OpenMS
2.5.0
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Representation of a digestion enzyme for RNA (RNase) More...
#include <OpenMS/CHEMISTRY/DigestionEnzymeRNA.h>
Public Member Functions | |
void | setCutsAfterRegEx (const String &value) |
sets the "cuts after ..." regular expression More... | |
String | getCutsAfterRegEx () const |
returns the "cuts after ..." regular expression More... | |
void | setCutsBeforeRegEx (const String &value) |
sets the "cuts before ..." regular expression More... | |
String | getCutsBeforeRegEx () const |
returns the "cuts before ..." regular expression More... | |
void | setThreePrimeGain (const String &value) |
sets the 3' gain (as a nucleotide modification code) More... | |
String | getThreePrimeGain () const |
returns the 3' gain (as a nucleotide modification code) More... | |
void | setFivePrimeGain (const String &value) |
sets the 5' gain (as a nucleotide modification code) More... | |
String | getFivePrimeGain () const |
returns the 5' gain (as a nucleotide modification code) More... | |
bool | setValueFromFile (const String &key, const String &value) override |
Set the value of a member variable based on an entry from an input file. More... | |
Public Member Functions inherited from DigestionEnzyme | |
DigestionEnzyme (const DigestionEnzyme &)=default | |
Copy constructor. More... | |
DigestionEnzyme (DigestionEnzyme &&)=default | |
Move constructor. More... | |
DigestionEnzyme (const String &name, const String &cleavage_regex, const std::set< String > &synonyms=std::set< String >(), String regex_description="") | |
Detailed constructor. More... | |
virtual | ~DigestionEnzyme () |
Destructor. More... | |
DigestionEnzyme & | operator= (const DigestionEnzyme &)=default |
Assignment operator. More... | |
DigestionEnzyme & | operator= (DigestionEnzyme &&) &=default |
Move assignment operator. More... | |
void | setName (const String &name) |
sets the name of the enzyme More... | |
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 cleavage regex More... | |
String | getRegEx () const |
returns the cleavage regex More... | |
void | setRegExDescription (const String &value) |
sets the regex description More... | |
String | getRegExDescription () const |
returns the regex description More... | |
bool | operator== (const DigestionEnzyme &enzyme) const |
equality operator More... | |
bool | operator!= (const DigestionEnzyme &enzyme) const |
inequality operator More... | |
bool | operator== (const String &cleavage_regex) const |
equality operator for regex More... | |
bool | operator!= (const String &cleavage_regex) const |
equality operator for regex More... | |
bool | operator< (const DigestionEnzyme &enzyme) const |
order operator More... | |
Protected Attributes | |
String | three_prime_gain_ |
String | five_prime_gain_ |
String | cuts_after_regex_ |
String | cuts_before_regex_ |
Protected Attributes inherited from DigestionEnzyme | |
String | name_ |
String | cleavage_regex_ |
std::set< String > | synonyms_ |
String | regex_description_ |
Additional Inherited Members | |
Protected Member Functions inherited from DigestionEnzyme | |
DigestionEnzyme () | |
default constructor More... | |
Representation of a digestion enzyme for RNA (RNase)
The cutting sites of these enzymes are defined using two different mechanisms: First, a single regular expression that is applied to strings of unmodified RNA sequence and defines cutting sites via zero-length matches (using lookahead/lookbehind assertions). This is the same mechanism that is used for proteases (
There is support for terminal (5'/3') modifications that may be generated on fragments as a result of RNase cleavage. A typical example is 3'-phosphate, resulting from cleavage of the phosphate backbone.
String getCutsAfterRegEx | ( | ) | const |
returns the "cuts after ..." regular expression
String getCutsBeforeRegEx | ( | ) | const |
returns the "cuts before ..." regular expression
String getFivePrimeGain | ( | ) | const |
returns the 5' gain (as a nucleotide modification code)
String getThreePrimeGain | ( | ) | const |
returns the 3' gain (as a nucleotide modification code)
void setCutsAfterRegEx | ( | const String & | value | ) |
sets the "cuts after ..." regular expression
void setCutsBeforeRegEx | ( | const String & | value | ) |
sets the "cuts before ..." regular expression
void setFivePrimeGain | ( | const String & | value | ) |
sets the 5' gain (as a nucleotide modification code)
void setThreePrimeGain | ( | const String & | value | ) |
sets the 3' gain (as a nucleotide modification code)
Set the value of a member variable based on an entry from an input file.
Returns whether the key was recognized and the value set successfully.
Reimplemented from DigestionEnzyme.
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