OpenMS
Tagging Class Reference

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

#include <OpenMS/METADATA/Tagging.h>

Inheritance diagram for Tagging:
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Collaboration diagram for Tagging:
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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...
 
Taggingoperator= (const Tagging &)=default
 Assignment operator. More...
 
Taggingoperator= (Tagging &&) &=default
 Move assignment operator. More...
 
bool operator== (const SampleTreatment &rhs) const override
 Equality operator. More...
 
SampleTreatmentclone () 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 IsotopeVariantgetVariant () 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...
 
Modificationoperator= (const Modification &)=default
 Assignment operator. More...
 
Modificationoperator= (Modification &&) &=default
 Move assignment operator. More...
 
const StringgetReagentName () 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 SpecificityTypegetSpecificityType () const
 returns the specificity of the reagent (default: AA) More...
 
void setSpecificityType (const SpecificityType &specificity_type)
 sets the specificity of the reagent More...
 
const StringgetAffectedAminoAcids () 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...
 
SampleTreatmentoperator= (const SampleTreatment &)=default
 Assignment operator. More...
 
SampleTreatmentoperator= (SampleTreatment &&) &=default
 Move assignment operator. More...
 
const StringgetType () const
 return the treatment type More...
 
const StringgetComment () 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...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 Assignment operator. More...
 
MetaInfoInterfaceoperator= (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 DataValuegetMetaValue (const String &name) const
 Returns the value corresponding to a string, or DataValue::EMPTY if not found. More...
 
DataValue getMetaValue (const String &name, const DataValue &default_value) const
 Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found. More...
 
const DataValuegetMetaValue (UInt index) const
 Returns the value corresponding to the index, or DataValue::EMPTY if not found. More...
 
DataValue getMetaValue (UInt index, const DataValue &default_value) const
 Returns the value corresponding to the index, or a default value (e.g.: 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 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
MetaInfometa_
 Pointer to the MetaInfo object (0 by default) More...
 

Additional Inherited Members

- Static Public Member Functions inherited from MetaInfoInterface
static MetaInfoRegistrymetaRegistry ()
 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

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