OpenMS  2.8.0
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DigestionEnzymeProtein Class Reference

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

#include <OpenMS/CHEMISTRY/DigestionEnzymeProtein.h>

Inheritance diagram for DigestionEnzymeProtein:
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Collaboration diagram for DigestionEnzymeProtein:
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Public Member Functions

Constructors
 DigestionEnzymeProtein ()
 Default constructor. More...
 
 DigestionEnzymeProtein (const DigestionEnzyme &d)
 Constructor from base class (adding defaults for the missing stuff) 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
DigestionEnzymeProteinoperator= (const DigestionEnzymeProtein &)=default
 Assignment operator. More...
 
DigestionEnzymeProteinoperator= (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...
 
void setCometID (Int value)
 sets the Comet enzyme ID More...
 
Int getCometID () const
 returns the Comet enzyme ID More...
 
void setCruxID (const String &value)
 sets the Crux enzyme ID More...
 
String getCruxID () const
 returns 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...
 
- 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...
 
 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...
 
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...
 
const StringgetName () 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...
 
const StringgetRegEx () const
 returns the cleavage regex More...
 
void setRegExDescription (const String &value)
 sets the regex description More...
 
const StringgetRegExDescription () 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...
 

Predicates

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_
 
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...
 
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...
 
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...
 
- Protected Attributes inherited from DigestionEnzyme
String name_
 
String cleavage_regex_
 
std::set< Stringsynonyms_
 
String regex_description_
 

Detailed Description

Representation of a digestion enzyme for proteins (protease)

Constructor & Destructor Documentation

◆ DigestionEnzymeProtein() [1/5]

Default constructor.

◆ DigestionEnzymeProtein() [2/5]

DigestionEnzymeProtein ( const DigestionEnzyme d)
explicit

Constructor from base class (adding defaults for the missing stuff)

◆ DigestionEnzymeProtein() [3/5]

Copy constructor.

◆ DigestionEnzymeProtein() [4/5]

Move constructor.

◆ DigestionEnzymeProtein() [5/5]

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 
)
overridevirtual

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