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Modification Class Reference

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

#include <OpenMS/METADATA/Modification.h>

Inheritance diagram for Modification:
SampleTreatment MetaInfoInterface Tagging

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 &)
 copy constructor More...
 
virtual ~Modification ()
 destructor More...
 
Modificationoperator= (const Modification &)
 assignment operator More...
 
virtual bool operator== (const SampleTreatment &rhs) const
 Equality operator. More...
 
virtual SampleTreatmentclone () const
 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...
 
DoubleReal getMass () const
 returns the mass change (default: 0.0) More...
 
void setMass (DoubleReal 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 NamesOfSpecificityType [SIZE_OF_SPECIFICITYTYPE]
 Names of specifitiy types. More...
 

Protected Attributes

String reagent_name_
 
DoubleReal 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 ()
 retuns 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

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-termiuns is modified

NTERM 

the N-termiuns is modified

SIZE_OF_SPECIFICITYTYPE 

Constructor & Destructor Documentation

default constructor

Modification ( const Modification )

copy constructor

virtual ~Modification ( )
virtual

destructor

Member Function Documentation

virtual SampleTreatment* clone ( ) const
virtual

clone method. See SampleTreatment

Implements SampleTreatment.

Reimplemented in Tagging.

const String& getAffectedAminoAcids ( ) const

returns a string containing the one letter code of the amino acids that are affected by the reagent. (default: "")

DoubleReal getMass ( ) const

returns the mass change (default: 0.0)

const String& getReagentName ( ) const

returns the name of the reagent that was used (default: "")

const SpecificityType& getSpecificityType ( ) const

returns the specificity of the the reagent (default: AA)

Modification& operator= ( const Modification )

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 SampleTreatment.

Reimplemented in Tagging.

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!

void setMass ( DoubleReal  mass)

sets the mass change

void setReagentName ( const String reagent_name)

sets the name of the reagent that was used

void setSpecificityType ( const SpecificityType specificity_type)

sets the specificity of the the reagent

Member Data Documentation

String affected_amino_acids_
protected
DoubleReal mass_
protected
const std::string NamesOfSpecificityType[SIZE_OF_SPECIFICITYTYPE]
static

Names of specifitiy types.

String reagent_name_
protected
SpecificityType specificity_type_
protected

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5