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Tagging Class Reference

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

#include <OpenMS/METADATA/Tagging.h>

Inheritance diagram for Tagging:
Modification SampleTreatment MetaInfoInterface

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 &)
 copy constructor More...
 
virtual ~Tagging ()
 destructor More...
 
Taggingoperator= (const Tagging &)
 assignment operator More...
 
virtual bool operator== (const SampleTreatment &rhs) const
 Equality operator. More...
 
virtual SampleTreatmentclone () const
 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 &)
 copy constructor More...
 
virtual ~Modification ()
 destructor More...
 
Modificationoperator= (const Modification &)
 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 the reagent (default: AA) More...
 
void setSpecificityType (const SpecificityType &specificity_type)
 sets the specificity of the 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 &)
 Copy constructor. More...
 
virtual ~SampleTreatment ()
 destructor More...
 
SampleTreatmentoperator= (const SampleTreatment &)
 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 ()
 destructor More...
 
MetaInfoInterfaceoperator= (const MetaInfoInterface &rhs)
 assignment operator 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 More...
 
const DataValuegetMetaValue (UInt index) const
 returns the value corresponding to an index More...
 
bool metaValueExists (const String &name) const
 returns if this MetaInfo is set More...
 
bool metaValueExists (UInt index) const
 returns if this MetaInfo is set 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
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

Isotope variants (light and heavy)

Enumerator
LIGHT 
HEAVY 
SIZE_OF_ISOTOPEVARIANT 

Constructor & Destructor Documentation

Tagging ( )

default constructor

Tagging ( const Tagging )

copy constructor

virtual ~Tagging ( )
virtual

destructor

Member Function Documentation

virtual SampleTreatment* clone ( ) const
virtual

clone method. See SampleTreatment

Reimplemented from Modification.

double getMassShift ( ) const

returns the mass difference between light and heavy variant (default is 0.0)

const IsotopeVariant& getVariant ( ) const

returns the isotope variant of the tag (default is LIGHT)

Tagging& operator= ( const Tagging )

assignment operator

virtual bool operator== ( const SampleTreatment rhs) const
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.

void setMassShift ( double  mass_shift)

sets the mass difference between light and heavy variant

void setVariant ( const IsotopeVariant variant)

sets the isotope variant of the tag

Member Data Documentation

double mass_shift_
protected
const std::string NamesOfIsotopeVariant[SIZE_OF_ISOTOPEVARIANT]
static

Names of isotope variants.

IsotopeVariant variant_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Wed Mar 30 2016 16:18:48 using doxygen 1.8.5