OpenMS
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Database for enzymes that digest RNA (RNases) More...
#include <OpenMS/CHEMISTRY/RNaseDB.h>
Protected Member Functions | |
RNaseDB () | |
constructor More... | |
Protected Member Functions inherited from DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB > | |
DigestionEnzymeDB & | operator= (const DigestionEnzymeDB &enzymes_db)=delete |
assignment operator More... | |
void | readEnzymesFromFile_ (const String &filename) |
reads enzymes from the given file More... | |
const DigestionEnzymeRNA * | parseEnzyme_ (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 DigestionEnzymeRNA * | getEnzyme (const String &name) const |
const DigestionEnzymeRNA * | getEnzymeByRegEx (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 RNaseDB * | getInstance () |
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... | |
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".
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