35 #ifndef OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
36 #define OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
94 virtual void setFastaFile(
const String & f);
100 virtual String getFastaFile();
107 virtual void setTolerance(
double t);
113 virtual double getTolerance();
120 virtual void setSpectrum(
const std::vector<double> & s);
126 virtual const std::vector<double> & getSpectrum();
133 virtual bool begin();
140 virtual bool isAtEnd();
146 virtual bool isDigestingEnd(
char,
char);
154 return "EdwardsLippertIterator";
172 virtual std::string next_();
189 virtual bool isInSpectrum_(
double & mass);
215 #endif //OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
A more convenient string class.
Definition: String.h:57
std::vector< double > spec_
given spectrum
Definition: EdwardsLippertIterator.h:195
bool is_at_end_
indicates if iterator is at end
Definition: EdwardsLippertIterator.h:201
Abstract base class for different peptide iterators.
Definition: PepIterator.h:48
finds all Peptide Candidates with given masses and given fasta file
Definition: EdwardsLippertIterator.h:48
String f_file_
fasta file location
Definition: EdwardsLippertIterator.h:191
PepIterator * f_iterator_
FastaIterator.
Definition: EdwardsLippertIterator.h:203
std::pair< String, String > FASTAEntry
Definition: EdwardsLippertIterator.h:54
static const String getProductName()
needed by Factory
Definition: EdwardsLippertIterator.h:152
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
FASTAEntry f_entry_
actual fasta entry
Definition: EdwardsLippertIterator.h:205
double tol_
tolerance
Definition: EdwardsLippertIterator.h:197
static PepIterator * create()
needed by Factory
Definition: EdwardsLippertIterator.h:161
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:421
double massMax_
mass and maximum masse
Definition: EdwardsLippertIterator.h:209
unsigned int e_
to ints representing a position within the actual string (b = begin, e = end)
Definition: EdwardsLippertIterator.h:207
std::string actual_pep_
actual peptide
Definition: EdwardsLippertIterator.h:193