IMSAlphabet Class Reference

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

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

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 ( 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

getElement() [2/2]

const element_type& getElement

(

const name_type &

name

)

const

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 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&)

push_back() [2/2]

void push_back ( const element_type &  element )

inline

Adds a new element element to the alphabet.

Parameters

element

The Element to be added.

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.