OpenMS
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Meta information about chemical modification of a sample. More...
#include <OpenMS/METADATA/Modification.h>
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 &)=default | |
Copy constructor. More... | |
Modification (Modification &&)=default | |
Move constructor. More... | |
~Modification () override | |
Destructor. More... | |
Modification & | operator= (const Modification &)=default |
Assignment operator. More... | |
Modification & | operator= (Modification &&) &=default |
Move assignment operator. More... | |
bool | operator== (const SampleTreatment &rhs) const override |
SampleTreatment * | clone () const override |
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 reagent (default: AA) More... | |
void | setSpecificityType (const SpecificityType &specificity_type) |
sets the specificity of 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 &)=default | |
Copy constructor. More... | |
SampleTreatment (SampleTreatment &&)=default | |
Move constructor. More... | |
virtual | ~SampleTreatment () |
Destructor. More... | |
SampleTreatment & | operator= (const SampleTreatment &)=default |
Assignment operator. More... | |
SampleTreatment & | operator= (SampleTreatment &&) &=default |
Move 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 (MetaInfoInterface &&) noexcept | |
Move constructor. More... | |
~MetaInfoInterface () | |
Destructor. More... | |
MetaInfoInterface & | operator= (const MetaInfoInterface &rhs) |
Assignment operator. More... | |
MetaInfoInterface & | operator= (MetaInfoInterface &&) noexcept |
Move assignment operator. More... | |
void | swap (MetaInfoInterface &rhs) |
Swap contents. 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... | |
DataValue | getMetaValue (const String &name, const DataValue &default_value) const |
Returns the value corresponding to a string, or a default value (e.g.: DataValue::EMPTY) if not found More... | |
const DataValue & | getMetaValue (UInt index) const |
Returns the value corresponding to the index, or DataValue::EMPTY if not found. More... | |
DataValue | getMetaValue (UInt index, const DataValue &default_value) const |
Returns the value corresponding to the index, or a default value (e.g.: 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 | addMetaValues (const MetaInfoInterface &from) |
function to copy all meta values from one object to this one 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... | |
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.
enum SpecificityType |
specificity of the reagent.
Modification | ( | ) |
Default constructor.
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default |
Copy constructor.
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default |
Move constructor.
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override |
Destructor.
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overridevirtual |
const String& getAffectedAminoAcids | ( | ) | const |
returns a string containing the one letter code of the amino acids that are affected by the reagent. (default: "")
double 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 reagent (default: AA)
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default |
Assignment operator.
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default |
Move assignment operator.
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overridevirtual |
@brief 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 | ( | double | 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 reagent
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protected |
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protected |
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static |
Names of specificity types.
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protected |
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protected |