OpenMS
2.4.0
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Digestion enzyme database (base class) More...
#include <OpenMS/CHEMISTRY/DigestionEnzymeDB.h>
Public Types | |
Typedefs | |
typedef std::set< const DigestionEnzymeType * >::const_iterator | ConstEnzymeIterator |
typedef std::set< const DigestionEnzymeType * >::iterator | EnzymeIterator |
Public Member Functions | |
Constructors and Destructors | |
virtual | ~DigestionEnzymeDB () |
destructor More... | |
Accessors | |
const DigestionEnzymeType * | getEnzyme (const String &name) const |
const DigestionEnzymeType * | 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... | |
Predicates | |
bool | hasEnzyme (const String &name) const |
returns true if the db contains a enzyme with the given name (supports synonym names) More... | |
bool | hasRegEx (const String &cleavage_regex) const |
returns true if the db contains a enzyme with the given regex More... | |
bool | hasEnzyme (const DigestionEnzymeType *enzyme) const |
returns true if the db contains the enzyme of the given pointer More... | |
Iterators | |
ConstEnzymeIterator | beginEnzyme () const |
ConstEnzymeIterator | endEnzyme () const |
Static Public Member Functions | |
static InstanceType * | getInstance () |
this member function serves as a replacement of the constructor More... | |
Protected Member Functions | |
DigestionEnzymeDB (const String &db_file="") | |
DigestionEnzymeDB (const DigestionEnzymeDB &enzymes_db)=delete | |
copy constructor More... | |
void | readEnzymesFromFile_ (const String &filename) |
reads enzymes from the given file More... | |
const DigestionEnzymeType * | parseEnzyme_ (Map< String, String > &values) const |
parses an enzyme, given the key/value pairs from an XML file More... | |
void | addEnzyme_ (const DigestionEnzymeType *enzyme) |
Assignment | |
DigestionEnzymeDB & | operator= (const DigestionEnzymeDB &enzymes_db)=delete |
assignment operator More... | |
Protected Attributes | |
boost::unordered_map< String, const DigestionEnzymeType * > | enzyme_names_ |
Map< String, const DigestionEnzymeType * > | enzyme_regex_ |
std::set< const DigestionEnzymeType * > | const_enzymes_ |
Digestion enzyme database (base class)
Template parameters: DigestionEnzymeType
should be a subclass of DigestionEnzyme. InstanceType
should be a subclass of DigestionEnzymeDB ("Curiously Recurring Template Pattern", see https://stackoverflow.com/a/34519373).
typedef std::set<const DigestionEnzymeType*>::const_iterator ConstEnzymeIterator |
typedef std::set<const DigestionEnzymeType*>::iterator EnzymeIterator |
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destructor
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inlineprotected |
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protecteddelete |
copy constructor
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inlineprotected |
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inline |
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returns all the enzyme names (does NOT include synonym names)
Referenced by SimpleSearchEngine::registerOptionsAndFlags_(), and RNPxlSearch::registerOptionsAndFlags_().
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returns a pointer to the enzyme with name (supports synonym names)
Exception::ElementNotFound | if enzyme is unknown |
Referenced by SimpleSearchEngine::postProcessHits_(), and RNPxlSearch::postProcessHits_().
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returns a pointer to the enzyme with cleavage regex
Exception::IllegalArgument | if enzyme regex is unregistered. |
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inlinestatic |
this member function serves as a replacement of the constructor
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inline |
returns true if the db contains a enzyme with the given name (supports synonym names)
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returns true if the db contains the enzyme of the given pointer
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inline |
returns true if the db contains a enzyme with the given regex
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protecteddelete |
assignment operator
parses an enzyme, given the key/value pairs from an XML file
Referenced by DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::readEnzymesFromFile_().
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inlineprotected |
reads enzymes from the given file
Referenced by DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::DigestionEnzymeDB().
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Referenced by DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::addEnzyme_(), DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::beginEnzyme(), DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::endEnzyme(), DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::getAllNames(), and DigestionEnzymeDB< DigestionEnzymeRNA, RNaseDB >::hasEnzyme().
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