OpenMS
RNaseDB Class Reference

Database for enzymes that digest RNA (RNases) More...

#include <OpenMS/CHEMISTRY/RNaseDB.h>

Inheritance diagram for RNaseDB:
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Collaboration diagram for RNaseDB:
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Protected Member Functions

 RNaseDB ()
 constructor More...
 
- Protected Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
DigestionEnzymeDBoperator= (const DigestionEnzymeDB &enzymes_db)=delete
 assignment operator More...
 
void readEnzymesFromFile_ (const String &filename)
 reads enzymes from the given file More...
 
const DigestionEnzymeRNAparseEnzyme_ (std::map< String, String > &values) const
 parses an enzyme, given the key/value pairs from an XML file More...
 
void addEnzyme_ (const DigestionEnzymeRNA *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< DigestionEnzymeRNA, RNaseDB >
 

Additional Inherited Members

- Public Types inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
typedef std::set< const DigestionEnzymeRNA * >::const_iterator ConstEnzymeIterator
 
typedef std::set< const DigestionEnzymeRNA * >::iterator EnzymeIterator
 
- Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
virtual ~DigestionEnzymeDB ()
 destructor More...
 
const DigestionEnzymeRNAgetEnzyme (const String &name) const
 
const DigestionEnzymeRNAgetEnzymeByRegEx (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 DigestionEnzymeRNA *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
 
- Static Public Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
static RNaseDBgetInstance ()
 this member function serves as a replacement of the constructor More...
 
- Protected Attributes inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
std::map< String, const DigestionEnzymeRNA * > enzyme_names_
 index by names More...
 
std::map< String, const DigestionEnzymeRNA * > enzyme_regex_
 index by regex More...
 
std::set< const DigestionEnzymeRNA * > const_enzymes_
 set of enzymes More...
 

Detailed Description

Database for enzymes that digest RNA (RNases)

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

Constructor & Destructor Documentation

◆ RNaseDB()

RNaseDB ( )
protected

constructor

Friends And Related Function Documentation

◆ DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >

friend class DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >
friend