35 #ifndef OPENMS_CHEMISTRY_TRYPTICITERATOR_H
36 #define OPENMS_CHEMISTRY_TRYPTICITERATOR_H
94 virtual void setFastaFile(
const String & f);
100 virtual String getFastaFile();
145 virtual bool begin();
152 virtual bool isAtEnd();
158 virtual bool isDigestingEnd(
char aa1,
char aa2);
166 return "TrypticIterator";
183 virtual std::string next_();
213 #endif //OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
static const String getProductName()
needed by Factory
Definition: TrypticIterator.h:164
A more convenient string class.
Definition: String.h:56
Abstract base class for different peptide iterators.
Definition: PepIterator.h:48
FASTAEntry f_entry_
actual fasta entry
Definition: TrypticIterator.h:204
static PepIterator * create()
needed by Factory
Definition: TrypticIterator.h:173
unsigned int e_
to ints representing a position within the actual string (b = begin, e = end)
Definition: TrypticIterator.h:206
std::string actual_pep_
actual peptide
Definition: TrypticIterator.h:198
virtual DoubleReal getTolerance()
getter for tolerance
Definition: TrypticIterator.h:116
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:415
bool is_at_end_
indicates if iterator is at end
Definition: TrypticIterator.h:200
virtual const std::vector< DoubleReal > & getSpectrum()
getter for spectrum
Definition: TrypticIterator.h:135
String f_file_
fasta file location
Definition: TrypticIterator.h:196
virtual void setTolerance(DoubleReal)
setter for tolerance
Definition: TrypticIterator.h:106
std::pair< String, String > FASTAEntry
Definition: TrypticIterator.h:54
finds all tryptic Peptides with every missed cleavage
Definition: TrypticIterator.h:48
std::pair< String, String > FASTAEntry
Definition: PepIterator.h:53
Not implemented exception.
Definition: Exception.h:437
PepIterator * f_iterator_
FastaIterator.
Definition: TrypticIterator.h:202
virtual void setSpectrum(const std::vector< DoubleReal > &)
setter for spectrum
Definition: TrypticIterator.h:125