finds all tryptic Peptides with every missed cleavage More...
#include <OpenMS/CHEMISTRY/TrypticIterator.h>
Public Types | |
| typedef std::pair< String, String > | FASTAEntry |
Public Types inherited from PepIterator | |
| typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
| TrypticIterator () | |
| Constructor. More... | |
| TrypticIterator (const TrypticIterator &) | |
| Copy Constructor. More... | |
| virtual | ~TrypticIterator () |
| Destructor. More... | |
| virtual FASTAEntry | operator* () |
| * operator for getting the value of the iterator More... | |
| virtual PepIterator & | operator++ () |
| opperator ++ for postincrement More... | |
| virtual PepIterator * | operator++ (int i) |
| opperator ++ for preincrement More... | |
| virtual void | setFastaFile (const String &f) |
| setter for fasta file More... | |
| virtual String | getFastaFile () |
| getter for FASTA file More... | |
| virtual void | setTolerance (DoubleReal) |
| setter for tolerance More... | |
| virtual DoubleReal | getTolerance () |
| getter for tolerance More... | |
| virtual void | setSpectrum (const std::vector< DoubleReal > &) |
| setter for spectrum More... | |
| virtual const std::vector < DoubleReal > & | getSpectrum () |
| getter for spectrum More... | |
| virtual bool | begin () |
| initializing iterator More... | |
| virtual bool | isAtEnd () |
| indicates whether iterator is at end More... | |
| virtual bool | isDigestingEnd (char aa1, char aa2) |
| indicated if a digesting enzyme will cut at this position More... | |
Public Member Functions inherited from PepIterator | |
| PepIterator () | |
| constructor More... | |
| virtual | ~PepIterator () |
| destructor More... | |
| PepIterator (const PepIterator &source) | |
| copy constructor More... | |
Static Public Member Functions | |
| static const String | getProductName () |
| needed by Factory More... | |
| static PepIterator * | create () |
| needed by Factory More... | |
Static Public Member Functions inherited from PepIterator | |
| static void | registerChildren () |
| all children has to be registered here More... | |
Protected Member Functions | |
| virtual std::string | next_ () |
| getting the next candidate More... | |
| bool | hasNext_ () |
| indicates if there will be a next element More... | |
| void | goToNextAA_ () |
| finds the next starting position where a digesting enzyme will cut the sequence More... | |
Protected Attributes | |
| String | f_file_ |
| fasta file location More... | |
| std::string | actual_pep_ |
| actual peptide More... | |
| bool | is_at_end_ |
| indicates if iterator is at end More... | |
| PepIterator * | f_iterator_ |
| FastaIterator. More... | |
| FASTAEntry | f_entry_ |
| actual fasta entry More... | |
| unsigned int | b_ |
| unsigned int | e_ |
| to ints representing a position within the actual string (b = begin, e = end) More... | |
finds all tryptic Peptides with every missed cleavage
| typedef std::pair<String, String> FASTAEntry |
| TrypticIterator | ( | ) |
Constructor.
| TrypticIterator | ( | const TrypticIterator & | ) |
Copy Constructor.
|
virtual |
Destructor.
|
virtual |
initializing iterator
| throws | InvalidIterator if begin iterator is not valid |
Implements PepIterator.
|
inlinestatic |
needed by Factory
|
virtual |
|
inlinestatic |
needed by Factory
|
inlinevirtual |
getter for spectrum
| NotImplemented | because its not available for tryptic iterator |
Implements PepIterator.
|
inlinevirtual |
getter for tolerance
| NotImplemented | because its not available for tryptic iterator |
Implements PepIterator.
|
protected |
finds the next starting position where a digesting enzyme will cut the sequence
|
protected |
indicates if there will be a next element
|
virtual |
indicates whether iterator is at end
Implements PepIterator.
|
virtual |
indicated if a digesting enzyme will cut at this position
|
protectedvirtual |
getting the next candidate
|
virtual |
* operator for getting the value of the iterator
| InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
|
virtual |
opperator ++ for postincrement
| InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
|
virtual |
opperator ++ for preincrement
| InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
|
virtual |
setter for fasta file
| f | String with fasta file location |
| FileNotFound | if file could not be found |
Implements PepIterator.
|
inlinevirtual |
setter for spectrum
| NotImplemented | because its not available for tryptic iterator |
Implements PepIterator.
|
inlinevirtual |
setter for tolerance
| NotImplemented | because its not available for tryptic iterator |
Implements PepIterator.
|
protected |
actual peptide
|
protected |
|
protected |
to ints representing a position within the actual string (b = begin, e = end)
|
protected |
actual fasta entry
|
protected |
fasta file location
|
protected |
|
protected |
indicates if iterator is at end
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:28 using doxygen 1.8.5 |