ModificationDefinitionsSet Class Reference [Chemistry]

Representation of a set of modification definitions. More...

#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>

List of all members.

Public Member Functions
Constructor and Destructors
	ModificationDefinitionsSet ()
	default constructor
	ModificationDefinitionsSet (const ModificationDefinitionsSet &rhs)
	copy constructor
	ModificationDefinitionsSet (const String &fixed_modifications, const String &variable_modifications="")
	detailed constructor with comma separated list of modifications
	ModificationDefinitionsSet (const StringList &fixed_modifications, const StringList &variable_modifications=StringList::create(""))
	detailed constructor with StringLists
virtual	~ModificationDefinitionsSet ()
	destructor
Accessors
void	setMaxModifications (Size max_mod)
	sets the maximal number of modifications allowed per peptide
Size	getMaxModifications () const
	return the maximal number of modifications allowed per peptide
Size	getNumberOfModifications () const
	returns the number of modifications stored in this set
Size	getNumberOfFixedModifications () const
	returns the number of fixed modifications stored in this set
Size	getNumberOfVariableModifications () const
	returns the number of variable modifications stored in this set
void	addModification (const ModificationDefinition &mod_def)
	adds a modification definition to the set
void	setModifications (const std::set< ModificationDefinition > &mod_defs)
	sets the modification definitions
void	setModifications (const String &fixed_modifications, const String &variable_modifications)
	set the modification definitions from a string
void	setModifications (const StringList &fixed_modifications, const StringList &variable_modifications)
	same as above, but using StringList instead of comma separated strings
std::set< ModificationDefinition >	getModifications () const
	returns the stored modification definitions
const std::set < ModificationDefinition > &	getFixedModifications () const
	returns the stored fixed modification definitions
const std::set < ModificationDefinition > &	getVariableModifications () const
	returns the stored variable modification definitions
std::set< String >	getModificationNames () const
	return only the names of the modifications stored in the set
std::set< String >	getFixedModificationNames () const
	return only the names of the fixed modifications
std::set< String >	getVariableModificationNames () const
	return only the names of the variable modifications
Assignment
ModificationDefinitionsSet &	operator= (const ModificationDefinitionsSet &element)
	assignment operator
Predicates
bool	isCompatible (const AASequence &peptide) const
	returns true if the peptide is compatible with the definitions, e.g. does not contain other modifications
bool	operator== (const ModificationDefinitionsSet &rhs) const
	equality operator
bool	operator!= (const ModificationDefinitionsSet &rhs) const
	inequality operator
Protected Attributes
std::set< ModificationDefinition >	variable_mods_
std::set< ModificationDefinition >	fixed_mods_
Size	max_mods_per_peptide_

---

Detailed Description

Representation of a set of modification definitions.

This class enhances the modification definitions as defined in the class ModificationDefinition into a set of definitions. This is also e.g. used as input parameters in search engines.

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Constructor & Destructor Documentation

ModificationDefinitionsSet

(

)

default constructor

ModificationDefinitionsSet

(

const ModificationDefinitionsSet &

rhs

)

copy constructor

ModificationDefinitionsSet	(	const String &	fixed_modifications,
		const String &	variable_modifications = ""
	)

detailed constructor with comma separated list of modifications

ModificationDefinitionsSet	(	const StringList &	fixed_modifications,
		const StringList &	variable_modifications = StringList::create("")
	)

detailed constructor with StringLists

virtual ~ModificationDefinitionsSet

(

)

[virtual]

destructor

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Member Function Documentation

void addModification

(

const ModificationDefinition &

mod_def

)

adds a modification definition to the set

std::set<String> getFixedModificationNames

(

)

const

return only the names of the fixed modifications

const std::set<ModificationDefinition>& getFixedModifications

(

)

const

returns the stored fixed modification definitions

Size getMaxModifications

(

)

const

return the maximal number of modifications allowed per peptide

std::set<String> getModificationNames

(

)

const

return only the names of the modifications stored in the set

std::set<ModificationDefinition> getModifications

(

)

const

returns the stored modification definitions

Size getNumberOfFixedModifications

(

)

const

returns the number of fixed modifications stored in this set

Size getNumberOfModifications

(

)

const

returns the number of modifications stored in this set

Size getNumberOfVariableModifications

(

)

const

returns the number of variable modifications stored in this set

std::set<String> getVariableModificationNames

(

)

const

return only the names of the variable modifications

const std::set<ModificationDefinition>& getVariableModifications

(

)

const

returns the stored variable modification definitions

bool isCompatible

(

const AASequence &

peptide

)

const

returns true if the peptide is compatible with the definitions, e.g. does not contain other modifications

bool operator!=

(

const ModificationDefinitionsSet &

rhs

)

const

inequality operator

ModificationDefinitionsSet& operator=

(

const ModificationDefinitionsSet &

element

)

assignment operator

bool operator==

(

const ModificationDefinitionsSet &

rhs

)

const

equality operator

void setMaxModifications

(

Size

max_mod

)

sets the maximal number of modifications allowed per peptide

void setModifications	(	const String &	fixed_modifications,
		const String &	variable_modifications
	)

set the modification definitions from a string

The strings should contain a comma separated list of modifications. The names can be PSI-MOD identifier or any other unique name supported by PSI-MOD. TermSpec definitions and other specific definitions are given by the modifications themselves.

void setModifications

(

const std::set< ModificationDefinition > &

mod_defs

)

sets the modification definitions

void setModifications	(	const StringList &	fixed_modifications,
		const StringList &	variable_modifications
	)

same as above, but using StringList instead of comma separated strings

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Member Data Documentation

std::set<ModificationDefinition> fixed_mods_ [protected]

Size max_mods_per_peptide_ [protected]

std::set<ModificationDefinition> variable_mods_ [protected]