Tagging Class Reference

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 &)=default
	Copy constructor. More...
	Tagging (Tagging &&)=default
	Move constructor. More...
	~Tagging () override
	Destructor. More...
Tagging &	operator= (const Tagging &)=default
	Assignment operator. More...
Tagging &	operator= (Tagging &&) &=default
	Move 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 &)=default
	Copy constructor. More...
	Modification (Modification &&)=default
	Move constructor. More...
	~Modification () override
	Destructor. More...
Modification &	operator= (const Modification &)=default
	Assignment operator. More...
Modification &	operator= (Modification &&) &=default
	Move 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 reagent (default: AA) More...
void	setSpecificityType (const SpecificityType &specificity_type)
	sets the specificity of 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 &)=default
	Copy constructor. More...
	SampleTreatment (SampleTreatment &&)=default
	Move constructor. More...
virtual	~SampleTreatment ()
	Destructor. More...
SampleTreatment &	operator= (const SampleTreatment &)=default
	Assignment operator. More...
SampleTreatment &	operator= (SampleTreatment &&) &=default
	Move 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 (MetaInfoInterface &&) noexcept
	Move constructor. More...
	~MetaInfoInterface ()
	Destructor. More...
MetaInfoInterface &	operator= (const MetaInfoInterface &rhs)
	Assignment operator. More...
MetaInfoInterface &	operator= (MetaInfoInterface &&) noexcept
	Move 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 DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to a string, or a default value (default: DataValue::EMPTY) if not found. More...
const DataValue &	getMetaValue (UInt index, const DataValue &default_value=DataValue::EMPTY) const
	Returns the value corresponding to an index, or a default value (default: 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() [1/3]

Tagging

(

)

Default constructor.

Tagging() [2/3]

Tagging ( const Tagging &  )

default

Copy constructor.

Tagging() [3/3]

Tagging ( Tagging &&  )

default

Move 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=() [1/2]

Tagging& operator= ( const Tagging &  )

default

Assignment operator.

operator=() [2/2]

Tagging& operator= ( Tagging &&  ) &

default

Move 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_

protected