Meta information about tagging of a sample e.g. ICAT labeling. More...

#include <OpenMS/METADATA/Tagging.h>

Inheritance diagram for Tagging:

Public Types
enum	IsotopeVariant { LIGHT, HEAVY, SIZE_OF_ISOTOPEVARIANT }
	Isotope variants (light and heavy) More...

Public Types inherited from Modification
enum	SpecificityType { AA, AA_AT_CTERM, AA_AT_NTERM, CTERM, NTERM, SIZE_OF_SPECIFICITYTYPE }
	specificity of the reagent. More...

Public Member Functions
	Tagging ()
	default constructor More...

	Tagging (const Tagging &)
	copy constructor More...

	~Tagging () override
	destructor More...

Tagging &	operator= (const Tagging &)
	assignment operator More...

bool	operator== (const SampleTreatment &rhs) const override
	Equality operator. More...

SampleTreatment *	clone () const override
	clone method. See SampleTreatment More...

double	getMassShift () const
	returns the mass difference between light and heavy variant (default is 0.0) More...

void	setMassShift (double mass_shift)
	sets the mass difference between light and heavy variant More...

const IsotopeVariant &	getVariant () const
	returns the isotope variant of the tag (default is LIGHT) More...

void	setVariant (const IsotopeVariant &variant)
	sets the isotope variant of the tag More...

Public Member Functions inherited from Modification
	Modification ()
	default constructor More...

	Modification (const Modification &)
	copy constructor More...

	~Modification () override
	destructor More...

Modification &	operator= (const Modification &)
	assignment operator More...

const String &	getReagentName () const
	returns the name of the reagent that was used (default: "") More...

void	setReagentName (const String &reagent_name)
	sets the name of the reagent that was used More...

double	getMass () const
	returns the mass change (default: 0.0) More...

void	setMass (double mass)
	sets the mass change More...

const SpecificityType &	getSpecificityType () const
	returns the specificity of the the reagent (default: AA) More...

void	setSpecificityType (const SpecificityType &specificity_type)
	sets the specificity of the the reagent More...

const String &	getAffectedAminoAcids () const
	returns a string containing the one letter code of the amino acids that are affected by the reagent. (default: "") More...

void	setAffectedAminoAcids (const String &affected_amino_acids)
	returns a string containing the one letter code of the amino acids that are affected by the reagent. Do not separate them by space, tab or comma! More...

Public Member Functions inherited from SampleTreatment
	SampleTreatment (const String &type)
	Constructor. More...

	SampleTreatment (const SampleTreatment &)
	Copy constructor. More...

virtual	~SampleTreatment ()
	destructor More...

SampleTreatment &	operator= (const SampleTreatment &)
	Assignment operator. More...

const String &	getType () const
	return the treatment type More...

const String &	getComment () const
	returns the description of the sample treatment More...

void	setComment (const String &comment)
	sets the description of the sample treatment More...

Public Member Functions inherited from MetaInfoInterface
	MetaInfoInterface ()
	Constructor. More...

	MetaInfoInterface (const MetaInfoInterface &rhs)
	Copy constructor. More...

	~MetaInfoInterface ()
	Destructor. More...

MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...

bool	operator== (const MetaInfoInterface &rhs) const
	Equality operator. More...

bool	operator!= (const MetaInfoInterface &rhs) const
	Equality operator. More...

const DataValue &	getMetaValue (const String &name) const
	Returns the value corresponding to a string (or DataValue::EMPTY if not found) More...

const DataValue &	getMetaValue (UInt index) const
	Returns the value corresponding to an index (or DataValue::EMPTY if not found) More...

bool	metaValueExists (const String &name) const
	Returns whether an entry with the given name exists. More...

bool	metaValueExists (UInt index) const
	Returns whether an entry with the given index exists. More...

void	setMetaValue (const String &name, const DataValue &value)
	Sets the DataValue corresponding to a name. More...

void	setMetaValue (UInt index, const DataValue &value)
	Sets the DataValue corresponding to an index. More...

void	removeMetaValue (const String &name)
	Removes the DataValue corresponding to `name` if it exists. More...

void	removeMetaValue (UInt index)
	Removes the DataValue corresponding to `index` if it exists. More...

void	getKeys (std::vector< String > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

void	getKeys (std::vector< UInt > &keys) const
	Fills the given vector with a list of all keys for which a value is set. More...

bool	isMetaEmpty () const
	Returns if the MetaInfo is empty. More...

void	clearMetaInfo ()
	Removes all meta values. More...

Static Public Attributes
static const std::string	NamesOfIsotopeVariant [SIZE_OF_ISOTOPEVARIANT]
	Names of isotope variants. More...

Static Public Attributes inherited from Modification
static const std::string	NamesOfSpecificityType [SIZE_OF_SPECIFICITYTYPE]
	Names of specificity types. More...

Protected Attributes
double	mass_shift_

IsotopeVariant	variant_

Protected Attributes inherited from Modification
String	reagent_name_

double	mass_

SpecificityType	specificity_type_

String	affected_amino_acids_

Protected Attributes inherited from SampleTreatment
String	type_

String	comment_

Protected Attributes inherited from MetaInfoInterface
MetaInfo *	meta_
	Pointer to the MetaInfo object (0 by default) More...

Additional Inherited Members
Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistry &	metaRegistry ()
	Returns a reference to the MetaInfoRegistry. More...

Protected Member Functions inherited from MetaInfoInterface
void	createIfNotExists_ ()
	Creates the MetaInfo object if it does not exist. More...

Detailed Description

Meta information about tagging of a sample e.g. ICAT labeling.

Holds information about the mass difference between light and heavy tag. All other relevant information is provided by Modification.

Member Enumeration Documentation

◆ IsotopeVariant

enum IsotopeVariant

Isotope variants (light and heavy)

Enumerator
LIGHT
HEAVY
SIZE_OF_ISOTOPEVARIANT

Constructor & Destructor Documentation

◆ Tagging() [1/2]

Tagging ( )

default constructor

◆ Tagging() [2/2]

Tagging ( const Tagging & )

copy constructor

◆ ~Tagging()

~Tagging ( )

override

destructor

Member Function Documentation

◆ clone()

SampleTreatment* clone ( ) const

overridevirtual

clone method. See SampleTreatment

Reimplemented from Modification.

◆ getMassShift()

double getMassShift ( ) const

returns the mass difference between light and heavy variant (default is 0.0)

◆ getVariant()

const IsotopeVariant& getVariant ( ) const

returns the isotope variant of the tag (default is LIGHT)

◆ operator=()

Tagging& operator= ( const Tagging & )

assignment operator

◆ operator==()

bool operator== ( const SampleTreatment & rhs ) const

overridevirtual

Equality operator.

Although this operator takes a reference to a SampleTreatment as argument it tests for the equality of Tagging instances!

Reimplemented from Modification.

◆ setMassShift()

void setMassShift ( double mass_shift )

sets the mass difference between light and heavy variant

◆ setVariant()

void setVariant ( const IsotopeVariant & variant )

sets the isotope variant of the tag

Member Data Documentation

◆ mass_shift_

double mass_shift_

protected

◆ NamesOfIsotopeVariant

const std::string NamesOfIsotopeVariant[SIZE_OF_ISOTOPEVARIANT]

static

Names of isotope variants.

◆ variant_

IsotopeVariant variant_