finds all Peptide Candidates with given masses and given fasta file More...
#include <OpenMS/CHEMISTRY/EdwardsLippertIterator.h>
 
  
 | Public Types | |
| typedef std::pair< String, String > | FASTAEntry | 
|  Public Types inherited from PepIterator | |
| typedef std::pair< String, String > | FASTAEntry | 
| Public Member Functions | |
| EdwardsLippertIterator () | |
| Constructor.  More... | |
| EdwardsLippertIterator (const EdwardsLippertIterator &) | |
| Copy Constructor.  More... | |
| virtual | ~EdwardsLippertIterator () | 
| 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 t) | 
| setter for tolerance  More... | |
| virtual DoubleReal | getTolerance () | 
| getter for tolerance  More... | |
| virtual void | setSpectrum (const std::vector< DoubleReal > &s) | 
| 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, char) | 
| 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... | |
| virtual bool | isInSpectrum_ (DoubleReal &mass) | 
| indicates if a mass is in spectrum  More... | |
| Protected Attributes | |
| String | f_file_ | 
| fasta file location  More... | |
| std::string | actual_pep_ | 
| actual peptide  More... | |
| std::vector< DoubleReal > | spec_ | 
| given spectrum  More... | |
| DoubleReal | tol_ | 
| tolerance  More... | |
| DoubleReal | masse_ [255] | 
| mass table  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... | |
| DoubleReal | m_ | 
| DoubleReal | massMax_ | 
| mass and maximum masse  More... | |
finds all Peptide Candidates with given masses and given fasta file
The used algorithm was described by Edwards and Lippert. The algorithm uses two pointers to iterator over a sequence. One pointer represents the start the other the end.
| typedef std::pair<String, String> FASTAEntry | 
Constructor.
| EdwardsLippertIterator | ( | const EdwardsLippertIterator & | ) | 
Copy Constructor.
| 
 | virtual | 
Destructor.
| 
 | virtual | 
initializing iterator
| InvalidIterator | is thrown if the begin iterator is invalid | 
Implements PepIterator.
| 
 | inlinestatic | 
needed by Factory
| 
 | virtual | 
| 
 | inlinestatic | 
needed by Factory
| 
 | virtual | 
| 
 | virtual | 
| 
 | 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
Reimplemented in EdwardsLippertIteratorTryptic.
| 
 | protectedvirtual | 
indicates if a mass is in spectrum
| 
 | 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.
| 
 | virtual | 
setter for spectrum
| s | spectrum as a vector of DoubleReals | 
| InvalidValue | if spectrum is not sorted | 
Implements PepIterator.
| 
 | virtual | 
setter for tolerance
| t | tolerance | 
| InvalidValue | if tolerance is negative | 
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
| 
 | protected | 
| 
 | protected | 
mass table
| 
 | protected | 
mass and maximum masse
| 
 | protected | 
given spectrum
| 
 | protected | 
tolerance
| OpenMS / TOPP release 1.11.1 | Documentation generated on Thu Nov 14 2013 11:19:27 using doxygen 1.8.5 |