OpenMS  2.4.0
Classes | Public Member Functions | Protected Attributes | List of all members
MSSpectrum Class Reference

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

#include <OpenMS/KERNEL/MSSpectrum.h>

Inheritance diagram for MSSpectrum:
RangeManager< 1 > SpectrumSettings MetaInfoInterface

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< PeakTypeContainerType
 Spectrum base type. More...
 
typedef OpenMS::DataArrays::FloatDataArray FloatDataArray
 Float data array vector type. More...
 
typedef std::vector< FloatDataArrayFloatDataArrays
 
typedef OpenMS::DataArrays::StringDataArray StringDataArray
 String data array vector type. More...
 
typedef std::vector< StringDataArrayStringDataArrays
 
typedef OpenMS::DataArrays::IntegerDataArray IntegerDataArray
 Integer data array vector type. More...
 
typedef std::vector< IntegerDataArrayIntegerDataArrays
 
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...
 
- 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 () override
 Destructor. More...
 
MSSpectrumoperator= (const MSSpectrum &source)
 Assignment operator. More...
 
MSSpectrumoperator= (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...
 
MSSpectrumselect (const std::vector< Size > &indices)
 
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 in milliseconds (-1 means it is not set) More...
 
void setDriftTime (double dt)
 Returns the ion mobility drift time in milliseconds. More...
 
UInt getMSLevel () const
 Returns the MS level. More...
 
void setMSLevel (UInt ms_level)
 Sets the MS level. More...
 
const StringgetName () 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 FloatDataArraysgetFloatDataArrays () const
 Returns a const reference to the float meta data arrays. More...
 
FloatDataArraysgetFloatDataArrays ()
 Returns a mutable reference to the float meta data arrays. More...
 
void setFloatDataArrays (const FloatDataArrays &fda)
 Sets the float meta data arrays. More...
 
const StringDataArraysgetStringDataArrays () const
 Returns a const reference to the string meta data arrays. More...
 
StringDataArraysgetStringDataArrays ()
 Returns a mutable reference to the string meta data arrays. More...
 
void setStringDataArrays (const StringDataArrays &sda)
 Sets the string meta data arrays. More...
 
const IntegerDataArraysgetIntegerDataArrays () const
 Returns a const reference to the integer meta data arrays. More...
 
IntegerDataArraysgetIntegerDataArrays ()
 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...
 
virtual ~RangeManager ()
 Destructor. More...
 
RangeManageroperator= (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 PositionTypegetMin () const
 Returns the minimum position. More...
 
const PositionTypegetMax () 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 &source)
 Copy constructor. More...
 
 ~SpectrumSettings ()
 Destructor. More...
 
SpectrumSettingsoperator= (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 (centroided (PEAKS) or profile data (RAW)) More...
 
void setType (SpectrumType type)
 sets the spectrum type More...
 
const StringgetNativeID () 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 StringgetComment () const
 returns the free-text comment More...
 
void setComment (const String &comment)
 sets the free-text comment More...
 
const InstrumentSettingsgetInstrumentSettings () const
 returns a const reference to the instrument settings of the current spectrum More...
 
InstrumentSettingsgetInstrumentSettings ()
 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 AcquisitionInfogetAcquisitionInfo () const
 returns a const reference to the acquisition info More...
 
AcquisitionInfogetAcquisitionInfo ()
 returns a mutable reference to the acquisition info More...
 
void setAcquisitionInfo (const AcquisitionInfo &acquisition_info)
 sets the acquisition info More...
 
const SourceFilegetSourceFile () const
 returns a const reference to the source file More...
 
SourceFilegetSourceFile ()
 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 ()
 Destructor. More...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (const String &name) const
 Returns the value corresponding to a string (or DataValue::EMPTY if not found) More...
 
const DataValuegetMetaValue (UInt index) const
 Returns the value corresponding to an index (or 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...
 
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< Precursorprecursors_
 
std::vector< Productproducts_
 
std::vector< PeptideIdentificationidentification_
 
std::vector< DataProcessingPtrdata_processing_
 
- Protected Attributes inherited from MetaInfoInterface
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 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

Coordinate (m/z) type.

◆ FloatDataArray

Float data array vector type.

◆ FloatDataArrays

typedef std::vector<FloatDataArray> FloatDataArrays

◆ IntegerDataArray

Integer data array vector type.

◆ IntegerDataArrays

typedef std::vector<IntegerDataArray> IntegerDataArrays

◆ Iterator

typedef ContainerType::iterator Iterator

Mutable iterator.

◆ PeakType

Peak type.

◆ ReverseIterator

typedef ContainerType::reverse_iterator ReverseIterator

Mutable reverse iterator.

◆ StringDataArray

String data array vector type.

◆ StringDataArrays

typedef std::vector<StringDataArray> StringDataArrays

Constructor & Destructor Documentation

◆ MSSpectrum() [1/2]

Constructor.

◆ MSSpectrum() [2/2]

MSSpectrum ( const MSSpectrum source)

Copy constructor.

◆ ~MSSpectrum()

~MSSpectrum ( )
inlineoverride

Destructor.

Member Function Documentation

◆ clear()

void clear ( bool  clear_meta_data)

◆ findNearest() [1/3]

Size findNearest ( CoordinateType  mz) const

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

Parameters
mzThe 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::Preconditionis thrown if the spectrum is empty (not only in debug mode)

◆ 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
mzThe searched for mass-to-charge ratio searched
toleranceThe 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
mzThe searched for mass-to-charge ratio searched
tolerance_leftThe non-negative tolerance applied left of mz
tolerance_rightThe 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

◆ getDriftTime()

double getDriftTime ( ) const

Returns the ion mobility drift time in milliseconds (-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.

◆ getFloatDataArrays() [1/2]

const FloatDataArrays& getFloatDataArrays ( ) const

◆ getFloatDataArrays() [2/2]

FloatDataArrays& getFloatDataArrays ( )
inline

Returns a mutable reference to the float meta data arrays.

◆ getIntegerDataArrays() [1/2]

const IntegerDataArrays& getIntegerDataArrays ( ) const

◆ getIntegerDataArrays() [2/2]

IntegerDataArrays& getIntegerDataArrays ( )

Returns a mutable reference to the integer meta data arrays.

◆ getMSLevel()

UInt getMSLevel ( ) const

◆ getName()

const String& getName ( ) const

Returns the name.

Referenced by PeakPickerIterative::pick().

◆ getRT()

double getRT ( ) const

◆ getStringDataArrays() [1/2]

const StringDataArrays& getStringDataArrays ( ) const

◆ getStringDataArrays() [2/2]

StringDataArrays& getStringDataArrays ( )

Returns a mutable reference to the string meta data arrays.

◆ isSorted()

bool isSorted ( ) const

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

◆ MZBegin() [1/4]

Iterator MZBegin ( CoordinateType  mz)

◆ 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 TOPPMetaProSIP::extractPeakSpectrum(), 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=() [1/2]

MSSpectrum& operator= ( const MSSpectrum source)

Assignment operator.

◆ operator=() [2/2]

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)

◆ setDriftTime()

void setDriftTime ( double  dt)

Returns the ion mobility drift time in milliseconds.

◆ setFloatDataArrays()

void setFloatDataArrays ( const FloatDataArrays fda)

Sets the float meta data arrays.

◆ setIntegerDataArrays()

void setIntegerDataArrays ( const IntegerDataArrays ida)

Sets the integer meta data arrays.

◆ setMSLevel()

void setMSLevel ( UInt  ms_level)

◆ setName()

void setName ( const String name)

Sets the name.

Referenced by DTAFile::load(), XMassFile::load(), and PeakPickerIterative::pick().

◆ setRT()

void setRT ( double  rt)

◆ 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 ( )

◆ updateRanges()

void updateRanges ( )
overridevirtual

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.

◆ 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.