OpenMS  2.6.0
Classes | Public Types | Public Member Functions | List of all members
IMSAlphabet Class Reference

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


Collaboration diagram for IMSAlphabet:


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_typecontainer
typedef container::size_type size_type
typedef container::iterator iterator
typedef container::const_iterator const_iterator
typedef std::vector< name_typename_container
typedef name_container::iterator name_iterator
typedef name_container::const_iterator const_name_iterator
typedef std::vector< mass_typemass_container
typedef mass_container::iterator mass_iterator
typedef mass_container::const_iterator const_mass_iterator
typedef std::vector< mass_typemasses_type

Public Member Functions

 IMSAlphabet ()
 IMSAlphabet (const container &elements)
 IMSAlphabet (const IMSAlphabet &alphabet)
size_type size () const
const element_typegetElement (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.

nameName of the element.
Element with the given name, or if there are no such element
container elements_
const element_typegetElement (const name_type &name) const
const name_typegetName (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

◆ iterator

typedef container::iterator iterator

◆ mass_container

typedef std::vector<mass_type> mass_container

◆ mass_iterator

typedef mass_container::iterator mass_iterator

◆ 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

◆ size_type

typedef container::size_type size_type

Constructor & Destructor Documentation

◆ IMSAlphabet() [1/3]

IMSAlphabet ( )

Empty constructor.

◆ IMSAlphabet() [2/3]

IMSAlphabet ( const container elements)

Constructor with elements.

elementsElements to be set

◆ IMSAlphabet() [3/3]

IMSAlphabet ( const IMSAlphabet alphabet)

Copy constructor.

alphabetAlphabet to be assigned

◆ ~IMSAlphabet()

virtual ~IMSAlphabet ( )

Default destructor.

Member Function Documentation

◆ clear()

void clear ( )

Clears the alphabet data.

◆ erase()

bool erase ( const name_type name)

Removes the element with name name from the alphabet.

nameThe name of the element to be removed from the alphabet.
A boolean indicating whether an element was removed (true) or not (false).

◆ getAverageMasses()

masses_type getAverageMasses ( ) const

Gets average masses of elements.

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

Gets the element with index index.

Operation takes constant time.
indexof the element
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.

nameSymbol of the element.
Mass of the element, or if there are no element
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.

indexIndex of the element.
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.

isotope_indexIndex of isotope
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.

indexof the element.
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.

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

◆ load() [1/2]

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

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

fnameThe file name to be loaded.
See also
load(const std::string& fname, AlphabetParser<>* parser)

◆ load() [2/2]

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

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

fnameFile name to be loaded.
parserParser to be used by loading.
See also
load(const std::string& fname)

◆ push_back() [1/2]

void push_back ( const element_type element)

Adds a new element element to the alphabet.

elementThe Element to be added.

◆ push_back() [2/2]

void push_back ( const name_type name,
mass_type  value 

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

nameName of the element to be added.
valueMass 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.

nameThe name of the element that should be replaced in (or appended to) the alphabet.
massThe new mass of the element in the alphabet.
forcedIndicates 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

Returns the alphabet size.

The size of alphabet.

◆ sortByNames()

virtual void sortByNames ( )

Sorts the alphabet by names.

See also

◆ sortByValues()

virtual void sortByValues ( )

Sorts the alphabet by mass values.

See also

Member Data Documentation

◆ elements_

container elements_

Elements of the alphabet.