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 &) | |
| copy constructor More... | |
| virtual | ~Modification () |
| destructor More... | |
| Modification & | operator= (const Modification &) |
| assignment operator More... | |
| virtual bool | operator== (const SampleTreatment &rhs) const |
| Equality operator. More... | |
| virtual SampleTreatment * | clone () const |
| 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 the reagent (default: AA) More... | |
| void | setSpecificityType (const SpecificityType &specificity_type) |
| sets the specificity of the 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 &) | |
| Copy constructor. More... | |
| virtual | ~SampleTreatment () |
| destructor More... | |
| SampleTreatment & | operator= (const SampleTreatment &) |
| 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 () | |
| Destructor. More... | |
| MetaInfoInterface & | operator= (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 DataValue & | getMetaValue (const String &name) const |
| Returns the value corresponding to a string (or DataValue::EMPTY if not found) More... | |
| const DataValue & | getMetaValue (UInt index) const |
| Returns the value corresponding to an index (or 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.
Constructor & Destructor Documentation
◆ Modification() [1/2]
| Modification | ( | ) |
default constructor
◆ Modification() [2/2]
| Modification | ( | const Modification & | ) |
copy constructor
◆ ~Modification()
|
virtual |
destructor
Member Function Documentation
◆ clone()
|
virtual |
◆ 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 the reagent (default: AA)
◆ operator=()
| Modification& operator= | ( | const Modification & | ) |
assignment operator
◆ operator==()
|
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 the reagent
Member Data Documentation
◆ affected_amino_acids_
|
protected |
◆ mass_
|
protected |
◆ NamesOfSpecificityType
|
static |
Names of specificity types.
◆ reagent_name_
|
protected |
◆ specificity_type_
|
protected |