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 |
![]() | |
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++ () |
operator ++ for postincrement More... | |
virtual PepIterator * | operator++ (int i) |
operator ++ 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 (double t) |
setter for tolerance More... | |
virtual double | getTolerance () |
getter for tolerance More... | |
virtual void | setSpectrum (const std::vector< double > &s) |
setter for spectrum More... | |
virtual const std::vector< double > & | 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... | |
![]() | |
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 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_ (double &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< double > | spec_ |
given spectrum More... | |
double | tol_ |
tolerance More... | |
double | 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... | |
double | m_ |
double | 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.
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 |
operator ++ for postincrement
InvalidIterator | if iterator has not been initialized |
Implements PepIterator.
|
virtual |
operator ++ 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 doubles |
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 2.0.0 | Documentation generated on Sat May 16 2015 16:13:49 using doxygen 1.8.9.1 |