Modification Class Reference

Meta information about chemical modification of a sample. More...

#include <OpenMS/METADATA/Modification.h>

Inheritance diagram for Modification:

Collaboration diagram for Modification:

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

Public Member Functions
	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...
bool	operator== (const SampleTreatment &rhs) const override
	Equality operator. More...
SampleTreatment *	clone () const override
	clone method. See SampleTreatment 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...
void	swap (MetaInfoInterface &rhs)
	Swap contents. 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	addMetaValues (const MetaInfoInterface &from)
	function to copy all meta values from one object to this one 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	NamesOfSpecificityType [SIZE_OF_SPECIFICITYTYPE]
	Names of specificity types. More...

Protected Attributes
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 chemical modification of a sample.

Representation of some kind of modification. It hold information about what amino acids are modified and how much the mass changes.

Member Enumeration Documentation

SpecificityType

enum SpecificityType

specificity of the reagent.

Enumerator
AA	specified amino acids are modified
AA_AT_CTERM	specified amino acids are modified, if they are at the C-terminus
AA_AT_NTERM	specified amino acids are modified, if they are at the N-terminus
CTERM	the C-terminus is modified
NTERM	the N-terminus is modified
SIZE_OF_SPECIFICITYTYPE

Constructor & Destructor Documentation

Modification() [1/3]

Modification

(

)

Default constructor.

Modification() [2/3]

Modification ( const Modification &  )

default

Copy constructor.

Modification() [3/3]

Modification ( Modification &&  )

default

Move constructor.

~Modification()

~Modification ( )

override

Destructor.

Member Function Documentation

clone()

SampleTreatment* clone ( ) const

overridevirtual

clone method. See SampleTreatment

Implements SampleTreatment.

Reimplemented in Tagging.

getAffectedAminoAcids()

const String& getAffectedAminoAcids

(

)

const

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

getMass()

double getMass

(

)

const

returns the mass change (default: 0.0)

getReagentName()

const String& getReagentName

(

)

const

returns the name of the reagent that was used (default: "")

getSpecificityType()

const SpecificityType& getSpecificityType

(

)

const

returns the specificity of the reagent (default: AA)

operator=() [1/2]

Modification& operator= ( const Modification &  )

default

Assignment operator.

operator=() [2/2]

Modification& operator= ( Modification &&  ) &

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 SampleTreatment.

Reimplemented in Tagging.

setAffectedAminoAcids()

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!

setMass()

void setMass

(

double

mass

)

sets the mass change

setReagentName()

void setReagentName

(

const String &

reagent_name

)

sets the name of the reagent that was used

setSpecificityType()

void setSpecificityType

(

const SpecificityType &

specificity_type

)

sets the specificity of the reagent

Member Data Documentation

affected_amino_acids_

String affected_amino_acids_

protected

mass_

double mass_

protected

NamesOfSpecificityType

const std::string NamesOfSpecificityType[SIZE_OF_SPECIFICITYTYPE]

static

Names of specificity types.

reagent_name_

String reagent_name_

protected

specificity_type_

SpecificityType specificity_type_

protected