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Modification Class Reference
[Metadata]

#include <OpenMS/METADATA/Modification.h>

Inheritance diagram for Modification:

SampleTreatment MetaInfoInterface Tagging

List of all members.


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.

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
 Modification (const Modification &)
 copy constructor
virtual ~Modification ()
 destructor
Modificationoperator= (const Modification &)
 assignment operator
virtual bool operator== (const SampleTreatment &rhs) const
 Equality operator.
virtual SampleTreatmentclone () const
 clone method. See SampleTreatment
const StringgetReagentName () const
 returns the name of the reagent that was used (default: "")
void setReagentName (const String &reagent_name)
 sets the name of the reagent that was used
float getMass () const
 returns the mass change (default: 0.0)
void setMass (float mass)
 sets the mass change
const SpecificityTypegetSpecificityType () const
 returns the specificity of the the reagent (default: AA)
void setSpecificityType (const SpecificityType &specificity_type)
 sets the specificity of the the reagent
const StringgetAffectedAminoAcids () const
 returns a string containing the one letter code of the amino acids that are affected by the reagent. (default: "")
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!

Static Public Attributes

static const std::string NamesOfSpecificityType [SIZE_OF_SPECIFICITYTYPE]
 Names of specifitiy types.

Protected Attributes

String reagent_name_
float mass_
SpecificityType specificity_type_
String affected_amino_acids_


Member Enumeration Documentation

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-termiuns is modified
NTERM  the N-termiuns is modified
SIZE_OF_SPECIFICITYTYPE 


Constructor & Destructor Documentation

Modification (  ) 

default constructor

Modification ( const Modification  ) 

copy constructor

virtual ~Modification (  )  [virtual]

destructor


Member Function Documentation

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.

virtual SampleTreatment* clone (  )  const [virtual]

clone method. See SampleTreatment

Implements SampleTreatment.

Reimplemented in Tagging.

const String& getReagentName (  )  const

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

void setReagentName ( const String reagent_name  ) 

sets the name of the reagent that was used

float getMass (  )  const

returns the mass change (default: 0.0)

void setMass ( float  mass  ) 

sets the mass change

const SpecificityType& getSpecificityType (  )  const

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

void setSpecificityType ( const SpecificityType specificity_type  ) 

sets the specificity of the the reagent

const String& getAffectedAminoAcids (  )  const

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

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!


Member Data Documentation

const std::string NamesOfSpecificityType[SIZE_OF_SPECIFICITYTYPE] [static]

Names of specifitiy types.

String reagent_name_ [protected]

float mass_ [protected]

SpecificityType specificity_type_ [protected]

String affected_amino_acids_ [protected]


The documentation for this class was generated from the following file:
Generated Tue Apr 1 15:36:46 2008 -- using doxygen 1.5.4 OpenMS / TOPP 1.1