The representation of a chromatogram. More...

#include <OpenMS/KERNEL/MSChromatogram.h>

Inheritance diagram for MSChromatogram< PeakT >:

Classes
class	FloatDataArray
	Float data array class. More...
class	IntegerDataArray
	Float data array class. More...
struct	MZLess
	Comparator for the retention time. More...
class	StringDataArray
	String data array class. More...
Public Types
Base type definitions
Peak type
typedef PeakT	PeakType
typedef PeakType::CoordinateType	CoordinateType
	Coordinate (RT) type.
typedef std::vector< PeakType >	ContainerType
	Chromatogram 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
	MSChromatogram ()
	Constructor.
	MSChromatogram (const MSChromatogram &source)
	Copy constructor.
virtual	~MSChromatogram ()
	Destructor.
MSChromatogram &	operator= (const MSChromatogram &source)
	Assignment operator.
bool	operator== (const MSChromatogram &rhs) const
	Equality operator.
bool	operator!= (const MSChromatogram &rhs) const
	Equality operator.
virtual void	updateRanges ()
DoubleReal	getMZ () const
	returns the mz of the product entry, makes sense especially for MRM scans
Accessors for meta information
Returns the name
const String &	getName () const
void	setName (const 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.
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 RT.
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).
void	clear (bool clear_meta_data)
	Clears all data and meta data.
Protected Member Functions
virtual void	clearChildIds_ ()
	Clears the persistence id of all sub-objects.
Protected Attributes
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 = ChromatogramPeak>
class OpenMS::MSChromatogram< PeakT >

The representation of a chromatogram.

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

Chromatogram base type.

typedef PeakType::CoordinateType CoordinateType

Coordinate (RT) 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

typedef ContainerType::reverse_iterator ReverseIterator

Mutable reverse iterator.

typedef std::vector<StringDataArray> StringDataArrays

String data array vector type.

Constructor & Destructor Documentation

MSChromatogram ( ) [inline]

Constructor.

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

Copy constructor.

virtual ~MSChromatogram ( ) [inline, virtual]

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 MSChromatogram< ChromatogramPeakType >::clear().

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

Clears the persistence id of all sub-objects.

Implements PersistentObject.

Size findNearest ( CoordinateType rt ) const [inline]

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)

const FloatDataArrays& getFloatDataArrays ( ) const [inline]

Returns a const reference to the float meta data arrays

Referenced by MzMLHandler< MapType >::fillChromatogramData_(), and MzMLHandler< 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 MzMLHandler< MapType >::fillChromatogramData_(), and MzMLHandler< MapType >::writeTo().

DoubleReal getMZ ( ) const [inline]

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

Referenced by MSChromatogram< PeakT >::MZLess::operator()().

const String& getName ( ) const [inline]

const StringDataArrays& getStringDataArrays ( ) const [inline]

Returns a const reference to the string meta data arrays.

Referenced by MzMLHandler< MapType >::fillChromatogramData_(), 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 RT.

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

Equality operator.

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

Assignment operator.

Referenced by MSChromatogram< ChromatogramPeakType >::clear(), and MSChromatogram< ChromatogramPeakType >::operator=().

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

Equality operator.

Referenced by MSChromatogram< ChromatogramPeakType >::operator!=(), and MSChromatogram< ChromatogramPeakType >::operator==().

Iterator RTBegin ( CoordinateType rt ) [inline]

Binary search for peak range begin.

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

Referenced by MSChromatogram< ChromatogramPeakType >::findNearest().

Iterator RTBegin	(	Iterator	begin,
		CoordinateType	rt,
		Iterator	end
	)			`[inline]`

Binary search for peak range begin.

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

ConstIterator RTBegin ( CoordinateType rt ) const [inline]

Binary search for peak range begin.

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

ConstIterator RTBegin	(	ConstIterator	begin,
		CoordinateType	rt,
		ConstIterator	end
	)			const `[inline]`

Binary search for peak range begin.

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

ConstIterator RTEnd ( CoordinateType rt ) const [inline]

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.

ConstIterator RTEnd	(	ConstIterator	begin,
		CoordinateType	rt,
		ConstIterator	end
	)			const `[inline]`

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.

Iterator RTEnd	(	Iterator	begin,
		CoordinateType	rt,
		Iterator	end
	)			`[inline]`

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.

Iterator RTEnd ( CoordinateType rt ) [inline]

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.

void setName ( const String & name ) [inline]

Sets the name.

Referenced by MzMLHandler< MapType >::handleCVParam_().

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.

void sortByPosition ( ) [inline]

Lexicographically sorts the peaks by their position.

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

virtual void updateRanges ( ) [inline, virtual]

Member Data Documentation

FloatDataArrays float_data_arrays_ [protected]

Float data arrays.

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

IntegerDataArrays integer_data_arrays_ [protected]

Intager data arrays.

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

String name_ [protected]

Name.

Referenced by MSChromatogram< ChromatogramPeakType >::clear(), MSChromatogram< ChromatogramPeakType >::getName(), MSChromatogram< ChromatogramPeakType >::operator=(), and MSChromatogram< ChromatogramPeakType >::setName().

StringDataArrays string_data_arrays_ [protected]

String data arrays.

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

OpenMS / TOPP release 1.10.0

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

MSChromatogram< PeakT > Class Template Reference [Kernel]

Classes

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

template<typename PeakT = ChromatogramPeak> class OpenMS::MSChromatogram< PeakT >

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

MSChromatogram< PeakT > Class Template Reference
[Kernel]

template<typename PeakT = ChromatogramPeak>
class OpenMS::MSChromatogram< PeakT >