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 std::string &value)
	sets the "cuts after ..." regular expression
std::string	getCutsAfterRegEx () const
	returns the "cuts after ..." regular expression
void	setCutsBeforeRegEx (const std::string &value)
	sets the "cuts before ..." regular expression
std::string	getCutsBeforeRegEx () const
	returns the "cuts before ..." regular expression
void	setThreePrimeGain (const std::string &value)
	sets the 3' gain (as a nucleotide modification code)
std::string	getThreePrimeGain () const
	returns the 3' gain (as a nucleotide modification code)
void	setFivePrimeGain (const std::string &value)
	sets the 5' gain (as a nucleotide modification code)
std::string	getFivePrimeGain () const
	returns the 5' gain (as a nucleotide modification code)
bool	setValueFromFile (const std::string &key, const std::string &value) override
	Set the value of a member variable based on an entry from an input file.
Public Member Functions inherited from DigestionEnzyme
	DigestionEnzyme (const DigestionEnzyme &)=default
	Copy constructor.
	DigestionEnzyme (DigestionEnzyme &&)=default
	Move constructor.
	DigestionEnzyme (const std::string &name, const std::string &cleavage_regex, const std::set< std::string > &synonyms=std::set< std::string >(), std::string regex_description="")
	Detailed constructor.
	DigestionEnzyme (const std::string &name, std::string cut_before, const std::string &nocut_after="", std::string sense="C", const std::set< std::string > &synonyms=std::set< std::string >(), std::string regex_description="")
	Detailed constructor 2.
virtual	~DigestionEnzyme ()
	Destructor.
DigestionEnzyme &	operator= (const DigestionEnzyme &)=default
	Assignment operator.
DigestionEnzyme &	operator= (DigestionEnzyme &&) &=default
	Move assignment operator.
void	setName (const std::string &name)
	sets the name of the enzyme
const std::string &	getName () const
	returns the name of the enzyme
void	setSynonyms (const std::set< std::string > &synonyms)
	sets the synonyms
void	addSynonym (const std::string &synonym)
	adds a synonym
const std::set< std::string > &	getSynonyms () const
	returns the synonyms
void	setRegEx (const std::string &cleavage_regex)
	sets the cleavage regex
const std::string &	getRegEx () const
	returns the cleavage regex
void	setRegExDescription (const std::string &value)
	sets the regex description
const std::string &	getRegExDescription () const
	returns the regex description
bool	operator== (const DigestionEnzyme &enzyme) const
	equality operator
bool	operator!= (const DigestionEnzyme &enzyme) const
	inequality operator
bool	operator== (const std::string &cleavage_regex) const
	equality operator for regex
bool	operator!= (const std::string &cleavage_regex) const
	equality operator for regex
bool	operator< (const DigestionEnzyme &enzyme) const
	order operator

Protected Attributes
std::string	three_prime_gain_
std::string	five_prime_gain_
std::string	cuts_after_regex_
std::string	cuts_before_regex_
Protected Attributes inherited from DigestionEnzyme
std::string	name_
std::string	cleavage_regex_
std::set< std::string >	synonyms_
std::string	regex_description_

Additional Inherited Members
Protected Member Functions inherited from DigestionEnzyme
	DigestionEnzyme ()
	default constructor

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()

std::string getCutsAfterRegEx

(

)

const

returns the "cuts after ..." regular expression

getCutsBeforeRegEx()

std::string getCutsBeforeRegEx

(

)

const

returns the "cuts before ..." regular expression

getFivePrimeGain()

std::string getFivePrimeGain

(

)

const

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

getThreePrimeGain()

std::string getThreePrimeGain

(

)

const

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

setCutsAfterRegEx()

void setCutsAfterRegEx

(

const std::string &

value

)

sets the "cuts after ..." regular expression

setCutsBeforeRegEx()

void setCutsBeforeRegEx

(

const std::string &

value

)

sets the "cuts before ..." regular expression

setFivePrimeGain()

void setFivePrimeGain

(

const std::string &

value

)

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

setThreePrimeGain()

void setThreePrimeGain

(

const std::string &

value

)

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

setValueFromFile()

bool setValueFromFile ( const std::string &  key, const std::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_

std::string cuts_after_regex_

protected

cuts_before_regex_

std::string cuts_before_regex_

protected

five_prime_gain_

std::string five_prime_gain_

protected

three_prime_gain_

std::string three_prime_gain_

protected