Holds an indexed list of bio-chemical elements used by mass-decomposition algorithms. 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

[in] 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 used by mass-decomposition algorithms.

Stores IMSElement instances and exposes them in two complementary ways: lookup by index is constant-time, lookup by element name is linear-time. Because IMSAlphabet keeps the full element representation, prefer the lighter ims::Weights when only the mass values are needed in performance-critical code.

An alphabet can be sorted either by element name or by mass; the file loaders always leave the alphabet sorted by mass, so files do not need to be pre-sorted.

To populate an alphabet from a flat text file with the default format, call load(const std::string&). To support a different format, derive a parser from IMSAlphabetParser and pass it to the two-argument load() overload. Both overloads report a missing or unreadable file by throwing Exception::IOException.

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

[in] elements Elements to be set

◆ IMSAlphabet() [3/3]

IMSAlphabet ( const IMSAlphabet & alphabet )

inline

Copy constructor.

Parameters

[in] alphabet Alphabet whose elements are copied.

◆ ~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

[in] 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

[in] 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

[in] 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

[in] 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

[in] 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

[in] 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

Replaces the alphabet's contents with the elements read from the text file fname (default OpenMS alphabet text format), sorted by mass.

Parameters

[in] fname File to read.

Exceptions

Exception::IOException if fname cannot be opened.

See also: load(const std::string&, IMSAlphabetParser<>&)

◆ load() [2/2]

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

virtual

Replaces the alphabet's contents with the elements read from fname through parser, sorted by mass.

Parameters

[in]	fname	File to read.
[in,out]	parser	Parser used to read the file.

Exceptions

Exception::IOException if fname cannot be opened by parser.

See also: load(const std::string&); IMSAlphabetParser

◆ push_back() [1/2]

void push_back ( const element_type & element )

inline

Adds a new element element to the alphabet.

Parameters

[in] 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

[in]	name	Name of the element to be added.
[in]	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

[in]	name	The name of the element that should be replaced in (or appended to) the alphabet.
[in]	mass	The new mass of the element in the alphabet.
[in]	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_