OpenMS  2.8.0
Public Member Functions | Protected Member Functions | Friends | List of all members
ProteaseDB Class Reference

Database for enzymes that digest proteins (proteases) More...

#include <OpenMS/CHEMISTRY/ProteaseDB.h>

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

void getAllXTandemNames (std::vector< String > &all_names) const
 returns all the enzyme names available for XTandem More...
 
void getAllCometNames (std::vector< String > &all_names) const
 returns all the enzyme names available for Comet More...
 
void getAllCruxNames (std::vector< String > &all_names) const
 returns all the enzyme names available for Crux More...
 
void getAllOMSSANames (std::vector< String > &all_names) const
 returns all the enzyme names available for OMSSA More...
 
void getAllMSGFNames (std::vector< String > &all_names) const
 returns all the enzyme names available for MSGFPlus More...
 
void writeTSV (const String &filename)
 writes the full names to a TSV file More...
 
- Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
virtual ~DigestionEnzymeDB ()
 destructor More...
 
const DigestionEnzymeProteingetEnzyme (const String &name) const
 
const DigestionEnzymeProteingetEnzymeByRegEx (const String &cleavage_regex) const
 
void getAllNames (std::vector< String > &all_names) const
 returns all the enzyme names (does NOT include synonym names) More...
 
bool hasEnzyme (const String &name) const
 returns true if the db contains a enzyme with the given name (supports synonym names) More...
 
bool hasEnzyme (const DigestionEnzymeProtein *enzyme) const
 returns true if the db contains the enzyme of the given pointer More...
 
bool hasRegEx (const String &cleavage_regex) const
 returns true if the db contains a enzyme with the given regex More...
 
ConstEnzymeIterator beginEnzyme () const
 
ConstEnzymeIterator endEnzyme () const
 

Protected Member Functions

 ProteaseDB ()
 constructor More...
 
- Protected Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
DigestionEnzymeDBoperator= (const DigestionEnzymeDB &enzymes_db)=delete
 assignment operator More...
 
void readEnzymesFromFile_ (const String &filename)
 reads enzymes from the given file More...
 
const DigestionEnzymeProteinparseEnzyme_ (Map< String, String > &values) const
 parses an enzyme, given the key/value pairs from an XML file More...
 
void addEnzyme_ (const DigestionEnzymeProtein *enzyme)
 add to internal data; also update indices for search by name and regex More...
 
 DigestionEnzymeDB (const String &db_file="")
 
 DigestionEnzymeDB (const DigestionEnzymeDB &enzymes_db)=delete
 copy constructor More...
 

Friends

class DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
 

Additional Inherited Members

- Public Types inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
typedef std::set< const DigestionEnzymeProtein * >::const_iterator ConstEnzymeIterator
 
typedef std::set< const DigestionEnzymeProtein * >::iterator EnzymeIterator
 
- Static Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
static ProteaseDBgetInstance ()
 this member function serves as a replacement of the constructor More...
 
- Protected Attributes inherited from DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >
Map< String, const DigestionEnzymeProtein * > enzyme_names_
 index by names More...
 
Map< String, const DigestionEnzymeProtein * > enzyme_regex_
 index by regex More...
 
std::set< const DigestionEnzymeProtein * > const_enzymes_
 set of enzymes More...
 

Detailed Description

Database for enzymes that digest proteins (proteases)

The enzymes stored in this DB are defined in an XML file under share/CHEMISTRY/Enzymes.xml.

Constructor & Destructor Documentation

◆ ProteaseDB()

ProteaseDB ( )
protected

constructor

Member Function Documentation

◆ getAllCometNames()

void getAllCometNames ( std::vector< String > &  all_names) const

returns all the enzyme names available for Comet

◆ getAllCruxNames()

void getAllCruxNames ( std::vector< String > &  all_names) const

returns all the enzyme names available for Crux

◆ getAllMSGFNames()

void getAllMSGFNames ( std::vector< String > &  all_names) const

returns all the enzyme names available for MSGFPlus

◆ getAllOMSSANames()

void getAllOMSSANames ( std::vector< String > &  all_names) const

returns all the enzyme names available for OMSSA

◆ getAllXTandemNames()

void getAllXTandemNames ( std::vector< String > &  all_names) const

returns all the enzyme names available for XTandem

◆ writeTSV()

void writeTSV ( const String filename)

writes the full names to a TSV file

Friends And Related Function Documentation

◆ DigestionEnzymeDB< DigestionEnzymeProtein, ProteaseDB >