DigestionEnzyme Class Reference

Base class for digestion enzymes. More...

#include <OpenMS/CHEMISTRY/DigestionEnzyme.h>

Inheritance diagram for DigestionEnzyme:

Collaboration diagram for DigestionEnzyme:

Public Member Functions
Constructors
	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.
Assignment
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

Predicates
std::string	name_
std::string	cleavage_regex_
std::set< std::string >	synonyms_
std::string	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
virtual bool	setValueFromFile (const std::string &key, const std::string &value)
	Set the value of a member variable based on an entry from an input file.
std::ostream &	operator<< (std::ostream &os, const DigestionEnzyme &enzyme)
	ostream iterator to write the enzyme to a stream
	DigestionEnzyme ()
	default constructor

Detailed Description

Base class for digestion enzymes.

Constructor & Destructor Documentation

DigestionEnzyme() [1/5]

DigestionEnzyme ( const DigestionEnzyme &  )

default

Copy constructor.

DigestionEnzyme() [2/5]

DigestionEnzyme ( DigestionEnzyme &&  )

default

Move constructor.

DigestionEnzyme() [3/5]

DigestionEnzyme ( const std::string &  name, const std::string &  cleavage_regex, const std::set< std::string > &  synonyms = std::set< std::string >(), std::string  regex_description = ""  )

explicit

Detailed constructor.

DigestionEnzyme() [4/5]

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 = ""  )

explicit

Detailed constructor 2.

~DigestionEnzyme()

virtual ~DigestionEnzyme ( )

virtual

Destructor.

DigestionEnzyme() [5/5]

DigestionEnzyme ( )

protected

default constructor

Member Function Documentation

addSynonym()

void addSynonym

(

const std::string &

synonym

)

adds a synonym

getName()

const std::string & getName

(

)

const

returns the name of the enzyme

getRegEx()

const std::string & getRegEx

(

)

const

returns the cleavage regex

getRegExDescription()

const std::string & getRegExDescription

(

)

const

returns the regex description

getSynonyms()

const std::set< std::string > & getSynonyms

(

)

const

returns the synonyms

operator!=() [1/2]

bool operator!=

(

const DigestionEnzyme &

enzyme

)

const

inequality operator

operator!=() [2/2]

bool operator!=

(

const std::string &

cleavage_regex

)

const

equality operator for regex

operator<()

bool operator<

(

const DigestionEnzyme &

enzyme

)

const

order operator

operator=() [1/2]

DigestionEnzyme & operator= ( const DigestionEnzyme &  )

default

Assignment operator.

operator=() [2/2]

DigestionEnzyme & operator= ( DigestionEnzyme &&  ) &

default

Move assignment operator.

operator==() [1/2]

bool operator==

(

const DigestionEnzyme &

enzyme

)

const

equality operator

operator==() [2/2]

bool operator==

(

const std::string &

cleavage_regex

)

const

equality operator for regex

setName()

void setName

(

const std::string &

name

)

sets the name of the enzyme

Accessors

setRegEx()

void setRegEx

(

const std::string &

cleavage_regex

)

sets the cleavage regex

setRegExDescription()

void setRegExDescription

(

const std::string &

value

)

sets the regex description

setSynonyms()

void setSynonyms

(

const std::set< std::string > &

synonyms

)

sets the synonyms

setValueFromFile()

virtual bool setValueFromFile ( const std::string &  key, const std::string &  value  )

virtual

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 in DigestionEnzymeProtein, and DigestionEnzymeRNA.

Friends And Related Symbol Documentation

operator<<

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

friend

ostream iterator to write the enzyme to a stream

Member Data Documentation

cleavage_regex_

std::string cleavage_regex_

protected

name_

std::string name_

protected

regex_description_

std::string regex_description_

protected

synonyms_

std::set<std::string> synonyms_

protected