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

#include <OpenMS/KERNEL/MSSpectrum.h>

Inheritance diagram for MSSpectrum< PeakT >:

Classes
class	FloatDataArray
	Float data array class. More...
class	IntegerDataArray
	Integer data array class. More...
struct	RTLess
	Comparator for the retention time. More...
class	StringDataArray
	String data array class. More...
Public Types
Base type definitions

typedef PeakT	PeakType
	Peak type.
typedef PeakType::CoordinateType	CoordinateType
	Coordinate (m/z) type.
typedef std::vector< PeakType >	ContainerType
	Spectrum base type.
typedef std::vector < FloatDataArray >	FloatDataArrays
	Float data array vector type.
typedef std::vector < StringDataArray >	StringDataArrays
	String data array vector type.
typedef std::vector < IntegerDataArray >	IntegerDataArrays
	Integer data array vector type.
Peak container iterator type definitions

typedef ContainerType::iterator	Iterator
	Mutable iterator.
typedef ContainerType::const_iterator	ConstIterator
	Non-mutable iterator.
typedef ContainerType::reverse_iterator	ReverseIterator
	Mutable reverse iterator.
typedef ContainerType::const_reverse_iterator	ConstReverseIterator
	Non-mutable reverse iterator.
Public Member Functions
	MSSpectrum ()
	Constructor.
	MSSpectrum (const MSSpectrum &source)
	Copy constructor.
	~MSSpectrum ()
	Destructor.
MSSpectrum &	operator= (const MSSpectrum &source)
	Assignment operator.
bool	operator== (const MSSpectrum &rhs) const
	Equality operator.
bool	operator!= (const MSSpectrum &rhs) const
	Equality operator.
virtual void	updateRanges ()
void	clear (bool clear_meta_data)
	Clears all data and meta data.
Accessors for meta information
Returns the absolute retention time (is seconds)
DoubleReal	getRT () const
void	setRT (DoubleReal rt)
	Sets the absolute retention time (is seconds).
UInt	getMSLevel () const
	Returns the MS level.
void	setMSLevel (UInt ms_level)
	Sets the MS level.
const String &	getName () const
	Returns the name.
void	setName (const String &name)
	Sets the name.
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.
FloatDataArrays &	getFloatDataArrays ()
	Returns a mutable reference to the float meta data arrays.
const StringDataArrays &	getStringDataArrays () const
	Returns a const reference to the string meta data arrays.
StringDataArrays &	getStringDataArrays ()
	Returns a mutable reference to the string meta data arrays.
const IntegerDataArrays &	getIntegerDataArrays () const
	Returns a const reference to the integer meta data arrays.
IntegerDataArrays &	getIntegerDataArrays ()
	Returns a mutable reference to the integer meta data arrays.
Sorting peaks

void	sortByIntensity (bool reverse=false)
	Lexicographically sorts the peaks by their intensity.
void	sortByPosition ()
	Lexicographically sorts the peaks by their position.
bool	isSorted () const
	Checks if all peaks are sorted with respect to ascending m/z.
Searching a peak or peak range

Size	findNearest (CoordinateType mz) const
	Binary search for the peak nearest to a specific m/z.
Iterator	MZBegin (CoordinateType mz)
	Binary search for peak range begin.
Iterator	MZBegin (Iterator begin, CoordinateType mz, Iterator end)
	Binary search for peak range begin.
Iterator	MZEnd (CoordinateType mz)
	Binary search for peak range end (returns the past-the-end iterator).
Iterator	MZEnd (Iterator begin, CoordinateType mz, Iterator end)
	Binary search for peak range end (returns the past-the-end iterator).
ConstIterator	MZBegin (CoordinateType mz) const
	Binary search for peak range begin.
ConstIterator	MZBegin (ConstIterator begin, CoordinateType mz, ConstIterator end) const
	Binary search for peak range begin.
ConstIterator	MZEnd (CoordinateType mz) const
	Binary search for peak range end (returns the past-the-end iterator).
ConstIterator	MZEnd (ConstIterator begin, CoordinateType mz, ConstIterator end) const
	Binary search for peak range end (returns the past-the-end iterator).
Protected Member Functions
virtual void	clearChildIds_ ()
	Clears the persistence id of all sub-objects.
Protected Attributes
DoubleReal	retention_time_
	Retention time.
UInt	ms_level_
	MS level.
String	name_
	Name.
FloatDataArrays	float_data_arrays_
	Float data arrays.
StringDataArrays	string_data_arrays_
	String data arrays.
IntegerDataArrays	integer_data_arrays_
	Intager data arrays.

Detailed Description

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!

Member Typedef Documentation

typedef ContainerType::const_iterator ConstIterator

Non-mutable iterator.

typedef ContainerType::const_reverse_iterator ConstReverseIterator

Non-mutable reverse iterator.

typedef std::vector<PeakType> ContainerType

Spectrum base type.

typedef PeakType::CoordinateType CoordinateType

Coordinate (m/z) type.

typedef std::vector<FloatDataArray> FloatDataArrays

Float data array vector type.

typedef std::vector<IntegerDataArray> IntegerDataArrays

Integer data array vector type.

typedef ContainerType::iterator Iterator

Mutable iterator.

typedef PeakT PeakType

Peak type.

typedef ContainerType::reverse_iterator ReverseIterator

Mutable reverse iterator.

typedef std::vector<StringDataArray> StringDataArrays

String data array vector type.

Constructor & Destructor Documentation

MSSpectrum ( ) [inline]

Constructor.

MSSpectrum ( const MSSpectrum< PeakT > & source ) [inline]

Copy constructor.

~MSSpectrum ( ) [inline]

Destructor.

Member Function Documentation

void clear ( bool clear_meta_data ) [inline]

Clears all data and meta data.

Parameters:

clear_meta_data

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

Referenced by MSSpectrum< RichPeak1D >::clear(), IDEvaluationBase::getPoints(), XMassFile::load(), TwoDOptimization::optimizeRegionsScanwise_(), and PeakPickerHiRes::pick().

virtual void clearChildIds_ ( ) [inline, protected, virtual]

Clears the persistence id of all sub-objects.

Implements PersistentObject.

Reimplemented in BinnedSpectrum.

Size findNearest ( CoordinateType mz ) const [inline]

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 FeatureFinderAlgorithmPicked< PeakType, FeatureType >::findIsotope_(), and FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run().

const FloatDataArrays& getFloatDataArrays ( ) const [inline]

Returns a const reference to the float meta data arrays.

Referenced by MetaDataBrowser::add(), MzDataHandler< MapType >::characters(), MzMLHandler< MapType >::fillData_(), MzDataHandler< MapType >::fillData_(), TwoDOptimization::optimizeRegionsScanwise_(), DataFilters::passes(), MzDataHandler< MapType >::startElement(), MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

FloatDataArrays& getFloatDataArrays ( ) [inline]

Returns a mutable reference to the float meta data arrays.

IntegerDataArrays& getIntegerDataArrays ( ) [inline]

Returns a mutable reference to the integer meta data arrays.

const IntegerDataArrays& getIntegerDataArrays ( ) const [inline]

Returns a const reference to the integer meta data arrays.

Referenced by MetaDataBrowser::add(), MzMLHandler< MapType >::fillData_(), DataFilters::passes(), and MzMLHandler< MapType >::writeTo().

UInt getMSLevel ( ) const [inline]

Returns the MS level.

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

Referenced by MzDataHandler< MapType >::cvParam_(), MzMLHandler< MapType >::handleCVParam_(), PeakPickerHiRes::pick(), MzDataHandler< MapType >::startElement(), CachedmzML::writeSpectrum_(), MzXMLHandler< MapType >::writeTo(), MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

const String& getName ( ) const [inline]

Returns the name.

Referenced by PeakPickerHiRes::pick().

DoubleReal getRT ( ) const [inline]

Referenced by IsotopeWaveletTransform< PeakType >::checkPositionForPlausibility_(), MzDataHandler< MapType >::cvParam_(), GaussFilter::filter(), IsotopeWaveletTransform< PeakType >::TransSpectrum::getRT(), MzMLHandler< MapType >::handleCVParam_(), IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), TOPPRNPxl::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), MSSpectrum< PeakT >::RTLess::operator()(), PeakPickerHiRes::pick(), FeatureFinderAlgorithmSH< PeakType, FeatureType >::run(), FeatureFinderAlgorithmPicked< PeakType, FeatureType >::run(), FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::run(), CachedmzML::writeSpectrum_(), MzXMLHandler< MapType >::writeTo(), MzMLHandler< MapType >::writeTo(), and MzDataHandler< MapType >::writeTo().

const StringDataArrays& getStringDataArrays ( ) const [inline]

Returns a const reference to the string meta data arrays.

Referenced by MetaDataBrowser::add(), MzMLHandler< MapType >::fillData_(), and MzMLHandler< MapType >::writeTo().

StringDataArrays& getStringDataArrays ( ) [inline]

Returns a mutable reference to the string meta data arrays.

bool isSorted ( ) const [inline]

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

Referenced by MRMTransitionGroupPicker::pickTransitionGroup().

ConstIterator MZBegin	(	ConstIterator	begin,
		CoordinateType	mz,
		ConstIterator	end
	)			const `[inline]`

Binary search for peak range begin.

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

Iterator MZBegin ( CoordinateType mz ) [inline]

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_(), MSSpectrum< RichPeak1D >::findNearest(), IsotopeWaveletTransform< PeakType >::identifyCharge(), IsotopeWaveletTransform< PeakType >::initializeScan(), IsotopeWaveletTransform< PeakType >::mapSeeds2Features(), IsotopeWaveletTransform< PeakType >::TransSpectrum::MZBegin(), and IsotopeWaveletTransform< PeakType >::scoreThis_().

Iterator MZBegin	(	Iterator	begin,
		CoordinateType	mz,
		Iterator	end
	)			`[inline]`

Binary search for peak range begin.

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

ConstIterator MZBegin ( CoordinateType mz ) const [inline]

Binary search for peak range begin.

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

Iterator MZEnd ( CoordinateType mz ) [inline]

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().

ConstIterator MZEnd ( CoordinateType mz ) const [inline]

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.

Iterator MZEnd	(	Iterator	begin,
		CoordinateType	mz,
		Iterator	end
	)			`[inline]`

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.

ConstIterator MZEnd	(	ConstIterator	begin,
		CoordinateType	mz,
		ConstIterator	end
	)			const `[inline]`

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.

bool operator!= ( const MSSpectrum< PeakT > & rhs ) const [inline]

Equality operator.

MSSpectrum& operator= ( const MSSpectrum< PeakT > & source ) [inline]

Assignment operator.

Referenced by MSSpectrum< RichPeak1D >::clear(), and MSSpectrum< RichPeak1D >::operator=().

bool operator== ( const MSSpectrum< PeakT > & rhs ) const [inline]

Equality operator.

Referenced by MSSpectrum< RichPeak1D >::operator!=(), and MSSpectrum< RichPeak1D >::operator==().

void setMSLevel ( UInt ms_level ) [inline]

Sets the MS level.

Referenced by MzDataHandler< MapType >::cvParam_(), MzMLHandler< MapType >::handleCVParam_(), XMassFile::load(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), PeakPickerHiRes::pick(), CachedmzML::readSpectrum_(), MSExperiment< SimPointType >::set2DData(), TOPPViewBase::showSpectrumGenerationDialog(), and MzDataHandler< MapType >::startElement().

void setName ( const String & name ) [inline]

Sets the name.

Referenced by XMassFile::load(), TOPPRNPxl::main_(), and PeakPickerHiRes::pick().

void setRT ( DoubleReal rt ) [inline]

Sets the absolute retention time (is seconds).

Referenced by FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::createHRData(), MzDataHandler< MapType >::cvParam_(), TwoDOptimization::getRegionEndpoints_(), MzMLHandler< MapType >::handleCVParam_(), XMassFile::load(), TOPPRNPxl::main_(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), TwoDOptimization::optimize(), PeakPickerHiRes::pick(), CachedmzML::readSpectrum_(), MSExperiment< SimPointType >::RTBegin(), MSExperiment< SimPointType >::RTEnd(), and MSExperiment< SimPointType >::set2DData().

void sortByIntensity ( bool reverse = false ) [inline]

Lexicographically sorts the peaks by their intensity.

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

Referenced by IsotopeWaveletTransform< PeakType >::identifyCharge(), OfflinePrecursorIonSelection::makePrecursorSelectionForKnownLCMSMap(), and MRMTransitionGroupPicker::pickTransitionGroup().

void sortByPosition ( ) [inline]

Lexicographically sorts the peaks by their position.

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

Referenced by FeatureFinderAlgorithmIsotopeWavelet< PeakType, FeatureType >::createHRData(), MarkerIonExtractor::extractMarkerIons(), and MRMTransitionGroupPicker::pickTransitionGroup().

virtual void updateRanges ( ) [inline, virtual]

Member Data Documentation

FloatDataArrays float_data_arrays_ [protected]

Float data arrays.

Referenced by MSSpectrum< RichPeak1D >::clear(), MSSpectrum< RichPeak1D >::getFloatDataArrays(), MSSpectrum< RichPeak1D >::operator=(), MSSpectrum< RichPeak1D >::operator==(), MSSpectrum< RichPeak1D >::sortByIntensity(), and MSSpectrum< RichPeak1D >::sortByPosition().

IntegerDataArrays integer_data_arrays_ [protected]

Intager data arrays.

Referenced by MSSpectrum< RichPeak1D >::clear(), MSSpectrum< RichPeak1D >::getIntegerDataArrays(), MSSpectrum< RichPeak1D >::operator=(), MSSpectrum< RichPeak1D >::operator==(), MSSpectrum< RichPeak1D >::sortByIntensity(), and MSSpectrum< RichPeak1D >::sortByPosition().

UInt ms_level_ [protected]

MS level.

Referenced by MSSpectrum< RichPeak1D >::clear(), MSSpectrum< RichPeak1D >::getMSLevel(), MSSpectrum< RichPeak1D >::operator=(), MSSpectrum< RichPeak1D >::operator==(), and MSSpectrum< RichPeak1D >::setMSLevel().

String name_ [protected]

Name.

Referenced by MSSpectrum< RichPeak1D >::clear(), MSSpectrum< RichPeak1D >::getName(), MSSpectrum< RichPeak1D >::operator=(), and MSSpectrum< RichPeak1D >::setName().

DoubleReal retention_time_ [protected]

Retention time.

Referenced by MSSpectrum< RichPeak1D >::clear(), MSSpectrum< RichPeak1D >::getRT(), MSSpectrum< RichPeak1D >::operator=(), MSSpectrum< RichPeak1D >::operator==(), and MSSpectrum< RichPeak1D >::setRT().

StringDataArrays string_data_arrays_ [protected]

String data arrays.

Referenced by MSSpectrum< RichPeak1D >::clear(), MSSpectrum< RichPeak1D >::getStringDataArrays(), MSSpectrum< RichPeak1D >::operator=(), MSSpectrum< RichPeak1D >::operator==(), MSSpectrum< RichPeak1D >::sortByIntensity(), and MSSpectrum< RichPeak1D >::sortByPosition().

OpenMS / TOPP release 1.10.0

Documentation generated on Thu Mar 7 2013 09:42:55 using doxygen 1.7.1

MSSpectrum< PeakT > Class Template Reference [Kernel]

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<typename PeakT = Peak1D> class OpenMS::MSSpectrum< PeakT >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

MSSpectrum< PeakT > Class Template Reference
[Kernel]

template<typename PeakT = Peak1D>
class OpenMS::MSSpectrum< PeakT >