The representation of a chromatogram. More...

#include <OpenMS/KERNEL/MSChromatogram.h>

Inheritance diagram for MSChromatogram:

Classes
struct	MZLess
	Comparator for the precursor m/z time. More...

Public Types
Base type definitions
Peak type
typedef ChromatogramPeak	PeakType

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

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

typedef RangeManager< RangeRT, RangeIntensity >	RangeManagerType
	RangeManager.

typedef OpenMS::DataArrays::FloatDataArray	FloatDataArray
	Float data array vector type.

typedef std::vector< FloatDataArray >	FloatDataArrays

typedef OpenMS::DataArrays::StringDataArray	StringDataArray
	std::string data array vector type

typedef std::vector< StringDataArray >	StringDataArrays

typedef OpenMS::DataArrays::IntegerDataArray	IntegerDataArray
	Integer data array vector type.

typedef std::vector< IntegerDataArray >	IntegerDataArrays

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 Types inherited from RangeManagerContainer< RangeRT, RangeIntensity >
using	ThisRangeType = typename RangeManager< RangeBases... >::ThisRangeType

Public Types inherited from RangeManager< RangeBases... >
using	ThisRangeType = RangeManager< RangeBases... >

Public Types inherited from ChromatogramSettings
enum class	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 Types inherited from MetaInfoInterface
using	MetaInfoConstIterator = MetaInfo::const_iterator
	Const iterator type for iterating over meta info entries.

Public Member Functions
double	getMZ () const
	returns the mz of the product entry, makes sense especially for MRM scans

void	mergePeaks (MSChromatogram &other, bool add_meta=false)
	Adds all the chromatogram peaks from another MSChromatogram and updates the metadata to indicate a merge.

Export methods from std::vector
	MSChromatogram ()=default
	Constructor.

	MSChromatogram (const MSChromatogram &)=default
	Copy constructor.

	MSChromatogram (MSChromatogram &&)=default
	Move constructor.

	~MSChromatogram ()=default
	Destructor.

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

MSChromatogram &	operator= (MSChromatogram &&) &=default
	Move assignment operator.

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

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

void	updateRanges () override

Accessors for meta information
Returns the name
const std::string &	getName () const

void	setName (const std::string &name)
	Sets the name.

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.

void	setFloatDataArrays (const FloatDataArrays &fda)
	Sets 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.

void	setStringDataArrays (const StringDataArrays &sda)
	Sets 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.

void	setIntegerDataArrays (const IntegerDataArrays &ida)
	Sets 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 RT.

template<class Predicate >
void	sort (const Predicate &lambda)
	Stably sorts the peaks (and all parallel data arrays) by a user-defined predicate.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

MSChromatogram &	select (const std::vector< Size > &indices)
	Subset the chromatogram by selecting only indices in `indices`, in that order.

MSChromatogram &	selectUnchecked (const std::vector< Size > &indices)
	Like select(), but without the per-index range check.

Public Member Functions inherited from RangeManagerContainer< RangeRT, RangeIntensity >
virtual	~RangeManagerContainer ()=default
	D'tor.

const ThisRangeType &	getRange () const
	get range of current data (call updateRanges() before to ensure the range is accurate)

ThisRangeType &	getRange ()
	get mutable range, provided for efficiency reasons (avoid updateRanges(), if only minor changes were made)

Public Member Functions inherited from RangeManager< RangeBases... >
bool	operator== (const RangeManager &rhs) const

bool	operator!= (const RangeManager &rhs) const

bool	assignUnsafe (const RangeManager< RangeBasesOther... > &rhs)

auto &	assign (const RangeManager< RangeBasesOther... > &rhs)

bool	extendUnsafe (const RangeManager< RangeBasesOther... > &rhs)

void	extend (const RangeManager< RangeBasesOther... > &rhs)

void	scaleBy (const double factor)
	calls RangeBase::scale() for each dimension

void	minSpanIfSingular (const double min_span)
	If any dimension is a single point, e.g. min==max, then extend this dimension by `min_span` / 2 on either side.

bool	pushIntoUnsafe (const RangeManager< RangeBasesOther... > &rhs)

void	pushInto (const RangeManager< RangeBasesOther... > &sandbox)

bool	clampToUnsafe (const RangeManager< RangeBasesOther... > &rhs)

void	clampTo (const RangeManager< RangeBasesOther... > &rhs)

const RangeBase &	getRangeForDim (MSDim dim) const
	obtain a range dimension at runtime using `dim`

RangeBase &	getRangeForDim (MSDim dim)
	obtain a range dimension at runtime using `dim`

HasRangeType	hasRange () const
	is any/some/all dimension in this range populated?

bool	containsAll (const RangeManager< RangeBasesOther... > &rhs) const

void	clearRanges ()
	Resets all ranges.

ThisRangeType &	clear (const DIM_UNIT range)

void	printRange (std::ostream &out) const
	print each dimension (base classes) to a stream

Public Member Functions inherited from ChromatogramSettings
	ChromatogramSettings ()
	Constructor.

	ChromatogramSettings (const ChromatogramSettings &)=default
	Copy constructor.

	ChromatogramSettings (ChromatogramSettings &&)=default
	Move constructor.

virtual	~ChromatogramSettings ()
	Destructor.

ChromatogramSettings &	operator= (const ChromatogramSettings &)=default

ChromatogramSettings &	operator= (ChromatogramSettings &&) &=default
	Move assignment operator.

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

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

const std::string &	getNativeID () const
	returns the native identifier for the spectrum, used by the acquisition software.

void	setNativeID (const std::string &native_id)
	sets the native identifier for the spectrum, used by the acquisition software.

const std::string &	getComment () const
	returns the free-text comment

void	setComment (const std::string &comment)
	sets the free-text comment

const InstrumentSettings &	getInstrumentSettings () const
	returns a const reference to the instrument settings of the current spectrum

InstrumentSettings &	getInstrumentSettings ()
	returns a mutable reference to the instrument settings of the current spectrum

void	setInstrumentSettings (const InstrumentSettings &instrument_settings)
	sets the instrument settings of the current spectrum

const AcquisitionInfo &	getAcquisitionInfo () const
	returns a const reference to the acquisition info

AcquisitionInfo &	getAcquisitionInfo ()
	returns a mutable reference to the acquisition info

void	setAcquisitionInfo (const AcquisitionInfo &acquisition_info)
	sets the acquisition info

const SourceFile &	getSourceFile () const
	returns a const reference to the source file

SourceFile &	getSourceFile ()
	returns a mutable reference to the source file

void	setSourceFile (const SourceFile &source_file)
	sets the source file

const Precursor &	getPrecursor () const
	returns a const reference to the precursors

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

void	setPrecursor (const Precursor &precursor)
	sets the precursors

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

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

void	setProduct (const Product &product)
	sets the products

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

void	setChromatogramType (ChromatogramType type)
	sets the chromatogram type

void	setDataProcessing (const std::vector< DataProcessingPtr > &data_processing)
	sets the description of the applied processing

std::vector< DataProcessingPtr > &	getDataProcessing ()
	returns a mutable reference to the description of the applied processing

const std::vector< std::shared_ptr< const DataProcessing > >	getDataProcessing () const
	returns a const reference to the description of the applied processing

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()=default
	Constructor.

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor.

	MetaInfoInterface (MetaInfoInterface &&) noexcept
	Move constructor.

	~MetaInfoInterface ()
	Destructor.

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

MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move assignment operator.

void	swap (MetaInfoInterface &rhs)
	Swap contents.

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

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

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

DataValue	getMetaValue (const std::string &name, const DataValue &default_value) const
	Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found

const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to the index, or DataValue::EMPTY if not found.

DataValue	getMetaValue (UInt index, const DataValue &default_value) const
	Returns the value corresponding to the index, or a default value (e.g.: DataValue::EMPTY) if not found

bool	metaValueExists (const std::string &name) const
	Returns whether an entry with the given name exists.

bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists.

void	setMetaValue (const std::string &name, const DataValue &value)
	Sets the DataValue corresponding to a name.

void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index.

void	removeMetaValue (const std::string &name)
	Removes the DataValue corresponding to `name` if it exists.

void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to `index` if it exists.

void	addMetaValues (const MetaInfoInterface &from)

void	getKeys (std::vector< std::string > &keys) const
	Fills the given vector with a list of all keys for which a value is set.

void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set.

bool	isMetaEmpty () const
	Returns if the MetaInfo is empty.

void	clearMetaInfo ()
	Removes all meta values.

MetaInfoConstIterator	metaBegin () const
	Returns a const iterator to the beginning of the meta info entries.

MetaInfoConstIterator	metaEnd () const
	Returns a const iterator to the end of the meta info entries.

Size	metaSize () const
	Returns the number of meta info entries.

Protected Member Functions
void	checkDataArraySizes_ () const
	Throws Exception::Precondition if any non-empty data array's size differs from the peak count.

Protected Member Functions inherited from RangeManager< RangeBases... >
void	for_each_base_ (Visitor &&visitor)
	use fold expression to iterate over all RangeBases of RangeManager and apply a lambda (Visitor) for each one

void	for_each_base_ (Visitor &&visitor) const
	.. and a const version

Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist.

Protected Attributes
std::string	name_
	Name.

FloatDataArrays	float_data_arrays_
	Float data arrays.

StringDataArrays	string_data_arrays_
	std::string data arrays

IntegerDataArrays	integer_data_arrays_
	Integer data arrays.

Protected Attributes inherited from ChromatogramSettings
std::string	native_id_

std::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_ = nullptr
	Pointer to the MetaInfo object.

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry.

Static Public Attributes inherited from ChromatogramSettings
static const char *const	ChromatogramNames [static_cast< size_t >(ChromatogramType::SIZE_OF_CHROMATOGRAM_TYPE)+1]
	Names of chromatogram types corresponding to enum ChromatogramType.

Static Protected Member Functions inherited from RangeManager< RangeBases... >
static void	static_for_each_base_ (Visitor &&visitor)
	use fold expression to iterate over all RangeBases of RangeManager and apply a lambda (Visitor) for each one (for static members)

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

◆ RangeManagerType

typedef RangeManager<RangeRT, RangeIntensity> RangeManagerType

RangeManager.

◆ ReverseIterator

typedef ContainerType::reverse_iterator ReverseIterator

Mutable reverse iterator.

◆ StringDataArray

typedef OpenMS::DataArrays::StringDataArray StringDataArray

std::string data array vector type

◆ StringDataArrays

typedef std::vector<StringDataArray> StringDataArrays

Constructor & Destructor Documentation

◆ MSChromatogram() [1/3]

MSChromatogram ( )

default

Constructor.

◆ MSChromatogram() [2/3]

MSChromatogram ( const MSChromatogram & )

default

Copy constructor.

◆ MSChromatogram() [3/3]

MSChromatogram ( MSChromatogram && )

default

Move constructor.

◆ ~MSChromatogram()

~MSChromatogram ( )

default

Destructor.

Member Function Documentation

◆ checkDataArraySizes_()

void checkDataArraySizes_ ( ) const

protected

Throws Exception::Precondition if any non-empty data array's size differs from the peak count.

Shared by sort() and select() so that permuting the peaks can never mis-associate a parallel data array or index one out of bounds.

Exceptions

Exception::Precondition if a non-empty float, string or integer data array's size differs from the number of peaks.

◆ clear()

void clear ( bool clear_meta_data )

Clears all data and meta data.

Will delete (clear) all peaks contained in the chromatogram as well as any associated data arrays (FloatDataArrays, IntegerDataArrays, StringDataArrays) and the ranges by default – those arrays are parallel to the peaks, so retaining them would leave the chromatogram inconsistent. If clear_meta_data is true, then also the descriptive meta data (ChromatogramSettings, name) will be deleted.

Parameters

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

◆ findNearest()

Size findNearest ( CoordinateType rt ) const

Binary search for the peak nearest to a specific RT.

Parameters

[in] 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]

FloatDataArrays & getFloatDataArrays ( )

Returns a mutable reference to the float meta data arrays.

◆ getFloatDataArrays() [2/2]

const FloatDataArrays & getFloatDataArrays ( ) const

Returns a const reference to the float meta data arrays

Referenced by DataFilters::passes().

◆ getIntegerDataArrays() [1/2]

IntegerDataArrays & getIntegerDataArrays ( )

Returns a mutable reference to the integer meta data arrays.

◆ getIntegerDataArrays() [2/2]

const IntegerDataArrays & getIntegerDataArrays ( ) const

Returns a const reference to the integer meta data arrays.

Referenced by DataFilters::passes().

◆ getMZ()

double getMZ ( ) const

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

◆ getName()

const std::string & getName ( ) const

◆ getStringDataArrays() [1/2]

StringDataArrays & getStringDataArrays ( )

Returns a mutable reference to the string meta data arrays.

◆ getStringDataArrays() [2/2]

const StringDataArrays & getStringDataArrays ( ) const

Returns a const reference to the string meta data arrays.

◆ isSorted()

bool isSorted ( ) const

Checks if all peaks are sorted with respect to ascending RT.

◆ mergePeaks()

void mergePeaks	(	MSChromatogram &	other,
		bool	add_meta = `false`
	)

Adds all the chromatogram peaks from another MSChromatogram and updates the metadata to indicate a merge.

Note: Make sure BOTH chromatograms are sorted with respect to RT. Otherwise the result is undefined.; Peak level metadata stored in float_array string_array and int_array of the destination MSChromatogram is not guaranteed to be correct after merging

MZ of the destination MSChromatogram remains unchanged.

Parameters

[in,out]	other	A reference to the MSChromatogram to take ChromatogramPeaks from
[in]	add_meta	If true, a metavalue "merged_chromatogram_mzs" is added with the m/z of `other`

◆ operator!=()

bool operator!= ( const MSChromatogram & rhs ) const

inline

Equality operator.

References OpenMS::Internal::operator==().

◆ operator=() [1/2]

MSChromatogram & operator= ( const MSChromatogram & source )

Assignment operator.

◆ operator=() [2/2]

MSChromatogram & operator= ( MSChromatogram && ) &

default

Move assignment operator.

◆ operator==()

bool operator== ( const MSChromatogram & rhs ) const

Equality operator.

◆ PosBegin() [1/4]

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

Binary search for peak range begin.

Alias for RTBegin()

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

◆ PosBegin() [2/4]

Iterator PosBegin ( CoordinateType rt )

Binary search for peak range begin.

Alias for RTBegin()

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

◆ PosBegin() [3/4]

ConstIterator PosBegin ( CoordinateType rt ) const

Binary search for peak range begin.

Alias for RTBegin()

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

◆ PosBegin() [4/4]

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

Binary search for peak range begin.

Alias for RTBegin()

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

◆ PosEnd() [1/4]

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

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

Alias for RTEnd()

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

◆ PosEnd() [2/4]

Iterator PosEnd ( CoordinateType rt )

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

Alias for RTEnd()

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

◆ PosEnd() [3/4]

ConstIterator PosEnd ( CoordinateType rt ) const

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

Alias for RTEnd()

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

◆ PosEnd() [4/4]

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

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

Alias for RTEnd()

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

◆ RTBegin() [1/4]

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.

◆ RTBegin() [2/4]

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() [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]

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.

◆ RTEnd() [1/4]

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.

◆ RTEnd() [2/4]

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() [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]

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.

◆ select()

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

Subset the chromatogram by selecting only indices in indices, in that order.

Every index is bounds-checked before anything is modified, so an out-of-range index is rejected with the chromatogram left unchanged. This is the safe, default entry point. Callers whose indices are in range by construction can use selectUnchecked() to skip the check.

Parameters

[in] indices Indices to keep, in the retained order. Must all be < size(); see selectUnchecked() for the duplicate-index restriction that applies to both overloads.

Returns: Reference to this MSChromatogram

Note: Cached ranges are NOT recomputed. A permutation preserves them, but selecting a subset can leave them too wide – call updateRanges() if you need them exact.

Exceptions

Exception::Precondition if an index is out of range, or if a non-empty data array's size differs from the number of peaks.

◆ selectUnchecked()

MSChromatogram & selectUnchecked ( const std::vector< Size > & indices )

Like select(), but without the per-index range check.

For hot paths whose indices are in range by construction (e.g. a sort permutation). The data-array size consistency is still checked, as it is cheap and guards a separate out-of-bounds.

Note: indices must be duplicate-free. Repeating an index is undefined behaviour: entries are moved, so a second reference would read a moved-from value. A debug build asserts uniqueness via OPENMS_PRECONDITION; release builds do not pay for the check.

Parameters

[in] indices Indices to keep, in the retained order. Every index must be < size() and unique.

Returns: Reference to this MSChromatogram

Exceptions

Exception::Precondition if a non-empty data array's size differs from the number of peaks.

◆ 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 std::string & name )

Sets the name.

◆ setStringDataArrays()

void setStringDataArrays ( const StringDataArrays & sda )

inline

Sets the string meta data arrays.

◆ sort()

template<class Predicate >

void sort ( const Predicate & lambda )

inline

Stably sorts the peaks (and all parallel data arrays) by a user-defined predicate.

You can pass any lambda with signature bool(Size index_1, Size index_2) which, given two indices into the MSChromatogram (either peaks or data arrays), returns a strict weak ordering. Capture the MSChromatogram in the lambda and operate on it based on the indices. The sort is stable, so peaks with equivalent keys keep their relative order.

Template Parameters

Predicate Callable with signature bool(Size, Size) expressing a strict weak ordering.

Parameters

[in] lambda The comparison predicate.

Note: All data arrays are reordered alongside the peaks.; Cached ranges are preserved (a permutation does not change them).

Exceptions

Exception::Precondition if a non-empty data array's size differs from the number of peaks. This is checked up front, before lambda is ever invoked, so the chromatogram is left unchanged.

◆ 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.

◆ updateRanges()

void updateRanges ( )

overridevirtual

implement this function to reflect the underlying data of the derived class (e.g. an MSSpectrum) Usually, call clearRanges() internally and then populate the dimensions.

Implements RangeManagerContainer< RangeRT, RangeIntensity >.

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_

std::string name_

protected

Name.

◆ string_data_arrays_

StringDataArrays string_data_arrays_

protected

std::string data arrays

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ ConstIterator

◆ ConstReverseIterator

◆ ContainerType

◆ CoordinateType

◆ FloatDataArray

◆ FloatDataArrays

◆ IntegerDataArray

◆ IntegerDataArrays

◆ Iterator

◆ PeakType

◆ RangeManagerType

◆ ReverseIterator

◆ StringDataArray

◆ StringDataArrays

Constructor & Destructor Documentation

◆ MSChromatogram() [1/3]

◆ MSChromatogram() [2/3]

◆ MSChromatogram() [3/3]

◆ ~MSChromatogram()

Member Function Documentation

◆ checkDataArraySizes_()

◆ clear()

◆ findNearest()

◆ getFloatDataArrays() [1/2]

◆ getFloatDataArrays() [2/2]

◆ getIntegerDataArrays() [1/2]

◆ getIntegerDataArrays() [2/2]

◆ getMZ()

◆ getName()

◆ getStringDataArrays() [1/2]

◆ getStringDataArrays() [2/2]

◆ isSorted()

◆ mergePeaks()

◆ operator!=()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==()

◆ PosBegin() [1/4]

◆ PosBegin() [2/4]

◆ PosBegin() [3/4]

◆ PosBegin() [4/4]

◆ PosEnd() [1/4]

◆ PosEnd() [2/4]

◆ PosEnd() [3/4]

◆ PosEnd() [4/4]

◆ RTBegin() [1/4]

◆ RTBegin() [2/4]

◆ RTBegin() [3/4]

◆ RTBegin() [4/4]

◆ RTEnd() [1/4]

◆ RTEnd() [2/4]

◆ RTEnd() [3/4]

◆ RTEnd() [4/4]

◆ select()

◆ selectUnchecked()

◆ setFloatDataArrays()

◆ setIntegerDataArrays()

◆ setName()

◆ setStringDataArrays()

◆ sort()

◆ sortByIntensity()

◆ sortByPosition()

◆ updateRanges()

Member Data Documentation

◆ float_data_arrays_

◆ integer_data_arrays_

◆ name_

◆ string_data_arrays_