OpenMS
Modification Class Reference

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

#include <OpenMS/METADATA/Modification.h>

Inheritance diagram for Modification:
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Collaboration diagram for Modification:
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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...
 
Modificationoperator= (const Modification &)=default
 Assignment operator. More...
 
Modificationoperator= (Modification &&) &=default
 Move assignment operator. More...
 
bool operator== (const SampleTreatment &rhs) const override
 Equality operator. More...
 
SampleTreatmentclone () const override
 clone method. See SampleTreatment 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 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
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 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

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]

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