| OpenMS 2.5.0

Public Types | Public Member Functions | Static Public Attributes | Protected Attributes | List of all members
Tagging Class Reference
Metadata

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

override virtual

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

override virtual

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