Meta information about tagging of a sample e.g. ICAT labeling. More...
#include <OpenMS/METADATA/Tagging.h>
Inheritance diagram for Tagging:
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... | |
| Tagging & | operator= (const Tagging &) |
| assignment operator More... | |
| virtual bool | operator== (const SampleTreatment &rhs) const |
| Equality operator. More... | |
| virtual SampleTreatment * | clone () 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 IsotopeVariant & | getVariant () 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... | |
| Modification & | operator= (const Modification &) |
| assignment operator 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 | 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 | |
| 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 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
◆ IsotopeVariant
| enum IsotopeVariant |
Constructor & Destructor Documentation
◆ Tagging() [1/2]
| Tagging | ( | ) |
default constructor
◆ Tagging() [2/2]
◆ ~Tagging()
|
virtual |
destructor
Member Function Documentation
◆ clone()
|
virtual |
clone method. See SampleTreatment
Reimplemented from Modification.
◆ getMassShift()
| double getMassShift | ( | ) | const |
returns the mass difference between light and heavy variant (default is 0.0)
◆ getVariant()
| const IsotopeVariant& getVariant | ( | ) | const |
returns the isotope variant of the tag (default is LIGHT)
◆ 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 Modification.
◆ setMassShift()
| void setMassShift | ( | double | mass_shift | ) |
sets the mass difference between light and heavy variant
◆ setVariant()
| void setVariant | ( | const IsotopeVariant & | variant | ) |
sets the isotope variant of the tag
Member Data Documentation
◆ mass_shift_
|
protected |
◆ NamesOfIsotopeVariant
|
static |
Names of isotope variants.
◆ variant_
|
protected |