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 &) | |
| 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... | |
| DoubleReal | getMass () const |
| returns the mass change (default: 0.0) More... | |
| void | setMass (DoubleReal 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 More... | |
| const DataValue & | getMetaValue (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 | |
| MetaInfo * | meta_ |
| pointer to the MetaInfo object. 0 by default More... | |
Additional Inherited Members | |
Static Public Member Functions inherited from MetaInfoInterface | |
| static MetaInfoRegistry & | metaRegistry () |
| 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... | |
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
| Modification | ( | const Modification & | ) |
copy constructor
|
virtual |
destructor
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virtual |
| 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 |
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
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protected |
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protected |
|
static |
Names of specifitiy types.
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protected |
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protected |
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:33 using doxygen 1.8.5 |