#include <OpenMS/CHEMISTRY/AASequence.h>
Public Types | |
Typedefs | |
typedef std::vector< const Residue * >::iterator | iterator |
typedef std::vector< const Residue * >::const_iterator | const_iterator |
typedef std::vector< const Residue * >::iterator | Iterator |
typedef std::vector< const Residue * >::const_iterator | ConstIterator |
Public Member Functions | |
AASequence & | operator= (const AASequence &rhs) |
assignment operator | |
Constructors and Destructors | |
AASequence () | |
default constructor | |
AASequence (const AASequence &rhs) | |
copy constructor | |
AASequence (const String &rhs) throw (Exception::ParseError) | |
copy constructor from a String | |
AASequence (ResidueDB *res_db) | |
constructor with given residue db pointer | |
AASequence (ConstIterator begin, ConstIterator end) | |
constructor with given a residue range | |
virtual | ~AASequence () |
destructor | |
Accessors | |
const Residue * | getResidue (Int index) const throw (Exception::IndexUnderflow, Exception::IndexOverflow) |
returns a pointer to the residue, which is at position index | |
const Residue * | getResidue (UInt index) const throw (Exception::IndexOverflow) |
returns a pointer to the residue, which is at position index | |
EmpiricalFormula | getFormula (Residue::ResidueType type=Residue::Full, Int charge=0) const |
returns the formula of the peptide | |
DoubleReal | getAverageWeight (Residue::ResidueType type=Residue::Full, Int charge=0) const |
returns the average weight of the peptide | |
DoubleReal | getMonoWeight (Residue::ResidueType type=Residue::Full, Int charge=0) const |
returns the mono isotopic weight of the peptide | |
HashMap< const EmpiricalFormula *, UInt > | getNeutralLosses () const |
fills in the map the neutral loss formulas associated with their occuring frequency | |
const Residue * | operator[] (Int index) const throw (Exception::IndexUnderflow, Exception::IndexOverflow) |
returns a pointer to the residue at given position | |
const Residue * | operator[] (UInt index) const throw (Exception::IndexOverflow) |
returns a pointer to the residue at given position | |
AASequence | operator+ (const AASequence &peptide) const |
adds the residues of the peptide | |
AASequence | operator+ (const String &peptide) const throw (Exception::ParseError) |
adds the residues of the peptide, which is given as a string | |
AASequence & | operator+= (const AASequence &) |
adds the residues of a peptide | |
AASequence & | operator+= (const String &) throw (Exception::ParseError) |
adds the residues of a peptide, which is given as a string | |
void | setResidueDB (ResidueDB *res_db=0) |
UInt | size () const |
returns the number of residues | |
AASequence | getPrefix (UInt index) const throw (Exception::IndexOverflow) |
returns a peptide sequence of the first index residues | |
AASequence | getSuffix (UInt index) const throw (Exception::IndexOverflow) |
returns a peptide sequence of the last index residues | |
AASequence | getSubsequence (UInt index, UInt number) const throw (Exception::IndexOverflow) |
returns a peptide sequence of number residues, beginning at position index | |
Predicates | |
bool | has (const Residue *residue) const |
returns true if the peptude contains the given residue | |
bool | has (const String &name) const |
returns true if the peptide contains the given residue | |
bool | hasSubsequence (const AASequence &peptide) const |
returns true if the peptide contains the given peptide | |
bool | hasSubsequence (const String &peptide) const throw (Exception::ParseError) |
returns true if the peptide contains the given peptide | |
bool | hasPrefix (const AASequence &peptide) const |
returns true if the peptide has the given prefix | |
bool | hasPrefix (const String &peptide) const throw (Exception::ParseError) |
returns true if the peptide has the given prefix | |
bool | hasSuffix (const AASequence &peptide) const |
returns true if the peptide has the given suffix | |
bool | hasSuffix (const String &peptide) const throw (Exception::ParseError) |
returns true if the peptide has the given suffix | |
bool | operator== (const AASequence &) const |
equality operator | |
bool | operator== (const String &) const throw (Exception::ParseError) |
equality operator given the peptide as a string | |
bool | operator!= (const AASequence &) const |
inequality operator | |
bool | operator!= (const String &) const throw (Exception::ParseError) |
inequality operator given the peptide as a string | |
Iterators | |
Iterator | begin () |
ConstIterator | begin () const |
Iterator | end () |
ConstIterator | end () const |
Protected Member Functions | |
ResidueDB * | getResidueDB_ () const |
void | parseString_ (std::vector< const Residue * > &sequence, const String &peptide) const throw (Exception::ParseError) |
Protected Attributes | |
std::vector< const Residue * > | peptide_ |
Static Protected Attributes | |
static ResidueDB * | custom_res_db_ |
Friends | |
std::ostream & | operator<< (std::ostream &os, const AASequence &peptide) |
writes a peptide to an output stream | |
std::istream & | operator>> (std::istream &is, const AASequence &peptide) |
reads a peptide from an input stream |
typedef std::vector<const Residue*>::const_iterator const_iterator |
typedef std::vector<const Residue*>::const_iterator ConstIterator |
AASequence | ( | ) |
default constructor
AASequence | ( | const AASequence & | rhs | ) |
copy constructor
AASequence | ( | const String & | rhs | ) | throw (Exception::ParseError) |
copy constructor from a String
AASequence | ( | ResidueDB * | res_db | ) |
constructor with given residue db pointer
AASequence | ( | ConstIterator | begin, | |
ConstIterator | end | |||
) |
constructor with given a residue range
virtual ~AASequence | ( | ) | [virtual] |
destructor
AASequence& operator= | ( | const AASequence & | rhs | ) |
assignment operator
const Residue* getResidue | ( | Int | index | ) | const throw (Exception::IndexUnderflow, Exception::IndexOverflow) |
returns a pointer to the residue, which is at position index
const Residue* getResidue | ( | UInt | index | ) | const throw (Exception::IndexOverflow) |
returns a pointer to the residue, which is at position index
EmpiricalFormula getFormula | ( | Residue::ResidueType | type = Residue::Full , |
|
Int | charge = 0 | |||
) | const |
returns the formula of the peptide
DoubleReal getAverageWeight | ( | Residue::ResidueType | type = Residue::Full , |
|
Int | charge = 0 | |||
) | const |
returns the average weight of the peptide
DoubleReal getMonoWeight | ( | Residue::ResidueType | type = Residue::Full , |
|
Int | charge = 0 | |||
) | const |
returns the mono isotopic weight of the peptide
HashMap<const EmpiricalFormula*, UInt> getNeutralLosses | ( | ) | const |
fills in the map the neutral loss formulas associated with their occuring frequency
const Residue* operator[] | ( | Int | index | ) | const throw (Exception::IndexUnderflow, Exception::IndexOverflow) |
returns a pointer to the residue at given position
const Residue* operator[] | ( | UInt | index | ) | const throw (Exception::IndexOverflow) |
returns a pointer to the residue at given position
AASequence operator+ | ( | const AASequence & | peptide | ) | const |
adds the residues of the peptide
AASequence operator+ | ( | const String & | peptide | ) | const throw (Exception::ParseError) |
adds the residues of the peptide, which is given as a string
AASequence& operator+= | ( | const AASequence & | ) |
adds the residues of a peptide
AASequence& operator+= | ( | const String & | ) | throw (Exception::ParseError) |
adds the residues of a peptide, which is given as a string
void setResidueDB | ( | ResidueDB * | res_db = 0 |
) |
sets the residue db from an residue db; ATTENTION this affects all instances! calling with no argument resets to the default residues db usage
UInt size | ( | ) | const |
returns the number of residues
AASequence getPrefix | ( | UInt | index | ) | const throw (Exception::IndexOverflow) |
returns a peptide sequence of the first index residues
AASequence getSuffix | ( | UInt | index | ) | const throw (Exception::IndexOverflow) |
returns a peptide sequence of the last index residues
AASequence getSubsequence | ( | UInt | index, | |
UInt | number | |||
) | const throw (Exception::IndexOverflow) |
returns a peptide sequence of number residues, beginning at position index
bool has | ( | const Residue * | residue | ) | const |
returns true if the peptude contains the given residue
bool has | ( | const String & | name | ) | const |
returns true if the peptide contains the given residue
bool hasSubsequence | ( | const AASequence & | peptide | ) | const |
returns true if the peptide contains the given peptide
bool hasSubsequence | ( | const String & | peptide | ) | const throw (Exception::ParseError) |
returns true if the peptide contains the given peptide
bool hasPrefix | ( | const AASequence & | peptide | ) | const |
returns true if the peptide has the given prefix
bool hasPrefix | ( | const String & | peptide | ) | const throw (Exception::ParseError) |
returns true if the peptide has the given prefix
bool hasSuffix | ( | const AASequence & | peptide | ) | const |
returns true if the peptide has the given suffix
bool hasSuffix | ( | const String & | peptide | ) | const throw (Exception::ParseError) |
returns true if the peptide has the given suffix
bool operator== | ( | const AASequence & | ) | const |
equality operator
bool operator== | ( | const String & | ) | const throw (Exception::ParseError) |
equality operator given the peptide as a string
bool operator!= | ( | const AASequence & | ) | const |
inequality operator
bool operator!= | ( | const String & | ) | const throw (Exception::ParseError) |
inequality operator given the peptide as a string
Iterator begin | ( | ) | [inline] |
ConstIterator begin | ( | ) | const [inline] |
Iterator end | ( | ) | [inline] |
ConstIterator end | ( | ) | const [inline] |
ResidueDB* getResidueDB_ | ( | ) | const [protected] |
void parseString_ | ( | std::vector< const Residue * > & | sequence, | |
const String & | peptide | |||
) | const throw (Exception::ParseError) [protected] |
std::ostream& operator<< | ( | std::ostream & | os, | |
const AASequence & | peptide | |||
) | [friend] |
writes a peptide to an output stream
std::istream& operator>> | ( | std::istream & | is, | |
const AASequence & | peptide | |||
) | [friend] |
reads a peptide from an input stream
ResidueDB* custom_res_db_ [static, protected] |
Generated Tue Apr 1 15:36:42 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |