Enzyme Class Reference

Representation of an enzyme. More...

#include <OpenMS/CHEMISTRY/Enzyme.h>

Public Member Functions
Constructors
	Enzyme (const Enzyme &enzyme)
	copy constructor More...
	Enzyme (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="", UInt comet_id=0, Int msgf_id=-1, UInt omssa_id=0)
	detailed constructor More...
virtual	~Enzyme ()
	destructor More...
Assignment
Enzyme &	operator= (const Enzyme &enzyme)
	assignment operator More...
void	setName (const String &name)
	sets the name of the enzyme More...
const 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 name as regex More...
const String &	getRegEx () const
	returns the name as regex More...
void	setRegExDescription (String value)
	sets the regex description More...
String	getRegExDescription () const
	returns the regex description More...
void	setNTermGain (EmpiricalFormula value)
	sets the N-terminal gain More...
EmpiricalFormula	getNTermGain () const
	returns N-terminal gain More...
void	setCTermGain (EmpiricalFormula value)
	sets the C-terminal gain More...
EmpiricalFormula	getCTermGain () const
	returns C-terminal gain More...
void	setPSIID (String value)
	sets the PSI ID More...
String	getPSIID () const
	returns the PSI ID More...
void	setXTandemID (String value)
	sets the X! Tandem enzyme ID More...
String	getXTandemID () const
	returns the X! Tandem enzyme ID More...
UInt	getCometID () const
	returns the Comet enzyme ID More...
void	setCometID (UInt value)
	sets the Comet enzyme ID More...
void	setMSGFID (Int value)
	sets the MSGFPlus enzyme id More...
Int	getMSGFID () const
	returns the MSGFPlus enzyme id More...
void	setOMSSAID (UInt value)
	sets the OMSSA enzyme ID More...
UInt	getOMSSAID () const
	returns the OMSSA enzyme ID More...
Predicates
bool	operator== (const Enzyme &enzyme) const
	equality operator More...
bool	operator!= (const Enzyme &enzyme) const
	inequality operator More...
bool	operator== (String cleavage_regex) const
	equality operator for regex More...
bool	operator!= (String cleavage_regex) const
	equality operator for regex More...
bool	operator< (const Enzyme &enzyme) const
	order operator More...

Protected Member Functions
	Enzyme ()
	default constructor More...

Protected Attributes
String	name_
String	cleavage_regex_
std::set< String >	synonyms_
String	regex_description_
EmpiricalFormula	n_term_gain_
EmpiricalFormula	c_term_gain_
String	psi_id_
String	xtandem_id_
UInt	comet_id_
Int	msgf_id_
UInt	omssa_id_

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

Detailed Description

Representation of an enzyme.

This class represents enzymes.

Constructor & Destructor Documentation

Enzyme() [1/3]

Enzyme

(

const Enzyme &

enzyme

)

copy constructor

Enzyme() [2/3]

Enzyme ( 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 = "", UInt  comet_id = 0, Int  msgf_id = -1, UInt  omssa_id = 0  )

explicit

detailed constructor

~Enzyme()

virtual ~Enzyme ( )

virtual

destructor

Enzyme() [3/3]

Enzyme ( )

protected

default constructor

Member Function Documentation

addSynonym()

void addSynonym

(

const String &

synonym

)

adds a synonym

getCometID()

UInt getCometID

(

)

const

returns the Comet enzyme ID

getCTermGain()

EmpiricalFormula getCTermGain

(

)

const

returns C-terminal gain

getMSGFID()

Int getMSGFID

(

)

const

returns the MSGFPlus enzyme id

getName()

const String& getName

(

)

const

returns the name of the enzyme

getNTermGain()

EmpiricalFormula getNTermGain

(

)

const

returns N-terminal gain

getOMSSAID()

UInt getOMSSAID

(

)

const

returns the OMSSA enzyme ID

getPSIID()

String getPSIID

(

)

const

returns the PSI ID

getRegEx()

const String& getRegEx

(

)

const

returns the name as regex

getRegExDescription()

String getRegExDescription

(

)

const

returns the regex description

getSynonyms()

const std::set<String>& getSynonyms

(

)

const

returns the synonyms

getXTandemID()

String getXTandemID

(

)

const

returns the X! Tandem enzyme ID

operator!=() [1/2]

bool operator!=

(

const Enzyme &

enzyme

)

const

inequality operator

operator!=() [2/2]

bool operator!=

(

String

cleavage_regex

)

const

equality operator for regex

operator<()

bool operator<

(

const Enzyme &

enzyme

)

const

order operator

operator=()

Enzyme& operator=

(

const Enzyme &

enzyme

)

assignment operator

operator==() [1/2]

bool operator==

(

const Enzyme &

enzyme

)

const

equality operator

operator==() [2/2]

bool operator==

(

String

cleavage_regex

)

const

equality operator for regex

setCometID()

void setCometID

(

UInt

value

)

sets the Comet enzyme ID

setCTermGain()

void setCTermGain

(

EmpiricalFormula

value

)

sets the C-terminal gain

setMSGFID()

void setMSGFID

(

Int

value

)

sets the MSGFPlus enzyme id

setName()

void setName

(

const String &

name

)

sets the name of the enzyme

Accessors

setNTermGain()

void setNTermGain

(

EmpiricalFormula

value

)

sets the N-terminal gain

setOMSSAID()

void setOMSSAID

(

UInt

value

)

sets the OMSSA enzyme ID

setPSIID()

void setPSIID

(

String

value

)

sets the PSI ID

setRegEx()

void setRegEx

(

const String &

cleavage_regex

)

sets the name as regex

setRegExDescription()

void setRegExDescription

(

String

value

)

sets the regex description

setSynonyms()

void setSynonyms

(

const std::set< String > &

synonyms

)

sets the synonyms

setXTandemID()

void setXTandemID

(

String

value

)

sets the X! Tandem enzyme ID

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  os, const Enzyme &  enzyme  )

friend

ostream iterator to write the enzyme to a stream

Member Data Documentation

c_term_gain_

EmpiricalFormula c_term_gain_

protected

cleavage_regex_

String cleavage_regex_

protected

comet_id_

UInt comet_id_

protected

msgf_id_

Int msgf_id_

protected

n_term_gain_

EmpiricalFormula n_term_gain_

protected

name_

String name_

protected

omssa_id_

UInt omssa_id_

protected

psi_id_

String psi_id_

protected

regex_description_

String regex_description_

protected

synonyms_

std::set<String> synonyms_

protected

xtandem_id_

String xtandem_id_

protected