Representation of a digestion enzyme for proteins (protease) More...

#include <OpenMS/CHEMISTRY/DigestionEnzymeProtein.h>

Inheritance diagram for DigestionEnzymeProtein:

Collaboration diagram for DigestionEnzymeProtein:

Public Member Functions
Constructors
	DigestionEnzymeProtein ()
	Default constructor.

	DigestionEnzymeProtein (const DigestionEnzyme &d)
	Constructor from base class (adding defaults for the missing stuff)

	DigestionEnzymeProtein (const DigestionEnzymeProtein &)=default
	Copy constructor.

	DigestionEnzymeProtein (DigestionEnzymeProtein &&)=default
	Move constructor.

	DigestionEnzymeProtein (const std::string &name, const std::string &cleavage_regex, const std::set< std::string > &synonyms=std::set< std::string >(), std::string regex_description="", EmpiricalFormula n_term_gain=EmpiricalFormula("H"), EmpiricalFormula c_term_gain=EmpiricalFormula("OH"), std::string psi_id="", std::string xtandem_id="", Int comet_id=-1, Int msgf_id=-1, Int omssa_id=-1)
	Detailed constructor.

	~DigestionEnzymeProtein () override
	Destructor.

Assignment
DigestionEnzymeProtein &	operator= (const DigestionEnzymeProtein &)=default
	Assignment operator.

DigestionEnzymeProtein &	operator= (DigestionEnzymeProtein &&) &=default
	Move assignment operator.

void	setNTermGain (const EmpiricalFormula &value)
	sets the N-terminal gain

EmpiricalFormula	getNTermGain () const
	returns N-terminal gain

void	setCTermGain (const EmpiricalFormula &value)
	sets the C-terminal gain

EmpiricalFormula	getCTermGain () const
	returns C-terminal gain

void	setPSIID (const std::string &value)
	sets the PSI ID

std::string	getPSIID () const
	returns the PSI ID

void	setXTandemID (const std::string &value)
	sets the X! Tandem enzyme ID

std::string	getXTandemID () const
	returns the X! Tandem enzyme ID

void	setCometID (Int value)
	sets the Comet enzyme ID

Int	getCometID () const
	returns the Comet enzyme ID

void	setMSGFID (Int value)
	sets the MSGFPlus enzyme id

Int	getMSGFID () const
	returns the MSGFPlus enzyme id

void	setOMSSAID (Int value)
	sets the OMSSA enzyme ID

Int	getOMSSAID () const
	returns the OMSSA enzyme ID

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

Predicates
EmpiricalFormula	n_term_gain_

EmpiricalFormula	c_term_gain_

std::string	psi_id_

std::string	xtandem_id_

Int	comet_id_

Int	msgf_id_

Int	omssa_id_

bool	operator== (const DigestionEnzymeProtein &enzyme) const
	equality operator

bool	operator!= (const DigestionEnzymeProtein &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 DigestionEnzymeProtein &enzyme) const
	order operator

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.

std::ostream &	operator<< (std::ostream &os, const DigestionEnzymeProtein &enzyme)
	ostream iterator to write the enzyme to a stream

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

Protected Attributes inherited from DigestionEnzyme
std::string	name_

std::string	cleavage_regex_

std::set< std::string >	synonyms_

std::string	regex_description_

Detailed Description

Representation of a digestion enzyme for proteins (protease)

Constructor & Destructor Documentation

◆ DigestionEnzymeProtein() [1/5]

DigestionEnzymeProtein ( )

Default constructor.

◆ DigestionEnzymeProtein() [2/5]

DigestionEnzymeProtein ( const DigestionEnzyme & d )

explicit

Constructor from base class (adding defaults for the missing stuff)

◆ DigestionEnzymeProtein() [3/5]

DigestionEnzymeProtein ( const DigestionEnzymeProtein & )

default

Copy constructor.

◆ DigestionEnzymeProtein() [4/5]

DigestionEnzymeProtein ( DigestionEnzymeProtein && )

default

Move constructor.

◆ DigestionEnzymeProtein() [5/5]

DigestionEnzymeProtein	(	const std::string &	name,
		const std::string &	cleavage_regex,
		const std::set< std::string > &	synonyms = `std::set< std::string >()`,
		std::string	regex_description = `""`,
		EmpiricalFormula	n_term_gain = `EmpiricalFormula("H")`,
		EmpiricalFormula	c_term_gain = `EmpiricalFormula("OH")`,
		std::string	psi_id = `""`,
		std::string	xtandem_id = `""`,
		Int	comet_id = `-1`,
		Int	msgf_id = `-1`,
		Int	omssa_id = `-1`
	)

explicit

Detailed constructor.

◆ ~DigestionEnzymeProtein()

~DigestionEnzymeProtein ( )

override

Destructor.

Member Function Documentation

◆ getCometID()

Int getCometID ( ) const

returns the Comet enzyme ID

◆ getCTermGain()

EmpiricalFormula getCTermGain ( ) const

returns C-terminal gain

◆ getMSGFID()

Int getMSGFID ( ) const

returns the MSGFPlus enzyme id

◆ getNTermGain()

EmpiricalFormula getNTermGain ( ) const

returns N-terminal gain

◆ getOMSSAID()

Int getOMSSAID ( ) const

returns the OMSSA enzyme ID

◆ getPSIID()

std::string getPSIID ( ) const

returns the PSI ID

◆ getXTandemID()

std::string getXTandemID ( ) const

returns the X! Tandem enzyme ID

◆ operator!=() [1/2]

bool operator!= ( const DigestionEnzymeProtein & enzyme ) const

inequality operator

◆ operator!=() [2/2]

bool operator!= ( const std::string & cleavage_regex ) const

equality operator for regex

◆ operator<()

bool operator< ( const DigestionEnzymeProtein & enzyme ) const

order operator

◆ operator=() [1/2]

DigestionEnzymeProtein & operator= ( const DigestionEnzymeProtein & )

default

Assignment operator.

◆ operator=() [2/2]

DigestionEnzymeProtein & operator= ( DigestionEnzymeProtein && ) &

default

Move assignment operator.

◆ operator==() [1/2]

bool operator== ( const DigestionEnzymeProtein & enzyme ) const

equality operator

◆ operator==() [2/2]

bool operator== ( const std::string & cleavage_regex ) const

equality operator for regex

◆ setCometID()

void setCometID ( Int value )

sets the Comet enzyme ID

◆ setCTermGain()

void setCTermGain ( const EmpiricalFormula & value )

sets the C-terminal gain

◆ setMSGFID()

void setMSGFID ( Int value )

sets the MSGFPlus enzyme id

◆ setNTermGain()

void setNTermGain ( const EmpiricalFormula & value )

sets the N-terminal gain

Accessors

◆ setOMSSAID()

void setOMSSAID ( Int value )

sets the OMSSA enzyme ID

◆ setPSIID()

void setPSIID ( const std::string & value )

sets the PSI ID

◆ 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.

◆ setXTandemID()

void setXTandemID ( const std::string & value )

sets the X! Tandem enzyme ID

Friends And Related Symbol Documentation

◆ operator<<

std::ostream & operator<<	(	std::ostream &	os,
		const DigestionEnzymeProtein &	enzyme
	)

friend

ostream iterator to write the enzyme to a stream

Member Data Documentation

◆ c_term_gain_

EmpiricalFormula c_term_gain_

protected

◆ comet_id_

Int comet_id_

protected

◆ msgf_id_

Int msgf_id_

protected

◆ n_term_gain_

EmpiricalFormula n_term_gain_

protected

◆ omssa_id_

Int omssa_id_

protected

◆ psi_id_

std::string psi_id_

protected

◆ xtandem_id_

std::string xtandem_id_

protected

Public Member Functions

Predicates

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DigestionEnzymeProtein() [1/5]

◆ DigestionEnzymeProtein() [2/5]

◆ DigestionEnzymeProtein() [3/5]

◆ DigestionEnzymeProtein() [4/5]

◆ DigestionEnzymeProtein() [5/5]

◆ ~DigestionEnzymeProtein()

Member Function Documentation

◆ getCometID()

◆ getCTermGain()

◆ getMSGFID()

◆ getNTermGain()

◆ getOMSSAID()

◆ getPSIID()

◆ getXTandemID()

◆ operator!=() [1/2]

◆ operator!=() [2/2]

◆ operator<()

◆ operator=() [1/2]

◆ operator=() [2/2]

◆ operator==() [1/2]

◆ operator==() [2/2]

◆ setCometID()

◆ setCTermGain()

◆ setMSGFID()

◆ setNTermGain()

◆ setOMSSAID()

◆ setPSIID()

◆ setValueFromFile()

◆ setXTandemID()

Friends And Related Symbol Documentation

◆ operator<<

Member Data Documentation

◆ c_term_gain_

◆ comet_id_

◆ msgf_id_

◆ n_term_gain_

◆ omssa_id_

◆ psi_id_

◆ xtandem_id_