ModificationDefinition Class Reference

#include <OpenMS/CHEMISTRY/ModificationDefinition.h>

Collaboration diagram for ModificationDefinition:

Public Member Functions
Constructor and Destructors
	ModificationDefinition ()
	default constructor More...
	ModificationDefinition (const ModificationDefinition &rhs)
	copy constructor More...
	ModificationDefinition (const String &mod, bool fixed=true, UInt max_occur=0)
	detailed constructor specifying the modification by name More...
	ModificationDefinition (const ResidueModification &mod, bool fixed=true, UInt max_occur=0)
	direct constructor from a residue modification More...
virtual	~ModificationDefinition ()
	destructor More...
Accessors
void	setFixedModification (bool fixed)
	sets whether this modification definition is fixed or variable (modification must occur vs. can occur) More...
bool	isFixedModification () const
	returns if the modification if fixed true, else false More...
void	setMaxOccurrences (UInt num)
	set the maximal number of occurrences per peptide (unbounded if 0) More...
UInt	getMaxOccurrences () const
	returns the maximal number of occurrences per peptide More...
String	getModificationName () const
	returns the name of the modification More...
void	setModification (const String &modification)
	sets the modification, allowed are unique names provided by ModificationsDB More...
const ResidueModification &	getModification () const
	Returns the modification. More...
Assignment
ModificationDefinition &	operator= (const ModificationDefinition &element)
	assignment operator More...

Predicates
const ResidueModification *	mod_
	the modification More...
bool	fixed_modification_
	fixed (true) or variable (false) More...
UInt	max_occurrences_
	maximal number of occurrences per peptide More...
bool	operator== (const ModificationDefinition &rhs) const
	equality operator More...
bool	operator!= (const ModificationDefinition &rhs) const
	inequality operator More...
bool	operator< (const OpenMS::ModificationDefinition &) const
	less than operator for e.g. usage in maps; only mod FullIds are compared! More...

Detailed Description

@brief Representation of modification definition

This class defines a modification type e.g. a input parameter of a search engine.
The modification is defined using an unique name of the modification present
in the modifications DB instance.

Constructor & Destructor Documentation

ModificationDefinition() [1/4]

ModificationDefinition

(

)

default constructor

ModificationDefinition() [2/4]

ModificationDefinition

(

const ModificationDefinition &

rhs

)

copy constructor

ModificationDefinition() [3/4]

ModificationDefinition ( const String &  mod, bool  fixed = true, UInt  max_occur = 0  )

explicit

detailed constructor specifying the modification by name

ModificationDefinition() [4/4]

ModificationDefinition ( const ResidueModification &  mod, bool  fixed = true, UInt  max_occur = 0  )

explicit

direct constructor from a residue modification

~ModificationDefinition()

virtual ~ModificationDefinition ( )

virtual

destructor

Member Function Documentation

getMaxOccurrences()

UInt getMaxOccurrences

(

)

const

returns the maximal number of occurrences per peptide

getModification()

const ResidueModification& getModification

(

)

const

Returns the modification.

Exceptions

Exception::InvalidValue

if no modification was set

getModificationName()

String getModificationName

(

)

const

returns the name of the modification

isFixedModification()

bool isFixedModification

(

)

const

returns if the modification if fixed true, else false

operator!=()

bool operator!=

(

const ModificationDefinition &

rhs

)

const

inequality operator

operator<()

bool operator<

(

const OpenMS::ModificationDefinition &

)

const

less than operator for e.g. usage in maps; only mod FullIds are compared!

operator=()

ModificationDefinition& operator=

(

const ModificationDefinition &

element

)

assignment operator

operator==()

bool operator==

(

const ModificationDefinition &

rhs

)

const

equality operator

setFixedModification()

void setFixedModification

(

bool

fixed

)

sets whether this modification definition is fixed or variable (modification must occur vs. can occur)

setMaxOccurrences()

void setMaxOccurrences

(

UInt

num

)

set the maximal number of occurrences per peptide (unbounded if 0)

setModification()

void setModification

(

const String &

modification

)

sets the modification, allowed are unique names provided by ModificationsDB

Member Data Documentation

fixed_modification_

bool fixed_modification_

protected

fixed (true) or variable (false)

max_occurrences_

UInt max_occurrences_

protected

maximal number of occurrences per peptide

mod_

const ResidueModification* mod_

protected

the modification