| OpenMS 2.5.0

Public Member Functions | Protected Member Functions | Protected Attributes | Friends | List of all members
DigestionEnzyme Class Reference
Chemistry

Abstract base class for digestion enzymes. More...

`#include <OpenMS/CHEMISTRY/DigestionEnzyme.h>`

Inheritance diagram for DigestionEnzyme:

## Public Member Functions

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...
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...
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
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...

## Protected Member Functions

| DigestionEnzyme ()
| default constructor More...

## Protected Attributes

String | name_
String | cleavage_regex_
std::set< String > | synonyms_
String | regex_description_

## Friends

std::ostream & | operator<< (std::ostream &os, const DigestionEnzyme &enzyme)
| ostream iterator to write the enzyme to a stream More...

## Detailed Description

Abstract base class for digestion enzymes.

## Constructor & Destructor Documentation

## ◆ DigestionEnzyme() [1/4]

DigestionEnzyme | ( | const DigestionEnzyme & |  | ) |

default

Copy constructor.

## ◆ DigestionEnzyme() [2/4]

DigestionEnzyme | ( | DigestionEnzyme && |  | ) |

default

Move constructor.

## ◆ DigestionEnzyme() [3/4]

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

explicit

Detailed constructor.

## ◆ ~DigestionEnzyme()

virtual ~DigestionEnzyme | ( |  | ) |

virtual

Destructor.

## ◆ DigestionEnzyme() [4/4]

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