ModificationDefinitionsSet Class Reference

#include <OpenMS/CHEMISTRY/ModificationDefinitionsSet.h>

Collaboration diagram for ModificationDefinitionsSet:

Public Member Functions
Constructor and Destructors
	ModificationDefinitionsSet ()
	default constructor More...
	ModificationDefinitionsSet (const ModificationDefinitionsSet &rhs)
	copy constructor More...
	ModificationDefinitionsSet (const StringList &fixed_modifications, const StringList &variable_modifications)
	detailed constructor with StringLists More...
virtual	~ModificationDefinitionsSet ()
	destructor More...
Accessors
void	setMaxModifications (Size max_mod)
	sets the maximal number of modifications allowed per peptide More...
Size	getMaxModifications () const
	return the maximal number of modifications allowed per peptide More...
Size	getNumberOfModifications () const
	returns the number of modifications stored in this set More...
Size	getNumberOfFixedModifications () const
	returns the number of fixed modifications stored in this set More...
Size	getNumberOfVariableModifications () const
	returns the number of variable modifications stored in this set More...
void	addModification (const ModificationDefinition &mod_def)
	adds a modification definition to the set More...
void	setModifications (const std::set< ModificationDefinition > &mod_defs)
	sets the modification definitions More...
void	setModifications (const String &fixed_modifications, const String &variable_modifications)
	set the modification definitions from a string More...
void	setModifications (const StringList &fixed_modifications, const StringList &variable_modifications)
	same as above, but using StringList instead of comma separated strings More...
std::set< ModificationDefinition >	getModifications () const
	returns the stored modification definitions More...
const std::set< ModificationDefinition > &	getFixedModifications () const
	returns the stored fixed modification definitions More...
const std::set< ModificationDefinition > &	getVariableModifications () const
	returns the stored variable modification definitions More...
std::set< String >	getModificationNames () const
	returns only the names of the modifications stored in the set More...
void	getModificationNames (StringList &fixed_modifications, StringList &variable_modifications) const
	populates the output lists with the modification names (use e.g. for ProteinIdentification::SearchParameters) More...
std::set< String >	getFixedModificationNames () const
	returns only the names of the fixed modifications More...
std::set< String >	getVariableModificationNames () const
	returns only the names of the variable modifications More...
Assignment
ModificationDefinitionsSet &	operator= (const ModificationDefinitionsSet &element)
	assignment operator More...

Predicates
std::set< ModificationDefinition >	variable_mods_
std::set< ModificationDefinition >	fixed_mods_
Size	max_mods_per_peptide_
bool	isCompatible (const AASequence &peptide) const
	returns true if the peptide is compatible with the definitions, e.g. does not contain other modifications More...
bool	operator== (const ModificationDefinitionsSet &rhs) const
	equality operator More...
bool	operator!= (const ModificationDefinitionsSet &rhs) const
	inequality operator More...
void	findMatches (std::multimap< double, ModificationDefinition > &matches, double mass, const String &residue="", ResidueModification::TermSpecificity term_spec=ResidueModification::NUMBER_OF_TERM_SPECIFICITY, bool consider_fixed=true, bool consider_variable=true, bool is_delta=true, double tolerance=0.01) const
	Finds modifications in the set that match a given (delta) mass. More...
void	inferFromPeptides (const std::vector< PeptideIdentification > &peptides)
	Infers the sets of defined modifications from the modifications present on peptide identifications. More...
static void	addMatches_ (std::multimap< double, ModificationDefinition > &matches, double mass, const String &residue, ResidueModification::TermSpecificity term_spec, const std::set< ModificationDefinition > &source, bool is_delta, double tolerance)
	helper function for findMatches() - finds matching modifications in source and adds them to matches More...

Detailed Description

@brief 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.

Constructor & Destructor Documentation

ModificationDefinitionsSet() [1/3]

ModificationDefinitionsSet

(

)

default constructor

ModificationDefinitionsSet() [2/3]

ModificationDefinitionsSet

(

const ModificationDefinitionsSet &

rhs

)

copy constructor

ModificationDefinitionsSet() [3/3]

ModificationDefinitionsSet	(	const StringList &	fixed_modifications,
		const StringList &	variable_modifications
	)

detailed constructor with StringLists

~ModificationDefinitionsSet()

virtual ~ModificationDefinitionsSet ( )

virtual

destructor

Member Function Documentation

addMatches_()

static void addMatches_ ( std::multimap< double, ModificationDefinition > &  matches, double  mass, const String &  residue, ResidueModification::TermSpecificity  term_spec, const std::set< ModificationDefinition > &  source, bool  is_delta, double  tolerance  )

staticprotected

helper function for findMatches() - finds matching modifications in source and adds them to matches

addModification()

void addModification

(

const ModificationDefinition &

mod_def

)

adds a modification definition to the set

findMatches()

void findMatches	(	std::multimap< double, ModificationDefinition > &	matches,
		double	mass,
		const String &	residue = "",
		ResidueModification::TermSpecificity	term_spec = ResidueModification::NUMBER_OF_TERM_SPECIFICITY,
		bool	consider_fixed = true,
		bool	consider_variable = true,
		bool	is_delta = true,
		double	tolerance = 0.01
	)		const

Finds modifications in the set that match a given (delta) mass.

Parameters

matches	Matching modifications (output), sorted by mass error
mass	Query mass
residue	Query residue
term_spec	Query term specificity
consider_variable	Consider the variable modifications?
consider_fixed	Consider the fixed modifications?
is_delta	Is mass a delta mass (mass difference)?
tolerance	Numeric tolerance (in Da) for mass matching

Exceptions

Exception::IllegalArgument

if both consider_variable and consider_fixed are false

getFixedModificationNames()

std::set<String> getFixedModificationNames

(

)

const

returns only the names of the fixed modifications

getFixedModifications()

const std::set<ModificationDefinition>& getFixedModifications

(

)

const

returns the stored fixed modification definitions

getMaxModifications()

Size getMaxModifications

(

)

const

return the maximal number of modifications allowed per peptide

getModificationNames() [1/2]

std::set<String> getModificationNames

(

)

const

returns only the names of the modifications stored in the set

getModificationNames() [2/2]

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

populates the output lists with the modification names (use e.g. for ProteinIdentification::SearchParameters)

getModifications()

std::set<ModificationDefinition> getModifications

(

)

const

returns the stored modification definitions

getNumberOfFixedModifications()

Size getNumberOfFixedModifications

(

)

const

returns the number of fixed modifications stored in this set

getNumberOfModifications()

Size getNumberOfModifications

(

)

const

returns the number of modifications stored in this set

getNumberOfVariableModifications()

Size getNumberOfVariableModifications

(

)

const

returns the number of variable modifications stored in this set

getVariableModificationNames()

std::set<String> getVariableModificationNames

(

)

const

returns only the names of the variable modifications

getVariableModifications()

const std::set<ModificationDefinition>& getVariableModifications

(

)

const

returns the stored variable modification definitions

inferFromPeptides()

void inferFromPeptides

(

const std::vector< PeptideIdentification > &

peptides

)

Infers the sets of defined modifications from the modifications present on peptide identifications.

isCompatible()

bool isCompatible

(

const AASequence &

peptide

)

const

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

operator!=()

bool operator!=

(

const ModificationDefinitionsSet &

rhs

)

const

inequality operator

operator=()

ModificationDefinitionsSet& operator=

(

const ModificationDefinitionsSet &

element

)

assignment operator

operator==()

bool operator==

(

const ModificationDefinitionsSet &

rhs

)

const

equality operator

setMaxModifications()

void setMaxModifications

(

Size

max_mod

)

sets the maximal number of modifications allowed per peptide

setModifications() [1/3]

void setModifications

(

const std::set< ModificationDefinition > &

mod_defs

)

sets the modification definitions

setModifications() [2/3]

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.

setModifications() [3/3]

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

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

Member Data Documentation

fixed_mods_

std::set<ModificationDefinition> fixed_mods_

protected

max_mods_per_peptide_

Size max_mods_per_peptide_

protected

variable_mods_

std::set<ModificationDefinition> variable_mods_

protected