#include <OpenMS/CHEMISTRY/EdwardsLippertIterator.h>
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.
Public Types | |
typedef std::pair< String, String > | FASTAEntry |
Public Member Functions | |
EdwardsLippertIterator () | |
Constructor. | |
EdwardsLippertIterator (const EdwardsLippertIterator &) | |
Copy Constructor. | |
virtual | ~EdwardsLippertIterator () |
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 t) throw (Exception::InvalidValue) |
setter for tolerance | |
virtual float | getTolerance () |
getter for tolerance | |
virtual void | setSpectrum (const std::vector< float > &s) throw (Exception::InvalidValue) |
setter for spectrum | |
virtual const std::vector < float > & | getSpectrum () |
getter for spectrum | |
virtual bool | begin () throw (Exception::InvalidIterator) |
initializing iterator | |
virtual bool | isAtEnd () |
indicates whether iterator is at end | |
virtual bool | isDigestingEnd (char, char) |
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 | |
virtual bool | isInSpectrum_ (float &mass) |
indicates if a mass is in spectrum | |
Protected Attributes | |
String | f_file_ |
fasta file location | |
std::string | actual_pep_ |
actual peptide | |
std::vector< float > | spec_ |
given spectrum | |
float | tol_ |
tolerance | |
float | masse_ [255] |
mass table | |
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) | |
float | m_ |
float | massMax_ |
mass and maximum masse |
typedef std::pair<String,String> FASTAEntry |
Reimplemented from PepIterator.
Constructor.
EdwardsLippertIterator | ( | const EdwardsLippertIterator & | ) |
Copy Constructor.
virtual ~EdwardsLippertIterator | ( | ) | [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 | t | ) | throw (Exception::InvalidValue) [virtual] |
setter for tolerance
t | tolerance |
Exception::InvalidValue | if tolerance is negative |
Implements PepIterator.
virtual float getTolerance | ( | ) | [virtual] |
virtual void setSpectrum | ( | const std::vector< float > & | s | ) | throw (Exception::InvalidValue) [virtual] |
setter for spectrum
s | spectrum as a vector of floats |
Exception::InvalidValue | if spectrum is not sorted |
Implements PepIterator.
virtual const std::vector<float>& getSpectrum | ( | ) | [virtual] |
virtual bool begin | ( | ) | throw (Exception::InvalidIterator) [virtual] |
virtual bool isAtEnd | ( | ) | [virtual] |
indicates whether iterator is at end
Implements PepIterator.
virtual bool isDigestingEnd | ( | char | , | |
char | ||||
) | [virtual] |
indicated if a digesting enzyme will cut at this position
Reimplemented in EdwardsLippertIteratorTryptic.
static const std::string getName | ( | ) | [inline, static] |
needed by FactoryProduct
Reimplemented in EdwardsLippertIteratorTryptic.
static PepIterator* create | ( | ) | [inline, static] |
needed by FactoryProduct
Reimplemented in EdwardsLippertIteratorTryptic.
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
virtual bool isInSpectrum_ | ( | float & | mass | ) | [protected, virtual] |
indicates if a mass is in spectrum
std::string actual_pep_ [protected] |
actual peptide
std::vector<float> spec_ [protected] |
given spectrum
float tol_ [protected] |
tolerance
float masse_[255] [protected] |
mass table
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)
float m_ [protected] |
float massMax_ [protected] |
mass and maximum masse
Generated Tue Apr 1 15:36:42 2008 -- using doxygen 1.5.4 | OpenMS / TOPP 1.1 |