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ResidueDB Class Reference

residue data base which holds residues More...

#include <OpenMS/CHEMISTRY/ResidueDB.h>

Public Types

Typedefs
typedef std::set< Residue * >::iterator ResidueIterator
 
typedef std::set< const Residue * >::const_iterator ResidueConstIterator
 

Public Member Functions

Constructors and Destructors
virtual ~ResidueDB ()
 destructor More...
 
Accessors
Size getNumberOfResidues () const
 returns the number of residues stored More...
 
Size getNumberOfModifiedResidues () const
 
const ResiduegetResidue (const String &name) const
 returns a pointer to the residue with name, 3 letter code or 1 letter code name More...
 
const ResiduegetResidue (const unsigned char &one_letter_code) const
 returns a pointer to the residue with 1 letter code name More...
 
const ResiduegetModifiedResidue (const String &name)
 
const ResiduegetModifiedResidue (const Residue *residue, const String &name)
 
const std::set< const Residue * > getResidues (const String &residue_set="All") const
 returns a set of all residues stored in this residue db More...
 
const std::set< String > & getResidueSets () const
 returns all residue sets that are registered which this instance More...
 
void setResidues (const String &filename)
 sets the residues from given file More...
 
void addResidue (const Residue &residue)
 adds a residue, i.e. a unknown residue, where only the weight is known More...
 
Predicates
bool hasResidue (const String &name) const
 returns true if the db contains a residue with the given name More...
 
bool hasResidue (const Residue *residue) const
 returns true if the db contains the residue of the given pointer More...
 
Iterators
ResidueIterator beginResidue ()
 
ResidueIterator endResidue ()
 
ResidueConstIterator beginResidue () const
 
ResidueConstIterator endResidue () const
 

Static Public Member Functions

static ResidueDBgetInstance ()
 this member function serves as a replacement of the constructor More...
 

Protected Member Functions

void readResiduesFromFile_ (const String &filename)
 reads residues from the given file More...
 
ResidueparseResidue_ (Map< String, String > &values)
 parses a residue, given the key/value pairs from i.e. an XML file More...
 
void clear_ ()
 deletes all sub-instances of the stored data like modifications and residues More...
 
void clearResidues_ ()
 clears the residues More...
 
void buildResidueNames_ ()
 builds an index of residue names for fast access, synonyms are also considered More...
 
void addResidue_ (Residue *residue)
 
Private Constructors
 ResidueDB ()
 default constructor More...
 
 ResidueDB (const ResidueDB &residue_db)
 copy constructor More...
 
Assignment
ResidueDBoperator= (const ResidueDB &aa)
 assignment operator More...
 

Protected Attributes

boost::unordered_map< String, Residue * > residue_names_
 
Residueresidue_by_one_letter_code_ [256]
 
Map< String, Map< String, Residue * > > residue_mod_names_
 
std::set< Residue * > residues_
 
std::set< const Residue * > const_residues_
 
std::set< Residue * > modified_residues_
 
std::set< const Residue * > const_modified_residues_
 
Map< String, std::set< const Residue * > > residues_by_set_
 
std::set< Stringresidue_sets_
 

Detailed Description

residue data base which holds residues

The residues stored in this DB are defined in a XML file under data/CHEMISTRY/residues.xml

By default no modified residues are stored in an instance. However, if one queries the instance with getModifiedResidue, a new modified residue is added.

Member Typedef Documentation

typedef std::set<const Residue *>::const_iterator ResidueConstIterator
typedef std::set<Residue *>::iterator ResidueIterator

Constructor & Destructor Documentation

virtual ~ResidueDB ( )
virtual

destructor

ResidueDB ( )
protected

default constructor

ResidueDB ( const ResidueDB residue_db)
protected

copy constructor

Member Function Documentation

void addResidue ( const Residue residue)

adds a residue, i.e. a unknown residue, where only the weight is known

void addResidue_ ( Residue residue)
protected
ResidueIterator beginResidue ( )
inline
ResidueConstIterator beginResidue ( ) const
inline
void buildResidueNames_ ( )
protected

builds an index of residue names for fast access, synonyms are also considered

void clear_ ( )
protected

deletes all sub-instances of the stored data like modifications and residues

void clearResidues_ ( )
protected

clears the residues

ResidueIterator endResidue ( )
inline
ResidueConstIterator endResidue ( ) const
inline
static ResidueDB* getInstance ( )
inlinestatic

this member function serves as a replacement of the constructor

const Residue* getModifiedResidue ( const String name)
const Residue* getModifiedResidue ( const Residue residue,
const String name 
)
Size getNumberOfModifiedResidues ( ) const
Size getNumberOfResidues ( ) const

returns the number of residues stored

const Residue* getResidue ( const String name) const

returns a pointer to the residue with name, 3 letter code or 1 letter code name

const Residue* getResidue ( const unsigned char &  one_letter_code) const

returns a pointer to the residue with 1 letter code name

const std::set<const Residue *> getResidues ( const String residue_set = "All") const

returns a set of all residues stored in this residue db

The possible residues are defined in share/OpenMS/CHEMISTRY/Residues.xml. At the moment the following sets are available: All - all residues stored in the file Natural20 - default 20 naturally occurring residues Natural19WithoutI - default natural amino acids, excluding isoleucine (isobaric to leucine) Natural19WithoutL - default natural amino acids, excluding leucine (isobaric to isoleucine) Natural19J - default natural amino acids, (isobaric leucine/isoleucine are marked by 'J') AmbiguousWithoutX - all amino acids, including ambiguous ones B (asparagine or aspartate) Z (glutamine or glutamate) J (isoleucine or leucine) Ambiguous - all amino acids including all ambiguous ones (X can be every other amino acid) AllNatural - naturally occurring residues, including selenocysteine (U)

const std::set<String>& getResidueSets ( ) const

returns all residue sets that are registered which this instance

bool hasResidue ( const String name) const

returns true if the db contains a residue with the given name

bool hasResidue ( const Residue residue) const

returns true if the db contains the residue of the given pointer

ResidueDB& operator= ( const ResidueDB aa)
protected

assignment operator

Residue* parseResidue_ ( Map< String, String > &  values)
protected

parses a residue, given the key/value pairs from i.e. an XML file

void readResiduesFromFile_ ( const String filename)
protected

reads residues from the given file

void setResidues ( const String filename)

sets the residues from given file

Member Data Documentation

std::set<const Residue *> const_modified_residues_
protected
std::set<const Residue *> const_residues_
protected
std::set<Residue *> modified_residues_
protected
Residue* residue_by_one_letter_code_[256]
protected
Map<String, Map<String, Residue *> > residue_mod_names_
protected
boost::unordered_map<String, Residue *> residue_names_
protected
std::set<String> residue_sets_
protected
std::set<Residue *> residues_
protected
Map<String, std::set<const Residue *> > residues_by_set_
protected

OpenMS / TOPP release 2.0.0 Documentation generated on Fri May 29 2015 17:20:43 using doxygen 1.8.9.1