| OpenMS 2.5.0

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

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

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

Inheritance diagram for DigestionEnzymeProtein:

## Public Member Functions

bool | setValueFromFile (const String &key, const String &value) override
| Set the value of a member variable based on an entry from an input file. More...
Constructors
| DigestionEnzymeProtein ()
| Default constructor. More...
| DigestionEnzymeProtein (const DigestionEnzymeProtein &)=default
| Copy constructor. More...
| DigestionEnzymeProtein (DigestionEnzymeProtein &&)=default
| Move constructor. More...
| DigestionEnzymeProtein (const String &name, const String &cleavage_regex, const std::set< String > &synonyms=std::set< String >(), String regex_description="", EmpiricalFormula n_term_gain=EmpiricalFormula("H"), EmpiricalFormula c_term_gain=EmpiricalFormula("OH"), String psi_id="", String xtandem_id="", Int comet_id=-1, String crux_id="", Int msgf_id=-1, Int omssa_id=-1)
| Detailed constructor. More...
| ~DigestionEnzymeProtein () override
| Destructor. More...
Assignment
DigestionEnzymeProtein & | operator= (const DigestionEnzymeProtein &)=default
| Assignment operator. More...
DigestionEnzymeProtein & | operator= (DigestionEnzymeProtein &&) &=default
| Move assignment operator. More...
void | setNTermGain (const EmpiricalFormula &value)
| sets the N-terminal gain More...
EmpiricalFormula | getNTermGain () const
| returns N-terminal gain More...
void | setCTermGain (const EmpiricalFormula &value)
| sets the C-terminal gain More...
EmpiricalFormula | getCTermGain () const
| returns C-terminal gain More...
void | setPSIID (const String &value)
| sets the PSI ID More...
String | getPSIID () const
| returns the PSI ID More...
void | setXTandemID (const String &value)
| sets the X! Tandem enzyme ID More...
String | getXTandemID () const
| returns the X! Tandem enzyme ID More...
Int | getCometID () const
| returns the Comet enzyme ID More...
void | setCometID (Int value)
| sets the Comet enzyme ID More...
String | getCruxID () const
| returns the Crux enzyme ID More...
void | setCruxID (const String &value)
| sets the Crux enzyme ID More...
void | setMSGFID (Int value)
| sets the MSGFPlus enzyme id More...
Int | getMSGFID () const
| returns the MSGFPlus enzyme id More...
void | setOMSSAID (Int value)
| sets the OMSSA enzyme ID More...
Int | getOMSSAID () const
| returns the OMSSA enzyme ID More...
Predicates
bool | operator== (const DigestionEnzymeProtein &enzyme) const
| equality operator More...
bool | operator!= (const DigestionEnzymeProtein &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 DigestionEnzymeProtein &enzyme) const
| order operator More...
Public Member Functions inherited from DigestionEnzyme
| 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...
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...
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 Attributes

EmpiricalFormula | n_term_gain_
EmpiricalFormula | c_term_gain_
String | psi_id_
String | xtandem_id_
Int | comet_id_
String | crux_id_
Int | msgf_id_
Int | omssa_id_
Protected Attributes inherited from DigestionEnzyme
String | name_
String | cleavage_regex_
std::set< String > | synonyms_
String | regex_description_

## Friends

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

## Additional Inherited Members

Protected Member Functions inherited from DigestionEnzyme
| DigestionEnzyme ()
| default constructor More...

## Detailed Description

Representation of a digestion enzyme for proteins (protease)

## Constructor & Destructor Documentation

## ◆ DigestionEnzymeProtein() [1/4]

DigestionEnzymeProtein | ( |  | ) |

Default constructor.

## ◆ DigestionEnzymeProtein() [2/4]

DigestionEnzymeProtein | ( | const DigestionEnzymeProtein & |  | ) |

default

Copy constructor.

## ◆ DigestionEnzymeProtein() [3/4]

DigestionEnzymeProtein | ( | DigestionEnzymeProtein && |  | ) |

default

Move constructor.

## ◆ DigestionEnzymeProtein() [4/4]

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

## ◆ getCruxID()

String getCruxID | ( |  | ) | const

returns the Crux 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()

String getPSIID | ( |  | ) | const

returns the PSI ID

## ◆ getXTandemID()

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 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 String & | cleavage_regex | ) | const

equality operator for regex

## ◆ setCometID()

void setCometID | ( | Int | value | ) |

sets the Comet enzyme ID

## ◆ setCruxID()

void setCruxID | ( | const String & | value | ) |

sets the Crux 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 String & | value | ) |

sets the PSI ID

## ◆ setValueFromFile()

bool setValueFromFile | ( | const String & | key,
|  | const String & | value
| ) |  |

override 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 from DigestionEnzyme.

## ◆ setXTandemID()

void setXTandemID | ( | const String & | value | ) |

sets the X! Tandem enzyme ID

## Friends And Related Function 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

## ◆ crux_id_

String crux_id_

protected

## ◆ msgf_id_

Int msgf_id_

protected

## ◆ n_term_gain_

EmpiricalFormula n_term_gain_

protected

## ◆ omssa_id_

Int omssa_id_

protected

## ◆ psi_id_

String psi_id_

protected

## ◆ xtandem_id_

String xtandem_id_

protected