| OpenMS 2.5.0

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

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

`#include <OpenMS/METADATA/Modification.h>`

Inheritance 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...
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 | 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

override virtual

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

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 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