OpenMS  2.6.0
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DigestionEnzyme Class Reference

Abstract base class for digestion enzymes. More...

#include <OpenMS/CHEMISTRY/DigestionEnzyme.h>

Inheritance diagram for DigestionEnzyme:
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Collaboration diagram for DigestionEnzyme:
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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
DigestionEnzymeoperator= (const DigestionEnzyme &)=default
 Assignment operator. More...
 
DigestionEnzymeoperator= (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< Stringsynonyms_
 
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