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FastaIterator.h
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34 
35 
36 #ifndef OPENMS_FORMAT_FASTAITERATOR_H
37 #define OPENMS_FORMAT_FASTAITERATOR_H
38 
41 #include <fstream>
42 #include <vector>
43 
44 namespace OpenMS
45 {
46 
53  class OPENMS_DLLAPI FastaIterator :
54  public PepIterator
55  {
56 
57 public:
58 
59  typedef std::pair<String, String> FASTAEntry;
63  FastaIterator();
64 
65 
69  virtual ~FastaIterator();
70 
76  virtual FASTAEntry operator*();
77 
83  virtual PepIterator & operator++();
84 
90  virtual PepIterator * operator++(int i);
91 
98  virtual void setFastaFile(const String & f);
99 
104  virtual String getFastaFile();
105 
111  virtual void setSpectrum(const std::vector<double> &)
112  {
113  throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
114  }
115 
121  virtual const std::vector<double> & getSpectrum()
122  {
123  throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
124  }
125 
131  virtual void setTolerance(double /* t */)
132  {
133  throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
134  }
135 
142  virtual double getTolerance()
143  {
144  throw Exception::NotImplemented(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION);
145  }
146 
152  virtual bool begin();
153 
158  virtual bool isAtEnd();
159 
164  static const String getProductName()
165  {
166  return "FastaIterator";
167  }
168 
173  static PepIterator * create()
174  {
175  return new FastaIterator;
176  }
177 
178 protected:
183  virtual std::string next_();
184 
185  bool is_at_end_;
186 
187  std::ifstream input_file_;
188 
190 
191  std::string actual_seq_;
192 
193  std::string header_;
194 
195  std::string last_header_;
196 
197 private:
201  FastaIterator(const FastaIterator &);
202 
206  FastaIterator & operator=(const FastaIterator &);
207 
208 
209  };
210 }
211 #endif // OPENMS_FORMAT_FASTAITERATOR_H
virtual double getTolerance()
getter for tolerance
Definition: FastaIterator.h:142
A more convenient string class.
Definition: String.h:57
Abstract base class for different peptide iterators.
Definition: PepIterator.h:48
virtual void setTolerance(double)
setter for tolerance
Definition: FastaIterator.h:131
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
bool is_at_end_
bool indicated whether iterator is at end
Definition: FastaIterator.h:185
virtual void setSpectrum(const std::vector< double > &)
setter for spectrum
Definition: FastaIterator.h:111
std::string actual_seq_
actual sequence
Definition: FastaIterator.h:191
std::string last_header_
last fasta header
Definition: FastaIterator.h:195
String fasta_file_
fasta file location
Definition: FastaIterator.h:189
virtual const std::vector< double > & getSpectrum()
getter for spectrum
Definition: FastaIterator.h:121
Iterator over FASTA file.
Definition: FastaIterator.h:53
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:421
std::ifstream input_file_
input file
Definition: FastaIterator.h:187
std::pair< String, String > FASTAEntry
Definition: FastaIterator.h:59
std::string header_
actual fasta header
Definition: FastaIterator.h:193
Not implemented exception.
Definition: Exception.h:437
static PepIterator * create()
needed by Factory
Definition: FastaIterator.h:173
static const String getProductName()
needed by Factory
Definition: FastaIterator.h:164

OpenMS / TOPP release 2.3.0 Documentation generated on Tue Jan 9 2018 18:22:00 using doxygen 1.8.13