Representation of an enzyme. More...
#include <OpenMS/CHEMISTRY/Enzyme.h>
Public Member Functions | |
Constructors | |
Enzyme (const Enzyme &enzyme) | |
copy constructor More... | |
Enzyme (const String &name, const String &cleavage_regex, const std::set< String > &synonyms=std::set< String >(), String regex_description="", EmpiricalFormula n_term_gain=EmpiricalFormula("H"), EmpiricalFormula c_term_gain=EmpiricalFormula("OH"), String psi_id="", String xtandem_id="", UInt comet_id=0, Int msgf_id=-1, UInt omssa_id=0) | |
detailed constructor More... | |
virtual | ~Enzyme () |
destructor More... | |
Assignment | |
Enzyme & | operator= (const Enzyme &enzyme) |
assignment operator More... | |
void | setName (const String &name) |
sets the name of the enzyme More... | |
const String & | getName () const |
returns the name of the enzyme More... | |
void | setSynonyms (const std::set< String > &synonyms) |
sets the synonyms More... | |
void | addSynonym (const String &synonym) |
adds a synonym More... | |
const std::set< String > & | getSynonyms () const |
returns the synonyms More... | |
void | setRegEx (const String &cleavage_regex) |
sets the name as regex More... | |
const String & | getRegEx () const |
returns the name as regex More... | |
void | setRegExDescription (String value) |
sets the regex description More... | |
String | getRegExDescription () const |
returns the regex description More... | |
void | setNTermGain (EmpiricalFormula value) |
sets the N-terminal gain More... | |
EmpiricalFormula | getNTermGain () const |
returns N-terminal gain More... | |
void | setCTermGain (EmpiricalFormula value) |
sets the C-terminal gain More... | |
EmpiricalFormula | getCTermGain () const |
returns C-terminal gain More... | |
void | setPSIID (String value) |
sets the PSI ID More... | |
String | getPSIID () const |
returns the PSI ID More... | |
void | setXTandemID (String value) |
sets the X! Tandem enzyme ID More... | |
String | getXTandemID () const |
returns the X! Tandem enzyme ID More... | |
UInt | getCometID () const |
returns the Comet enzyme ID More... | |
void | setCometID (UInt value) |
sets the Comet enzyme ID More... | |
void | setMSGFID (Int value) |
sets the MSGFPlus enzyme id More... | |
Int | getMSGFID () const |
returns the MSGFPlus enzyme id More... | |
void | setOMSSAID (UInt value) |
sets the OMSSA enzyme ID More... | |
UInt | getOMSSAID () const |
returns the OMSSA enzyme ID More... | |
Predicates | |
bool | operator== (const Enzyme &enzyme) const |
equality operator More... | |
bool | operator!= (const Enzyme &enzyme) const |
inequality operator More... | |
bool | operator== (String cleavage_regex) const |
equality operator for regex More... | |
bool | operator!= (String cleavage_regex) const |
equality operator for regex More... | |
bool | operator< (const Enzyme &enzyme) const |
order operator More... | |
Protected Member Functions | |
Enzyme () | |
default constructor More... | |
Protected Attributes | |
String | name_ |
String | cleavage_regex_ |
std::set< String > | synonyms_ |
String | regex_description_ |
EmpiricalFormula | n_term_gain_ |
EmpiricalFormula | c_term_gain_ |
String | psi_id_ |
String | xtandem_id_ |
UInt | comet_id_ |
Int | msgf_id_ |
UInt | omssa_id_ |
Friends | |
std::ostream & | operator<< (std::ostream &os, const Enzyme &enzyme) |
ostream iterator to write the enzyme to a stream More... | |
Representation of an enzyme.
This class represents enzymes.
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explicit |
detailed constructor
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virtual |
destructor
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protected |
default constructor
void addSynonym | ( | const String & | synonym | ) |
adds a synonym
UInt getCometID | ( | ) | const |
returns the Comet enzyme ID
EmpiricalFormula getCTermGain | ( | ) | const |
returns C-terminal gain
Int getMSGFID | ( | ) | const |
returns the MSGFPlus enzyme id
const String& getName | ( | ) | const |
returns the name of the enzyme
EmpiricalFormula getNTermGain | ( | ) | const |
returns N-terminal gain
UInt getOMSSAID | ( | ) | const |
returns the OMSSA enzyme ID
String getPSIID | ( | ) | const |
returns the PSI ID
const String& getRegEx | ( | ) | const |
returns the name as regex
String getRegExDescription | ( | ) | const |
returns the regex description
const std::set<String>& getSynonyms | ( | ) | const |
returns the synonyms
String getXTandemID | ( | ) | const |
returns the X! Tandem enzyme ID
bool operator!= | ( | const Enzyme & | enzyme | ) | const |
inequality operator
bool operator!= | ( | String | cleavage_regex | ) | const |
equality operator for regex
bool operator< | ( | const Enzyme & | enzyme | ) | const |
order operator
bool operator== | ( | const Enzyme & | enzyme | ) | const |
equality operator
bool operator== | ( | String | cleavage_regex | ) | const |
equality operator for regex
void setCometID | ( | UInt | value | ) |
sets the Comet enzyme ID
void setCTermGain | ( | EmpiricalFormula | value | ) |
sets the C-terminal gain
void setMSGFID | ( | Int | value | ) |
sets the MSGFPlus enzyme id
void setName | ( | const String & | name | ) |
sets the name of the enzyme
Accessors
void setNTermGain | ( | EmpiricalFormula | value | ) |
sets the N-terminal gain
void setOMSSAID | ( | UInt | value | ) |
sets the OMSSA enzyme ID
void setPSIID | ( | String | value | ) |
sets the PSI ID
void setRegEx | ( | const String & | cleavage_regex | ) |
sets the name as regex
void setRegExDescription | ( | String | value | ) |
sets the regex description
void setSynonyms | ( | const std::set< String > & | synonyms | ) |
sets the synonyms
void setXTandemID | ( | String | value | ) |
sets the X! Tandem enzyme ID
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friend |
ostream iterator to write the enzyme to a stream
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OpenMS / TOPP release 2.3.0 | Documentation generated on Tue Jan 9 2018 18:22:08 using doxygen 1.8.13 |