The representation of a chromatogram. More...

#include <OpenMS/KERNEL/MSChromatogram.h>

Inheritance diagram for MSChromatogram:

Classes
struct	MZLess
	Comparator for the retention time. More...

Public Types
Base type definitions
Peak type
typedef ChromatogramPeak	PeakType

typedef PeakType::CoordinateType	CoordinateType
	Coordinate (RT) type. More...

typedef std::vector< PeakType >	ContainerType
	Chromatogram 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...

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 ChromatogramSettings
enum	ChromatogramType { MASS_CHROMATOGRAM = 0, TOTAL_ION_CURRENT_CHROMATOGRAM, SELECTED_ION_CURRENT_CHROMATOGRAM, BASEPEAK_CHROMATOGRAM, SELECTED_ION_MONITORING_CHROMATOGRAM, SELECTED_REACTION_MONITORING_CHROMATOGRAM, ELECTROMAGNETIC_RADIATION_CHROMATOGRAM, ABSORPTION_CHROMATOGRAM, EMISSION_CHROMATOGRAM, SIZE_OF_CHROMATOGRAM_TYPE }

Public Member Functions
	MSChromatogram ()
	Constructor. More...

	MSChromatogram (const MSChromatogram &source)
	Copy constructor. More...

virtual	~MSChromatogram ()
	Destructor. More...

MSChromatogram &	operator= (const MSChromatogram &source)
	Assignment operator. More...

bool	operator== (const MSChromatogram &rhs) const
	Equality operator. More...

bool	operator!= (const MSChromatogram &rhs) const
	Equality operator. More...

virtual void	updateRanges ()
	Updates minimum and maximum position/intensity. More...

double	getMZ () const
	returns the mz of the product entry, makes sense especially for MRM scans More...

Accessors for meta information
Returns the name
const String &	getName () const

void	setName (const String &name)
	Sets the name. More...

Peak data array methods
These methods are used to annotate each peak in a chromatogram 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

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 RT. More...

Searching a peak or peak range
Size	findNearest (CoordinateType rt) const
	Binary search for the peak nearest to a specific RT. More...

Iterator	RTBegin (CoordinateType rt)
	Binary search for peak range begin. More...

Iterator	RTBegin (Iterator begin, CoordinateType rt, Iterator end)
	Binary search for peak range begin. More...

Iterator	RTEnd (CoordinateType rt)
	Binary search for peak range end (returns the past-the-end iterator) More...

Iterator	RTEnd (Iterator begin, CoordinateType rt, Iterator end)
	Binary search for peak range end (returns the past-the-end iterator) More...

ConstIterator	RTBegin (CoordinateType rt) const
	Binary search for peak range begin. More...

ConstIterator	RTBegin (ConstIterator begin, CoordinateType rt, ConstIterator end) const
	Binary search for peak range begin. More...

ConstIterator	RTEnd (CoordinateType rt) const
	Binary search for peak range end (returns the past-the-end iterator) More...

ConstIterator	MZEnd (CoordinateType rt) const

ConstIterator	RTEnd (ConstIterator begin, CoordinateType rt, ConstIterator end) const
	Binary search for peak range end (returns the past-the-end iterator) More...

void	clear (bool clear_meta_data)
	Clears all data and meta data. More...

Public Member Functions inherited from RangeManager< 1 >
	RangeManager ()
	Default constructor. More...

	RangeManager (const RangeManager &rhs)
	Copy constructor. More...

virtual	~RangeManager ()
	Destructor. More...

RangeManager &	operator= (const RangeManager &rhs)
	Assignment operator. More...

bool	operator== (const RangeManager &rhs) const
	Equality operator. More...

bool	operator!= (const RangeManager &rhs) const
	Equality operator. More...

const PositionType &	getMin () const
	Returns the minimum position. More...

const PositionType &	getMax () const
	Returns the maximum position. More...

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 ChromatogramSettings
	ChromatogramSettings ()
	Constructor. More...

	ChromatogramSettings (const ChromatogramSettings &source)
	Copy constructor. More...

virtual	~ChromatogramSettings ()
	Destructor. More...

ChromatogramSettings &	operator= (const ChromatogramSettings &source)

bool	operator== (const ChromatogramSettings &rhs) const
	Equality operator. More...

bool	operator!= (const ChromatogramSettings &rhs) const
	Equality operator. 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 Precursor &	getPrecursor () const
	returns a const reference to the precursors More...

Precursor &	getPrecursor ()
	returns a mutable reference to the precursors More...

void	setPrecursor (const Precursor &precursor)
	sets the precursors More...

const Product &	getProduct () const
	returns a const reference to the products More...

Product &	getProduct ()
	returns a mutable reference to the products More...

void	setProduct (const Product &product)
	sets the products More...

ChromatogramType	getChromatogramType () const
	returns the chromatogram type, e.g. a SRM chromatogram More...

void	setChromatogramType (ChromatogramType type)
	sets the chromatogram type 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...

MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...

bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...

bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...

const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string (or DataValue::EMPTY if not found) More...

const DataValue &	getMetaValue (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
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 ChromatogramSettings
String	native_id_

String	comment_

InstrumentSettings	instrument_settings_

SourceFile	source_file_

AcquisitionInfo	acquisition_info_

Precursor	precursor_

Product	product_

std::vector< DataProcessingPtr >	data_processing_

ChromatogramType	type_

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 ChromatogramSettings
static const char *const	ChromatogramNames [SIZE_OF_CHROMATOGRAM_TYPE+1]
	Names of chromatogram types corresponding to enum ChromatogramType. 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 chromatogram.

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

Chromatogram base type.

◆ CoordinateType

typedef PeakType::CoordinateType CoordinateType

Coordinate (RT) type.

◆ 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 ChromatogramPeak PeakType

◆ 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

◆ MSChromatogram() [1/2]

MSChromatogram ( )

inline

Constructor.

◆ MSChromatogram() [2/2]

MSChromatogram ( const MSChromatogram & source )

inline

Copy constructor.

◆ ~MSChromatogram()

virtual ~MSChromatogram ( )

inlinevirtual

Destructor.

References KDTree::operator==().

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 MSDataCachedConsumer::consumeChromatogram(), and PeakPickerHiRes::pick().

◆ findNearest()

Size findNearest ( CoordinateType rt ) const

Binary search for the peak nearest to a specific RT.

Parameters

rt	The searched for mass-to-charge ratio searched

Returns: Returns the index of the peak.

Note: Make sure the chromatogram is sorted with respect to RT! Otherwise the result is undefined.

Exceptions

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

◆ getFloatDataArrays() [1/2]

const FloatDataArrays& getFloatDataArrays ( ) const

Returns a const reference to the float meta data arrays

Referenced by PeakPickerHiRes::pick().

◆ getFloatDataArrays() [2/2]

FloatDataArrays& getFloatDataArrays ( )

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.

◆ getIntegerDataArrays() [2/2]

IntegerDataArrays& getIntegerDataArrays ( )

Returns a mutable reference to the integer meta data arrays.

◆ getMZ()

double getMZ ( ) const

returns the mz of the product entry, makes sense especially for MRM scans

Referenced by GaussFilter::filter().

◆ getName()

const String& getName ( ) const

Referenced by PeakPickerHiRes::pick().

◆ getStringDataArrays() [1/2]

const StringDataArrays& getStringDataArrays ( ) const

Returns a const reference to the string meta data arrays.

◆ 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 RT.

Referenced by MRMTransitionGroupPicker::pickTransitionGroup().

◆ MZEnd()

ConstIterator MZEnd ( CoordinateType rt ) const

◆ operator!=()

bool operator!= ( const MSChromatogram & rhs ) const

inline

Equality operator.

References KDTree::operator==().

◆ operator=()

MSChromatogram& operator= ( const MSChromatogram & source )

Assignment operator.

◆ operator==()

bool operator== ( const MSChromatogram & rhs ) const

Equality operator.

◆ RTBegin() [1/4]

Iterator RTBegin ( CoordinateType rt )

Binary search for peak range begin.

Note: Make sure the chromatogram is sorted with respect to retention time! Otherwise the result is undefined.

◆ RTBegin() [2/4]

Iterator RTBegin	(	Iterator	begin,
		CoordinateType	rt,
		Iterator	end
	)

Binary search for peak range begin.

Note: Make sure the chromatogram is sorted with respect to RT! Otherwise the result is undefined.

◆ RTBegin() [3/4]

ConstIterator RTBegin ( CoordinateType rt ) const

Binary search for peak range begin.

Note: Make sure the chromatogram is sorted with respect to RT! Otherwise the result is undefined.

◆ RTBegin() [4/4]

ConstIterator RTBegin	(	ConstIterator	begin,
		CoordinateType	rt,
		ConstIterator	end
	)		const

Binary search for peak range begin.

Note: Make sure the chromatogram is sorted with respect to RT! Otherwise the result is undefined.

◆ RTEnd() [1/4]

Iterator RTEnd ( CoordinateType rt )

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

Note: Make sure the chromatogram is sorted with respect to RT. Otherwise the result is undefined.

◆ RTEnd() [2/4]

Iterator RTEnd	(	Iterator	begin,
		CoordinateType	rt,
		Iterator	end
	)

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

Note: Make sure the chromatogram is sorted with respect to RT. Otherwise the result is undefined.

◆ RTEnd() [3/4]

ConstIterator RTEnd ( CoordinateType rt ) const

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

Note: Make sure the chromatogram is sorted with respect to RT. Otherwise the result is undefined.

◆ RTEnd() [4/4]

ConstIterator RTEnd	(	ConstIterator	begin,
		CoordinateType	rt,
		ConstIterator	end
	)		const

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

Note: Make sure the chromatogram is sorted with respect to RT. Otherwise the result is undefined.

◆ setFloatDataArrays()

void setFloatDataArrays ( const FloatDataArrays & fda )

inline

Sets the float meta data arrays.

◆ setIntegerDataArrays()

void setIntegerDataArrays ( const IntegerDataArrays & ida )

inline

Sets the integer meta data arrays.

◆ setName()

void setName ( const String & name )

Sets the name.

Referenced by PeakPickerHiRes::pick().

◆ setStringDataArrays()

void setStringDataArrays ( const StringDataArrays & sda )

inline

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 MRMTransitionGroupPicker::pickTransitionGroup().

◆ sortByPosition()

void sortByPosition ( )

Lexicographically sorts the peaks by their position.

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

Referenced by MRMTransitionGroupPicker::pickTransitionGroup().

◆ updateRanges()

virtual void updateRanges ( )

inlinevirtual

Updates minimum and maximum position/intensity.

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

Implements RangeManager< 1 >.

Member Data Documentation

◆ float_data_arrays_

FloatDataArrays float_data_arrays_

protected

Float data arrays.

◆ integer_data_arrays_

IntegerDataArrays integer_data_arrays_

protected

Integer data arrays.

◆ name_

String name_

protected

Name.

◆ string_data_arrays_

StringDataArrays string_data_arrays_

protected

String data arrays.

Classes

Public Types

Public Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConstIterator

◆ ConstReverseIterator

◆ ContainerType

◆ CoordinateType

◆ FloatDataArray

◆ FloatDataArrays

◆ IntegerDataArray

◆ IntegerDataArrays

◆ Iterator

◆ PeakType

◆ ReverseIterator

◆ StringDataArray

◆ StringDataArrays

Constructor & Destructor Documentation

◆ MSChromatogram() [1/2]

◆ MSChromatogram() [2/2]

◆ ~MSChromatogram()

Member Function Documentation

◆ clear()

◆ findNearest()

◆ getFloatDataArrays() [1/2]

◆ getFloatDataArrays() [2/2]

◆ getIntegerDataArrays() [1/2]

◆ getIntegerDataArrays() [2/2]

◆ getMZ()

◆ getName()

◆ getStringDataArrays() [1/2]

◆ getStringDataArrays() [2/2]

◆ isSorted()

◆ MZEnd()

◆ operator!=()

◆ operator=()

◆ operator==()

◆ RTBegin() [1/4]

◆ RTBegin() [2/4]

◆ RTBegin() [3/4]

◆ RTBegin() [4/4]

◆ RTEnd() [1/4]

◆ RTEnd() [2/4]

◆ RTEnd() [3/4]

◆ RTEnd() [4/4]

◆ setFloatDataArrays()

◆ setIntegerDataArrays()

◆ setName()

◆ setStringDataArrays()

◆ sortByIntensity()

◆ sortByPosition()

◆ updateRanges()

Member Data Documentation

◆ float_data_arrays_

◆ integer_data_arrays_

◆ name_

◆ string_data_arrays_