DigestionEnzyme Class Reference

Abstract 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. 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...
Assignment
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...

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

Detailed Description

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

explicit

Detailed constructor.

DigestionEnzyme() [4/5]

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 = ""  )

explicit

Detailed constructor 2.

~DigestionEnzyme()

virtual ~DigestionEnzyme ( )

virtual

Destructor.

DigestionEnzyme() [5/5]

DigestionEnzyme ( )

protected

default constructor

Member Function Documentation

addSynonym()

void addSynonym

(

const String &

synonym

)

adds a synonym

getName()

String getName

(

)

const

returns the name of the enzyme

getRegEx()

String getRegEx

(

)

const

returns the cleavage regex

getRegExDescription()

String getRegExDescription

(

)

const

returns the regex description

getSynonyms()

const std::set<String>& getSynonyms

(

)

const

returns the synonyms

operator!=() [1/2]

bool operator!=

(

const DigestionEnzyme &

enzyme

)

const

inequality operator

operator!=() [2/2]

bool operator!=

(

const 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 String &

cleavage_regex

)

const

equality operator for regex

setName()

void setName

(

const String &

name

)

sets the name of the enzyme

Accessors

setRegEx()

void setRegEx

(

const String &

cleavage_regex

)

sets the cleavage regex

setRegExDescription()

void setRegExDescription

(

const String &

value

)

sets the regex description

setSynonyms()

void setSynonyms

(

const std::set< String > &

synonyms

)

sets the synonyms

setValueFromFile()

virtual bool setValueFromFile ( const String &  key, const 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 Function 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_

String cleavage_regex_

protected

name_

String name_

protected

regex_description_

String regex_description_

protected

synonyms_

std::set<String> synonyms_

protected