Representation of a modification. More...
#include <OpenMS/CHEMISTRY/ResidueModification.h>
Public Types | |
| enum | Term_Specificity { ANYWHERE = 0, C_TERM = 1, N_TERM = 2, NUMBER_OF_TERM_SPECIFICITY } |
| Position where the modification is allowed to occur. More... | |
| enum | Source_Classification { ARTIFACT = 0, HYPOTHETICAL, NATURAL, POSTTRANSLATIONAL, MULTIPLE, CHEMICAL_DERIVATIVE, ISOTOPIC_LABEL, PRETRANSLATIONAL, OTHER_GLYCOSYLATION, NLINKED_GLYCOSYLATION, AA_SUBSTITUTION, OTHER, NONSTANDARD_RESIDUE, COTRANSLATIONAL, OLINKED_GLYCOSYLATION, UNKNOWN, NUMBER_OF_SOURCE_CLASSIFICATIONS } |
| Classification of the modification. More... | |
Public Member Functions | |
Constructors and Destructors | |
| ResidueModification () | |
| default constructor More... | |
| ResidueModification (const ResidueModification &modification) | |
| copy constructor More... | |
| virtual | ~ResidueModification () |
| destructor More... | |
Assignment operator | |
| ResidueModification & | operator= (const ResidueModification &modification) |
| assignment operator More... | |
Accessors | |
| void | setId (const String &id) |
| set the identifier of the modification More... | |
| const String & | getId () const |
| returns the identifier of the modification More... | |
| void | setFullId (const String &full_id) |
| set full identifier (UniMod Accession + origin, if available) More... | |
| const String & | getFullId () const |
| returns the full id of the mod (UniMod accession + origin, if available) More... | |
| void | setUniModAccession (const String &id) |
| sets the unimod accession More... | |
| const String & | getUniModAccession () const |
| returns the unimod accession if available More... | |
| void | setPSIMODAccession (const String &id) |
| set the MOD:XXXXX accession of PSI-MOD More... | |
| const String & | getPSIMODAccession () const |
| returns the PSI-MOD accession if available More... | |
| void | setFullName (const String &full_name) |
| sets the full name of the modification More... | |
| const String & | getFullName () const |
| returns the full name of the modification More... | |
| void | setName (const String &name) |
| sets the name of modification More... | |
| const String & | getName () const |
| returns the PSI-MS-label if available; e.g. Mascot uses this name More... | |
| void | setTermSpecificity (Term_Specificity term_spec) |
| sets the term specificity More... | |
| void | setTermSpecificity (const String &name) |
| sets the terminal specificity using a name (valid: "C-term","N-term","none") More... | |
| Term_Specificity | getTermSpecificity () const |
| returns terminal specificity More... | |
| String | getTermSpecificityName (Term_Specificity=NUMBER_OF_TERM_SPECIFICITY) const |
| returns the terminal specificity name which is set or given as parameter More... | |
| void | setOrigin (const String &origin) |
| sets the origin (ie amino acid) More... | |
| const String & | getOrigin () const |
| returns the origin (ie amino acid) if set More... | |
| void | setSourceClassification (const String &classification) |
| classification as defined by the PSI-MOD More... | |
| void | setSourceClassification (Source_Classification classification) |
| sets the source classification More... | |
| Source_Classification | getSourceClassification () const |
| returns the source classification, if none was set, it is unspecific More... | |
| String | getSourceClassificationName (Source_Classification classification=NUMBER_OF_SOURCE_CLASSIFICATIONS) const |
| returns the classification More... | |
| void | setAverageMass (DoubleReal mass) |
| sets the average mass More... | |
| DoubleReal | getAverageMass () const |
| returns the average mass if set More... | |
| void | setMonoMass (DoubleReal mass) |
| sets the monoisotopic mass More... | |
| DoubleReal | getMonoMass () const |
| return the monoisotopic mass, if set More... | |
| void | setDiffAverageMass (DoubleReal mass) |
| set the difference average mass More... | |
| DoubleReal | getDiffAverageMass () const |
| returns the difference average mass if set More... | |
| void | setDiffMonoMass (DoubleReal mass) |
| sets the difference monoisotopic mass More... | |
| DoubleReal | getDiffMonoMass () const |
| returns the diff monoisotopic mass if set More... | |
| void | setFormula (const String &composition) |
| set the formula More... | |
| const String & | getFormula () const |
| returns the chemical formula if set More... | |
| void | setDiffFormula (const EmpiricalFormula &diff_formula) |
| sets diff formula More... | |
| const EmpiricalFormula & | getDiffFormula () const |
| returns the diff formula if one was set More... | |
| void | setSynonyms (const std::set< String > &synonyms) |
| sets the synonyms of that modification More... | |
| void | addSynonym (const String &synonym) |
| adds a synonym to the unique list More... | |
| const std::set< String > & | getSynonyms () const |
| returns the set of synonyms More... | |
| void | setNeutralLossDiffFormula (const EmpiricalFormula &loss) |
| sets the neutral loss formula More... | |
| const EmpiricalFormula & | getNeutralLossDiffFormula () const |
| returns the neutral loss diff formula (if available) More... | |
| void | setNeutralLossMonoMass (DoubleReal mono_mass) |
| set the neutral loss mono weight More... | |
| DoubleReal | getNeutralLossMonoMass () const |
| returns the neutral loss mono weight More... | |
| void | setNeutralLossAverageMass (DoubleReal average_mass) |
| set the neutral loss average weight More... | |
| DoubleReal | getNeutralLossAverageMass () const |
| returns the neutral loss average weight More... | |
Predicates | |
| bool | hasNeutralLoss () const |
| returns true if a neutral loss formula is set More... | |
| bool | operator== (const ResidueModification &modification) const |
| equality operator More... | |
| bool | operator!= (const ResidueModification &modification) const |
| inequality operator More... | |
Representation of a modification.
This class represents a modification of a residue. A residue modification has several attributes like the diff formula, a terminal specificity a mass and maybe an origin which means a specific residue which it can be applied to. A residue modification can be represented by its UniMod name identifier, e.g. "Oxidation (M)" or "Oxidation". This is a unique key which only occurs once in an OpenMS instance stored in the ModificationsDB.
Classification of the modification.
| enum Term_Specificity |
default constructor
| ResidueModification | ( | const ResidueModification & | modification | ) |
copy constructor
|
virtual |
destructor
| void addSynonym | ( | const String & | synonym | ) |
adds a synonym to the unique list
| DoubleReal getAverageMass | ( | ) | const |
returns the average mass if set
| DoubleReal getDiffAverageMass | ( | ) | const |
returns the difference average mass if set
| const EmpiricalFormula& getDiffFormula | ( | ) | const |
returns the diff formula if one was set
| DoubleReal getDiffMonoMass | ( | ) | const |
returns the diff monoisotopic mass if set
| const String& getFormula | ( | ) | const |
returns the chemical formula if set
| const String& getFullId | ( | ) | const |
returns the full id of the mod (UniMod accession + origin, if available)
| const String& getFullName | ( | ) | const |
returns the full name of the modification
| const String& getId | ( | ) | const |
returns the identifier of the modification
| DoubleReal getMonoMass | ( | ) | const |
return the monoisotopic mass, if set
| const String& getName | ( | ) | const |
returns the PSI-MS-label if available; e.g. Mascot uses this name
| DoubleReal getNeutralLossAverageMass | ( | ) | const |
returns the neutral loss average weight
| const EmpiricalFormula& getNeutralLossDiffFormula | ( | ) | const |
returns the neutral loss diff formula (if available)
| DoubleReal getNeutralLossMonoMass | ( | ) | const |
returns the neutral loss mono weight
| const String& getOrigin | ( | ) | const |
returns the origin (ie amino acid) if set
| const String& getPSIMODAccession | ( | ) | const |
returns the PSI-MOD accession if available
| Source_Classification getSourceClassification | ( | ) | const |
returns the source classification, if none was set, it is unspecific
| String getSourceClassificationName | ( | Source_Classification | classification = NUMBER_OF_SOURCE_CLASSIFICATIONS | ) | const |
returns the classification
| const std::set<String>& getSynonyms | ( | ) | const |
returns the set of synonyms
| Term_Specificity getTermSpecificity | ( | ) | const |
returns terminal specificity
| String getTermSpecificityName | ( | Term_Specificity | = NUMBER_OF_TERM_SPECIFICITY | ) | const |
returns the terminal specificity name which is set or given as parameter
| const String& getUniModAccession | ( | ) | const |
returns the unimod accession if available
| bool hasNeutralLoss | ( | ) | const |
returns true if a neutral loss formula is set
| bool operator!= | ( | const ResidueModification & | modification | ) | const |
inequality operator
| ResidueModification& operator= | ( | const ResidueModification & | modification | ) |
assignment operator
| bool operator== | ( | const ResidueModification & | modification | ) | const |
equality operator
| void setAverageMass | ( | DoubleReal | mass | ) |
sets the average mass
| void setDiffAverageMass | ( | DoubleReal | mass | ) |
set the difference average mass
| void setDiffFormula | ( | const EmpiricalFormula & | diff_formula | ) |
sets diff formula
| void setDiffMonoMass | ( | DoubleReal | mass | ) |
sets the difference monoisotopic mass
| void setFormula | ( | const String & | composition | ) |
set the formula
| void setFullId | ( | const String & | full_id | ) |
set full identifier (UniMod Accession + origin, if available)
| void setFullName | ( | const String & | full_name | ) |
sets the full name of the modification
| void setId | ( | const String & | id | ) |
set the identifier of the modification
| void setMonoMass | ( | DoubleReal | mass | ) |
sets the monoisotopic mass
| void setName | ( | const String & | name | ) |
sets the name of modification
| void setNeutralLossAverageMass | ( | DoubleReal | average_mass | ) |
set the neutral loss average weight
| void setNeutralLossDiffFormula | ( | const EmpiricalFormula & | loss | ) |
sets the neutral loss formula
| void setNeutralLossMonoMass | ( | DoubleReal | mono_mass | ) |
set the neutral loss mono weight
| void setOrigin | ( | const String & | origin | ) |
sets the origin (ie amino acid)
| void setPSIMODAccession | ( | const String & | id | ) |
set the MOD:XXXXX accession of PSI-MOD
| void setSourceClassification | ( | const String & | classification | ) |
classification as defined by the PSI-MOD
| void setSourceClassification | ( | Source_Classification | classification | ) |
sets the source classification
| void setSynonyms | ( | const std::set< String > & | synonyms | ) |
sets the synonyms of that modification
| void setTermSpecificity | ( | Term_Specificity | term_spec | ) |
sets the term specificity
| void setTermSpecificity | ( | const String & | name | ) |
sets the terminal specificity using a name (valid: "C-term","N-term","none")
| void setUniModAccession | ( | const String & | id | ) |
sets the unimod accession
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| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5 |