#include <OpenMS/CHEMISTRY/TrypticIterator.h>
Public Types | |
typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
TrypticIterator () | |
Constructor. | |
TrypticIterator (const TrypticIterator &) | |
Copy Constructor. | |
virtual | ~TrypticIterator () |
Destructor. | |
virtual FASTAEntry | operator * () throw (Exception::InvalidIterator) |
* operator for getting the value of the iterator | |
virtual PepIterator & | operator++ () throw (Exception::InvalidIterator) |
opperator ++ for postincrement | |
virtual PepIterator * | operator++ (int i) throw (Exception::InvalidIterator) |
opperator ++ for preincrement | |
virtual void | setFastaFile (const String &f) throw (Exception::FileNotFound) |
setter for fasta file | |
virtual String | getFastaFile () |
getter for FASTA file | |
virtual void | setTolerance (float) throw (Exception::InvalidValue, Exception::NotImplemented) |
setter for tolerance | |
virtual float | getTolerance () throw (Exception::InvalidValue, Exception::NotImplemented) |
getter for tolerance | |
virtual void | setSpectrum (const std::vector< float > &) throw (Exception::InvalidValue, Exception::NotImplemented) |
setter for spectrum | |
virtual const std::vector < float > & | getSpectrum () throw (Exception::InvalidValue, Exception::NotImplemented) |
getter for spectrum | |
virtual bool | begin () throw (Exception::InvalidIterator) |
initializing iterator | |
virtual bool | isAtEnd () |
indicates whether iterator is at end | |
virtual bool | isDigestingEnd (char aa1, char aa2) |
indicated if a digesting enzyme will cut at this position | |
Static Public Member Functions | |
static const std::string | getName () |
needed by FactoryProduct | |
static PepIterator * | create () |
needed by FactoryProduct | |
Protected Member Functions | |
virtual std::string | next_ () |
getting the next candidate | |
bool | hasNext_ () |
indicates if there will be a next element | |
void | goToNextAA_ () |
finds the next starting position where a digesting enzyme will cut the sequence | |
Protected Attributes | |
String | f_file_ |
fasta file location | |
std::string | actual_pep_ |
actual peptide | |
bool | is_at_end_ |
indicates if iterator is at end | |
PepIterator * | f_iterator_ |
FastaIterator. | |
FASTAEntry | f_entry_ |
actual fasta entry | |
unsigned int | b_ |
unsigned int | e_ |
to ints representing a position within the actual string (b = begin, e = end) |
typedef std::pair<String,String> FASTAEntry |
Reimplemented from PepIterator.
TrypticIterator | ( | ) |
Constructor.
TrypticIterator | ( | const TrypticIterator & | ) |
Copy Constructor.
virtual ~TrypticIterator | ( | ) | [virtual] |
Destructor.
virtual FASTAEntry operator * | ( | ) | throw (Exception::InvalidIterator) [virtual] |
* operator for getting the value of the iterator
Exception::InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
virtual PepIterator& operator++ | ( | ) | throw (Exception::InvalidIterator) [virtual] |
opperator ++ for postincrement
Exception::InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
virtual PepIterator* operator++ | ( | int | i | ) | throw (Exception::InvalidIterator) [virtual] |
opperator ++ for preincrement
Exception::InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
virtual void setFastaFile | ( | const String & | f | ) | throw (Exception::FileNotFound) [virtual] |
setter for fasta file
f | String with fasta file location |
Exception::FileNotFound | if file could not be found |
Implements PepIterator.
virtual String getFastaFile | ( | ) | [virtual] |
virtual void setTolerance | ( | float | ) | throw (Exception::InvalidValue, Exception::NotImplemented) [inline, virtual] |
setter for tolerance
Exception::NotImplemented | because its not available for tryptic iterator |
Implements PepIterator.
virtual float getTolerance | ( | ) | throw (Exception::InvalidValue, Exception::NotImplemented) [inline, virtual] |
getter for tolerance
Exception::NotImplemented | because its not available for tryptic iterator |
Implements PepIterator.
virtual void setSpectrum | ( | const std::vector< float > & | ) | throw (Exception::InvalidValue, Exception::NotImplemented) [inline, virtual] |
setter for spectrum
Exception::NotImplemented | because its not available for tryptic iterator |
Implements PepIterator.
virtual const std::vector<float>& getSpectrum | ( | ) | throw (Exception::InvalidValue, Exception::NotImplemented) [inline, virtual] |
getter for spectrum
Exception::NotImplemented | because its not available for tryptic iterator |
Implements PepIterator.
virtual bool begin | ( | ) | throw (Exception::InvalidIterator) [virtual] |
virtual bool isAtEnd | ( | ) | [virtual] |
indicates whether iterator is at end
Implements PepIterator.
virtual bool isDigestingEnd | ( | char | aa1, | |
char | aa2 | |||
) | [virtual] |
indicated if a digesting enzyme will cut at this position
static const std::string getName | ( | ) | [inline, static] |
static PepIterator* create | ( | ) | [inline, static] |
virtual std::string next_ | ( | ) | [protected, virtual] |
getting the next candidate
bool hasNext_ | ( | ) | [protected] |
indicates if there will be a next element
void goToNextAA_ | ( | ) | [protected] |
finds the next starting position where a digesting enzyme will cut the sequence
std::string actual_pep_ [protected] |
actual peptide
bool is_at_end_ [protected] |
indicates if iterator is at end
PepIterator* f_iterator_ [protected] |
FASTAEntry f_entry_ [protected] |
actual fasta entry
unsigned int b_ [protected] |
unsigned int e_ [protected] |
to ints representing a position within the actual string (b = begin, e = end)
Generated Tue Apr 1 15:36:43 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |