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EdwardsLippertIterator.h
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34 
35 #ifndef OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
36 #define OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
37 
39 
40 namespace OpenMS
41 {
42 
48  class OPENMS_DLLAPI EdwardsLippertIterator :
49  public PepIterator
50  {
51 
52 public:
53 
54  typedef std::pair<String, String> FASTAEntry;
66  virtual ~EdwardsLippertIterator();
67 
73  virtual FASTAEntry operator*();
74 
80  virtual PepIterator & operator++();
81 
87  virtual PepIterator * operator++(int i);
88 
94  virtual void setFastaFile(const String & f);
95 
100  virtual String getFastaFile();
101 
107  virtual void setTolerance(DoubleReal t);
108 
113  virtual DoubleReal getTolerance();
114 
120  virtual void setSpectrum(const std::vector<DoubleReal> & s);
121 
126  virtual const std::vector<DoubleReal> & getSpectrum();
127 
133  virtual bool begin();
134 
140  virtual bool isAtEnd();
141 
146  virtual bool isDigestingEnd(char, char);
147 
152  static const String getProductName()
153  {
154  return "EdwardsLippertIterator";
155  }
156 
161  static PepIterator * create()
162  {
163  return new EdwardsLippertIterator;
164  }
165 
166 protected:
171  virtual std::string next_();
172 
177  bool hasNext_();
178 
182  void goToNextAA_();
183 
188  virtual bool isInSpectrum_(DoubleReal & mass);
189 
191 
192  std::string actual_pep_;
193 
194  std::vector<DoubleReal> spec_;
195 
197 
198  DoubleReal masse_[255];
199 
200  bool is_at_end_;
201 
203 
205 
206  unsigned int b_, e_;
207 
209 
210 
211  };
212 
213 }
214 #endif //OPENMS_CHEMISTRY_EDWARDSLIPPERTITERATOR_H
A more convenient string class.
Definition: String.h:56
bool is_at_end_
indicates if iterator is at end
Definition: EdwardsLippertIterator.h:200
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:190
PepIterator * f_iterator_
FastaIterator.
Definition: EdwardsLippertIterator.h:202
std::pair< String, String > FASTAEntry
Definition: EdwardsLippertIterator.h:54
static const String getProductName()
needed by Factory
Definition: EdwardsLippertIterator.h:152
FASTAEntry f_entry_
actual fasta entry
Definition: EdwardsLippertIterator.h:204
std::vector< DoubleReal > spec_
given spectrum
Definition: EdwardsLippertIterator.h:194
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:415
unsigned int e_
to ints representing a position within the actual string (b = begin, e = end)
Definition: EdwardsLippertIterator.h:206
std::string actual_pep_
actual peptide
Definition: EdwardsLippertIterator.h:192
DoubleReal massMax_
mass and maximum masse
Definition: EdwardsLippertIterator.h:208
DoubleReal tol_
tolerance
Definition: EdwardsLippertIterator.h:196

OpenMS / TOPP release 1.11.1 Documentation generated on Thu Nov 14 2013 11:19:13 using doxygen 1.8.5