DigestionEnzymeRNA Class Reference

Representation of a digestion enzyme for RNA (RNase) More...

#include <OpenMS/CHEMISTRY/DigestionEnzymeRNA.h>

Inheritance diagram for DigestionEnzymeRNA:

Collaboration diagram for DigestionEnzymeRNA:

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...
	DigestionEnzyme (const String &name, String cut_before, const String &nocut_after="", String sense="C", const std::set< String > &synonyms=std::set< String >(), String regex_description="")
	Detailed constructor 2. 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...
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 cleavage regex More...
const String &	getRegEx () const
	returns the cleavage regex More...
void	setRegExDescription (const String &value)
	sets the regex description More...
const 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...

Detailed Description

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 (

See also

ProteaseDigestion). However, due to the complex notation involved, this approach is not practical for modification-aware digestion. Thus, the second mechanism uses two regular expressions ("cuts after"/"cuts before"), which are applied to the short codes (e.g. "m6A") of sequential ribonucleotides. If both expressions match, then there is a cutting site between the two ribonucleotides.

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.

Member Function Documentation

getCutsAfterRegEx()

String getCutsAfterRegEx

(

)

const

returns the "cuts after ..." regular expression

getCutsBeforeRegEx()

String getCutsBeforeRegEx

(

)

const

returns the "cuts before ..." regular expression

getFivePrimeGain()

String getFivePrimeGain

(

)

const

returns the 5' gain (as a nucleotide modification code)

getThreePrimeGain()

String getThreePrimeGain

(

)

const

returns the 3' gain (as a nucleotide modification code)

setCutsAfterRegEx()

void setCutsAfterRegEx

(

const String &

value

)

sets the "cuts after ..." regular expression

setCutsBeforeRegEx()

void setCutsBeforeRegEx

(

const String &

value

)

sets the "cuts before ..." regular expression

setFivePrimeGain()

void setFivePrimeGain

(

const String &

value

)

sets the 5' gain (as a nucleotide modification code)

setThreePrimeGain()

void setThreePrimeGain

(

const String &

value

)

sets the 3' gain (as a nucleotide modification code)

setValueFromFile()

bool setValueFromFile ( const String &  key, const String &  value  )

overridevirtual

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.

Member Data Documentation

cuts_after_regex_

String cuts_after_regex_

protected

cuts_before_regex_

String cuts_before_regex_

protected

five_prime_gain_

String five_prime_gain_

protected

three_prime_gain_

String three_prime_gain_

protected