Holds an indexed list of bio-chemical elements. More...

#include <OpenMS/CHEMISTRY/MASSDECOMPOSITION/IMS/IMSAlphabet.h>

Collaboration diagram for IMSAlphabet:

Classes
class	MassSortingCriteria_
	Private class-functor to sort out elements in mass ascending order. More...

Public Types
typedef IMSElement	element_type

typedef element_type::mass_type	mass_type

typedef element_type::name_type	name_type

typedef std::vector< element_type >	container

typedef container::size_type	size_type

typedef container::iterator	iterator

typedef container::const_iterator	const_iterator

typedef std::vector< name_type >	name_container

typedef name_container::iterator	name_iterator

typedef name_container::const_iterator	const_name_iterator

typedef std::vector< mass_type >	mass_container

typedef mass_container::iterator	mass_iterator

typedef mass_container::const_iterator	const_mass_iterator

typedef std::vector< mass_type >	masses_type

Public Member Functions
	IMSAlphabet ()

	IMSAlphabet (const container &elements)

	IMSAlphabet (const IMSAlphabet &alphabet)

size_type	size () const

const element_type &	getElement (size_type index) const

void	setElement (const name_type &name, mass_type mass, bool forced=false)

bool	erase (const name_type &name)

. If there is

Gets the element with the symbol no such element, throws Exception::InvalidValue.

Parameters

name	Name of the element.

Returns: Element with the given name, or if there are no such element

Exceptions

Exception::InvalidValue.

container

elements_

const element_type & getElement (const name_type &name) const

const name_type & getName (size_type index) const

mass_type getMass (const name_type &name) const

mass_type getMass (size_type index) const

masses_type getMasses (size_type isotope_index=0) const

masses_type getAverageMasses () const

bool hasName (const name_type &name) const

void push_back (const name_type &name, mass_type value)

void push_back (const element_type &element)

void clear ()

virtual void sortByNames ()

virtual void sortByValues ()

virtual void load (const std::string &fname)

virtual void load (const std::string &fname, IMSAlphabetParser<> &parser)

virtual ~IMSAlphabet ()

Detailed Description

Holds an indexed list of bio-chemical elements.

Presents an indexed list of bio-chemical elements of type (or derived from type) Element. Due to indexed structure Alphabet can be used similar to std::vector, for example to add a new element to Alphabet function push_back(element_type) can be used. Elements or their properties (such as element's mass) can be accessed by index in a constant time. On the other hand accessing elements by their names takes linear time. Due to this and also the fact that Alphabet is 'heavy-weighted' (consisting of Element -s or their derivatives where the depth of derivation as well is undefined resulting in possibly 'heavy' access operations) it is recommended not use Alphabet directly in operations where fast access to Element 's properties is required. Instead consider to use 'light-weighted' equivalents, such as Weights.

Elements in Alphabet can be sorted by the Element 's properties: sequence and mass. When alphabet's data is loaded from file it is automatically sorted by mass. To load data from file default function load(str::string& fname) can be used. Then elements have to be stored in a flat file fname in a predefined format. To read more on this format, please,

See also: AlphabetParser. If one wants to load data stored differently or in its own file format (i.e. xml) one has to define a new parser derived from AlphabetParser and pass its pointer together with the file name to function load(const std::string& fname, AlphabetParser<>* parser). If there is any error happened while loading data, IOException will be thrown.

Member Typedef Documentation

◆ const_iterator

typedef container::const_iterator const_iterator

◆ const_mass_iterator

typedef mass_container::const_iterator const_mass_iterator

◆ const_name_iterator

typedef name_container::const_iterator const_name_iterator

◆ container

typedef std::vector<element_type> container

◆ element_type

typedef IMSElement element_type

◆ iterator

typedef container::iterator iterator

◆ mass_container

typedef std::vector<mass_type> mass_container

◆ mass_iterator

typedef mass_container::iterator mass_iterator

◆ mass_type

typedef element_type::mass_type mass_type

◆ masses_type

typedef std::vector<mass_type> masses_type

◆ name_container

typedef std::vector<name_type> name_container

◆ name_iterator

typedef name_container::iterator name_iterator

◆ name_type

typedef element_type::name_type name_type

◆ size_type

typedef container::size_type size_type

Constructor & Destructor Documentation

◆ IMSAlphabet() [1/3]

IMSAlphabet ( )

inline

Empty constructor.

◆ IMSAlphabet() [2/3]

IMSAlphabet ( const container & elements )

inlineexplicit

Constructor with elements.

Parameters

elements Elements to be set

◆ IMSAlphabet() [3/3]

IMSAlphabet ( const IMSAlphabet & alphabet )

inline

Copy constructor.

Parameters

alphabet Alphabet to be assigned

◆ ~IMSAlphabet()

virtual ~IMSAlphabet ( )

inlinevirtual

Default destructor.

Member Function Documentation

◆ clear()

void clear ( )

inline

Clears the alphabet data.

◆ erase()

bool erase ( const name_type & name )

Removes the element with name name from the alphabet.

Parameters

name	The name of the element to be removed from the alphabet.

Returns: A boolean indicating whether an element was removed (true) or not (false).

◆ getAverageMasses()

masses_type getAverageMasses ( ) const

Gets average masses of elements.

Returns: Average masses of elements.

◆ getElement() [1/2]

const element_type& getElement ( const name_type & name ) const

◆ getElement() [2/2]

const element_type& getElement ( size_type index ) const

inline

Gets the element with index index.

Note: Operation takes constant time.

Parameters

index of the element

Returns: Element with the given index in alphabet

◆ getMass() [1/2]

mass_type getMass ( const name_type & name ) const

Gets mono isotopic mass of the element with the symbol name. If there is no such element, throws an Exception::InvalidValue.

Parameters

name	Symbol of the element.

Returns: Mass of the element, or if there are no element

Exceptions

Exception::InvalidValue.

See also: getMass(size_type index)

◆ getMass() [2/2]

mass_type getMass ( size_type index ) const

Gets mass of the element with an index index in alphabet.

Parameters

index Index of the element.

Returns: Mass of the element.

See also: getMass(const std::string& name)

◆ getMasses()

masses_type getMasses ( size_type isotope_index = 0 ) const

Gets masses of elements isotopes given by isotope_index.

Parameters

isotope_index Index of isotope

Returns: Masses of elements isotopes with the given index.

◆ getName()

const name_type& getName ( size_type index ) const

Gets the symbol of the element with an index index in alphabet.

Parameters

index of the element.

Returns: Name of the element.

◆ hasName()

bool hasName ( const name_type & name ) const

Returns true if there is an element with symbol name in the alphabet, false - otherwise.

Returns: True, if there is an element with symbol name, false - otherwise.

◆ load() [1/2]

virtual void load ( const std::string & fname )

virtual

Loads the alphabet data from the file fname using the default parser. If there is no file fname, throws an IOException.

Parameters

fname The file name to be loaded.

Exceptions

Exception::IOException

See also: load(const std::string& fname, AlphabetParser<>* parser)

◆ load() [2/2]

virtual void load	(	const std::string &	fname,
		IMSAlphabetParser<> &	parser
	)

virtual

Loads the alphabet data from the file fname using parser. If there is no file fname found, throws an IOException.

Parameters

fname	File name to be loaded.
parser	Parser to be used by loading.

Exceptions

Exception::IOException

See also: load(const std::string& fname); AlphabetParser

◆ push_back() [1/2]

void push_back ( const element_type & element )

inline

Adds a new element element to the alphabet.

Parameters

element The Element to be added.

◆ push_back() [2/2]

void push_back	(	const name_type &	name,
		mass_type	value
	)

inline

Adds a new element with name name and mass value to the alphabet.

Parameters

name	Name of the element to be added.
value	Mass of the element to be added.

See also: push_back(const element_type&)

◆ setElement()

void setElement	(	const name_type &	name,
		mass_type	mass,
		bool	forced = `false`
	)

Overwrites an element in the alphabet with the name with a new element constructed from the given name name and mass mass. If the parameter forced is set to true, a new element will be appended to the alphabet in the case the alphabet contains no element with the name name.

Parameters

name	The name of the element that should be replaced in (or appended to) the alphabet.
mass	The new mass of the element in the alphabet.
forced	Indicates whether a new element should be created (if set to `true`) if there is no element with the name `name` or not (if set to `false`).

◆ size()

size_type size ( ) const

inline

Returns the alphabet size.

Returns: The size of alphabet.

◆ sortByNames()

virtual void sortByNames ( )

virtual

Sorts the alphabet by names.

See also: sortByValues()

◆ sortByValues()

virtual void sortByValues ( )

virtual

Sorts the alphabet by mass values.

See also: sortByNames()

Member Data Documentation

◆ elements_

container elements_

private

Elements of the alphabet.

Classes

Public Types

Public Member Functions

. If there is

Detailed Description

Member Typedef Documentation

◆ const_iterator

◆ const_mass_iterator

◆ const_name_iterator

◆ container

◆ element_type

◆ iterator

◆ mass_container

◆ mass_iterator

◆ mass_type

◆ masses_type

◆ name_container

◆ name_iterator

◆ name_type

◆ size_type

Constructor & Destructor Documentation

◆ IMSAlphabet() [1/3]

◆ IMSAlphabet() [2/3]

◆ IMSAlphabet() [3/3]

◆ ~IMSAlphabet()

Member Function Documentation

◆ clear()

◆ erase()

◆ getAverageMasses()

◆ getElement() [1/2]

◆ getElement() [2/2]

◆ getMass() [1/2]

◆ getMass() [2/2]

◆ getMasses()

◆ getName()

◆ hasName()

◆ load() [1/2]

◆ load() [2/2]

◆ push_back() [1/2]

◆ push_back() [2/2]

◆ setElement()

◆ size()

◆ sortByNames()

◆ sortByValues()

Member Data Documentation

◆ elements_