) |  |

Binary search for peak range begin.

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

## ◆ MZBegin() [3/4]

ConstIterator MZBegin | ( | CoordinateType | mz | ) | const

Binary search for peak range begin.

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

## ◆ MZBegin() [4/4]

ConstIterator MZBegin | ( | ConstIterator | begin,
|  | CoordinateType | mz,
|  | ConstIterator | end
| ) |  | const

Binary search for peak range begin.

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

## ◆ MZEnd() [1/4]

Iterator MZEnd | ( | CoordinateType | mz | ) |

Binary search for peak range end (returns the past-the-end iterator)

Note
  Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), and IsotopeWaveletTransform< PeakType >::TransSpectrum::MZEnd().

## ◆ MZEnd() [2/4]

Iterator MZEnd | ( | Iterator | begin,
|  | CoordinateType | mz,
|  | Iterator | end
| ) |  |

Binary search for peak range end (returns the past-the-end iterator)

Note
  Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

## ◆ MZEnd() [3/4]

ConstIterator MZEnd | ( | CoordinateType | mz | ) | const

Binary search for peak range end (returns the past-the-end iterator)

Note
  Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

## ◆ MZEnd() [4/4]

ConstIterator MZEnd | ( | ConstIterator | begin,
|  | CoordinateType | mz,
|  | ConstIterator | end
| ) |  | const

Binary search for peak range end (returns the past-the-end iterator)

Note
  Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

## ◆ operator!=()

bool operator!= | ( | const MSSpectrum & | rhs | ) | const

inline

Equality operator.

References KDTree::operator==().

## ◆ operator=() [1/3]

MSSpectrum& operator= | ( | const MSSpectrum & | source | ) |

Assignment operator.

## ◆ operator=() [2/3]

MSSpectrum& operator= | ( | MSSpectrum && |  | ) | &

default

Move assignment operator.

## ◆ operator=() [3/3]

MSSpectrum& operator= | ( | const SpectrumSettings & | source | ) |

Assignment operator.

## ◆ operator==()

bool operator== | ( | const MSSpectrum & | rhs | ) | const

Equality operator.

## ◆ PosBegin() [1/4]

Iterator PosBegin | ( | CoordinateType | mz | ) |

Binary search for peak range begin.

Alias for MZBegin()

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

## ◆ PosBegin() [2/4]

Iterator PosBegin | ( | Iterator | begin,
|  | CoordinateType | mz,
|  | Iterator | end
| ) |  |

Binary search for peak range begin.

Alias for MZBegin()

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

## ◆ PosBegin() [3/4]

ConstIterator PosBegin | ( | CoordinateType | mz | ) | const

Binary search for peak range begin.

Alias for MZBegin()

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

## ◆ PosBegin() [4/4]

ConstIterator PosBegin | ( | ConstIterator | begin,
|  | CoordinateType | mz,
|  | ConstIterator | end
| ) |  | const

Binary search for peak range begin.

Alias for MZBegin()

Note
  Make sure the spectrum is sorted with respect to m/z! Otherwise the result is undefined.

## ◆ PosEnd() [1/4]

Iterator PosEnd | ( | CoordinateType | mz | ) |

Binary search for peak range end (returns the past-the-end iterator)

Alias for MZEnd()

Note
  Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

## ◆ PosEnd() [2/4]

Iterator PosEnd | ( | Iterator | begin,
|  | CoordinateType | mz,
|  | Iterator | end
| ) |  |

Binary search for peak range end (returns the past-the-end iterator)

Alias for MZEnd()

Note
  Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

## ◆ PosEnd() [3/4]

ConstIterator PosEnd | ( | CoordinateType | mz | ) | const

Binary search for peak range end (returns the past-the-end iterator)

Alias for MZEnd()

Note
  Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

## ◆ PosEnd() [4/4]

ConstIterator PosEnd | ( | ConstIterator | begin,
|  | CoordinateType | mz,
|  | ConstIterator | end
| ) |  | const

Binary search for peak range end (returns the past-the-end iterator)

Alias for MZEnd()

Note
  Make sure the spectrum is sorted with respect to m/z. Otherwise the result is undefined.

## ◆ select()

MSSpectrum& select | ( | const std::vector< Size > & | indices | ) |

Referenced by WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), WindowMower::filterPeakSpectrumForTopNInSlidingWindow(), ThresholdMower::filterSpectrum(), and NLargest::filterSpectrum().

## ◆ setDriftTime()

void setDriftTime | ( | double | dt | ) |

Sets the ion mobility drift time.

Referenced by OpenMS::expandIMSpectrum(), and OpenMS::processDriftTimeStack().

## ◆ setDriftTimeUnit()

void setDriftTimeUnit | ( | DriftTimeUnit | dt | ) |

Sets the ion mobility drift time unit.

Referenced by OpenMS::expandIMSpectrum(), and OpenMS::processDriftTimeStack().

## ◆ setFloatDataArrays()

void setFloatDataArrays | ( | const FloatDataArrays & | fda | ) |

Sets the float meta data arrays.

Referenced by OpenMS::expandIMSpectrum(), and OpenMS::processDriftTimeStack().

## ◆ setIntegerDataArrays()

void setIntegerDataArrays | ( | const IntegerDataArrays & | ida | ) |

Sets the integer meta data arrays.

## ◆ setMSLevel()

void setMSLevel | ( | UInt | ms_level | ) |

Sets the MS level.

Referenced by MS2File::load(), DTAFile::load(), MascotInfile::load(), XMassFile::load(), MascotGenericFile::load(), SpectraMerger::mergeSpectra_(), PeakPickerIterative::pick(), TOPPViewBase::showCurrentPeaksAsDIA(), and TOPPViewBase::showSpectrumGenerationDialog().

## ◆ setName()

void setName | ( | const String & | name | ) |

Sets the name.

Referenced by OpenMS::expandIMSpectrum(), DTAFile::load(), XMassFile::load(), NucleicAcidSearchEngine::main_(), and PeakPickerIterative::pick().

## ◆ setRT()

void setRT | ( | double | rt | ) |

Sets the absolute retention time (in seconds)

Referenced by MascotGenericFile::getNextSpectrum_(), TwoDOptimization::getRegionEndpoints_(), MascotInfile::load(), XMassFile::load(), DTA2DFile::load(), SpectraMerger::mergeSpectra_(), TwoDOptimization::optimize(), and PeakPickerIterative::pick().

## ◆ setStringDataArrays()

void setStringDataArrays | ( | const StringDataArrays & | sda | ) |

Sets the string meta data arrays.

## ◆ sortByIntensity()

void sortByIntensity | ( | bool | reverse = `false` | ) |

Lexicographically sorts the peaks by their intensity.

Sorts the peaks according to ascending intensity. Meta data arrays will be sorted accordingly.

Referenced by WindowMower::filterPeakSpectrumForTopNInSlidingWindow(), Scaler::filterSpectrum(), and NLargest::filterSpectrum().

## ◆ sortByPosition()

void sortByPosition | ( |  | ) |

Lexicographically sorts the peaks by their position.

The spectrum is sorted with respect to position. Meta data arrays will be sorted accordingly.

Referenced by ComplementFilter::apply(), ComplementMarker::apply(), NeutralLossMarker::apply(), IsotopeMarker::apply(), NucleicAcidSearchEngine::deisotopeAndSingleChargeMSSpectrum_(), WindowMower::filterPeakSpectrumForTopNInJumpingWindow(), WindowMower::filterPeakSpectrumForTopNInSlidingWindow(), BernNorm::filterSpectrum(), SpectraMerger::mergeSpectra_(), PeakPickerIterative::pick(), NucleicAcidSearchEngine::preprocessSpectra_(), and LayerData::sortCurrentSpectrumByPosition().

## ◆ updateRanges()

void updateRanges | ( |  | ) |

override virtual

Updates minimum and maximum position/intensity.

This method is usually implemented by calling clearRanges() and updateRanges_().

Implements RangeManager< 1 >.

## Member Data Documentation

## ◆ drift_time_

double drift_time_

protected

Drift time.

## ◆ drift_time_unit_

DriftTimeUnit drift_time_unit_

protected

Drift time unit.

## ◆ float_data_arrays_

FloatDataArrays float_data_arrays_

protected

Float data arrays.

## ◆ integer_data_arrays_

IntegerDataArrays integer_data_arrays_

protected

Integer data arrays.

## ◆ ms_level_

UInt ms_level_

protected

MS level.

## ◆ name_

String name_

protected

Name.

## ◆ retention_time_

double retention_time_

protected

Retention time.

## ◆ string_data_arrays_

StringDataArrays string_data_arrays_

protected

String data arrays.