#include <OpenMS/CHEMISTRY/ResidueDB.h>
The residues stored in this DB are defined in a XML file under data/CHEMISTRY/residues.xml
Public Types | |
Typedefs | |
typedef std::set< Residue * > ::iterator | ResidueIterator |
typedef std::set< const Residue * >::const_iterator | ResidueConstIterator |
typedef std::set < ResidueModification * > ::iterator | ResidueModificationIterator |
typedef std::set< const ResidueModification * > ::const_iterator | ResidueModificationConstIterator |
Public Member Functions | |
Constructors and Destructors | |
ResidueDB () | |
default constructor | |
ResidueDB (const ResidueDB &residue_db) | |
copy constructor | |
ResidueDB (const String &res_filename, const String &mod_filename) throw (Exception::FileNotFound, Exception::ParseError) | |
constructor with filename where the residues are stored in | |
virtual | ~ResidueDB () |
destructor | |
Assignment | |
ResidueDB & | operator= (const ResidueDB &aa) |
assignment operator | |
Accessors | |
UInt | getNumberOfResidues () const |
returns the number of residues stored | |
UInt | getNumberOfResidueModifications () const |
returns the number of modifications stored in this residue db | |
const ResidueModification * | getModification (const String &name) const |
resturns a pointer to modification with name name, if non is found 0 is returned | |
std::set< const ResidueModification * > | getModifications (const Residue *residue) const |
returns a set of modifications which can be applied to the given residue | |
std::set< const ResidueModification * > | getModifications (const String &res_name) const |
returns a set of modifications which can be applied to the given residue | |
const std::set< const ResidueModification * > & | getModifications () const |
returns a set of all modifications stored in this residue db | |
const Residue * | getResidue (const String &name) const |
returns a pointer to the residue with name, 3 letter code or 1 letter code name | |
std::set< const Residue * > | getResidues (const ResidueModification *modification) const |
returns a set of residues which can have the given modification | |
std::set< const Residue * > | getResidues (const String &mod_name) const |
returns a set of residues which can have the given modification | |
const std::set< const Residue * > & | getResidues () const |
returns a set of all residues stored in this residue db | |
void | setModifications (const String &filename) throw (Exception::FileNotFound, Exception::ParseError) |
sets the modifications from given file | |
void | addResidueModification (ResidueModification modification) |
adds a modification, i.e. an unknown modification, where only the weights are known | |
void | setResidues (const String &filename) throw (Exception::FileNotFound, Exception::ParseError) |
sets the residues from given file | |
void | addResidue (const Residue &residue) |
adds a residue, i.e. a unkown residue, where only the weight is known | |
Predicates | |
bool | hasResidueModification (const String &name) const |
returns true if the db contains a modification with the given name | |
bool | hasResidue (const String &name) const |
returns true if the db contains a residue with the given name | |
bool | operator== (const ResidueDB &rhs) const |
equality operator | |
bool | operator!= (const ResidueDB &rhs) const |
inequality operator | |
Iterators | |
ResidueIterator | beginResidue () |
ResidueIterator | endResidue () |
ResidueConstIterator | beginResidue () const |
ResidueConstIterator | endResidue () const |
ResidueModificationIterator | beginResidueModification () |
ResidueModificationIterator | endResidueModification () |
ResidueModificationConstIterator | beginResidueModification () const |
ResidueModificationConstIterator | endResidueModification () const |
Protected Member Functions | |
void | readResiduesFromFile_ (const String &filename) throw (Exception::FileNotFound, Exception::ParseError) |
Residue * | parseResidue_ (HashMap< String, String > &values) throw () |
void | readResidueModificationsFromFile_ (const String &filename) throw (Exception::FileNotFound, Exception::ParseError) |
void | clear_ () |
void | clearResidues_ () |
void | clearResidueModifications_ () |
void | buildResidueNames_ () |
void | buildResidueModificationNames_ () |
void | buildModifiedResidues_ () |
Protected Attributes | |
HashMap< String, Residue * > | residue_names_ |
std::set< Residue * > | residues_ |
std::set< const Residue * > | const_residues_ |
HashMap< String, ResidueModification * > | modification_names_ |
std::set< ResidueModification * > | modifications_ |
std::set< const ResidueModification * > | const_modifications_ |
typedef std::set<Residue*>::iterator ResidueIterator |
typedef std::set<const Residue*>::const_iterator ResidueConstIterator |
typedef std::set<ResidueModification*>::iterator ResidueModificationIterator |
typedef std::set<const ResidueModification*>::const_iterator ResidueModificationConstIterator |
ResidueDB | ( | ) |
default constructor
ResidueDB | ( | const String & | res_filename, | |
const String & | mod_filename | |||
) | throw (Exception::FileNotFound, Exception::ParseError) |
constructor with filename where the residues are stored in
virtual ~ResidueDB | ( | ) | [virtual] |
destructor
UInt getNumberOfResidues | ( | ) | const |
returns the number of residues stored
UInt getNumberOfResidueModifications | ( | ) | const |
returns the number of modifications stored in this residue db
const ResidueModification* getModification | ( | const String & | name | ) | const |
resturns a pointer to modification with name name, if non is found 0 is returned
std::set<const ResidueModification*> getModifications | ( | const Residue * | residue | ) | const |
returns a set of modifications which can be applied to the given residue
std::set<const ResidueModification*> getModifications | ( | const String & | res_name | ) | const |
returns a set of modifications which can be applied to the given residue
const std::set<const ResidueModification*>& getModifications | ( | ) | const |
returns a set of all modifications stored in this residue db
returns a pointer to the residue with name, 3 letter code or 1 letter code name
std::set<const Residue*> getResidues | ( | const ResidueModification * | modification | ) | const |
returns a set of residues which can have the given modification
returns a set of residues which can have the given modification
const std::set<const Residue*>& getResidues | ( | ) | const |
returns a set of all residues stored in this residue db
void setModifications | ( | const String & | filename | ) | throw (Exception::FileNotFound, Exception::ParseError) |
sets the modifications from given file
void addResidueModification | ( | ResidueModification | modification | ) |
adds a modification, i.e. an unknown modification, where only the weights are known
void setResidues | ( | const String & | filename | ) | throw (Exception::FileNotFound, Exception::ParseError) |
sets the residues from given file
void addResidue | ( | const Residue & | residue | ) |
adds a residue, i.e. a unkown residue, where only the weight is known
bool hasResidueModification | ( | const String & | name | ) | const |
returns true if the db contains a modification with the given name
bool hasResidue | ( | const String & | name | ) | const |
returns true if the db contains a residue with the given name
bool operator== | ( | const ResidueDB & | rhs | ) | const |
equality operator
bool operator!= | ( | const ResidueDB & | rhs | ) | const |
inequality operator
ResidueIterator beginResidue | ( | ) | [inline] |
ResidueIterator endResidue | ( | ) | [inline] |
ResidueConstIterator beginResidue | ( | ) | const [inline] |
ResidueConstIterator endResidue | ( | ) | const [inline] |
ResidueModificationIterator beginResidueModification | ( | ) | [inline] |
ResidueModificationIterator endResidueModification | ( | ) | [inline] |
ResidueModificationConstIterator beginResidueModification | ( | ) | const [inline] |
ResidueModificationConstIterator endResidueModification | ( | ) | const [inline] |
void readResiduesFromFile_ | ( | const String & | filename | ) | throw (Exception::FileNotFound, Exception::ParseError) [protected] |
void readResidueModificationsFromFile_ | ( | const String & | filename | ) | throw (Exception::FileNotFound, Exception::ParseError) [protected] |
void clear_ | ( | ) | [protected] |
void clearResidues_ | ( | ) | [protected] |
void clearResidueModifications_ | ( | ) | [protected] |
void buildResidueNames_ | ( | ) | [protected] |
void buildResidueModificationNames_ | ( | ) | [protected] |
void buildModifiedResidues_ | ( | ) | [protected] |
HashMap<String, Residue*> residue_names_ [protected] |
std::set<const Residue*> const_residues_ [protected] |
HashMap<String, ResidueModification*> modification_names_ [protected] |
std::set<ResidueModification*> modifications_ [protected] |
std::set<const ResidueModification*> const_modifications_ [protected] |
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |