KmerIterator.hpp

#ifndef BFG_KMER_ITERATOR_HPP
#define BFG_KMER_ITERATOR_HPP

#include <iterator>
#include "Kmer.hpp"


/* Short description:
 *  - Easily iterate through kmers in a read
 *  - If the read contains any N, then the N is skipped and checked whether
 *    there is a kmer to the right of the N
 * */
class KmerIterator : public std::iterator<std::input_iterator_tag, std::pair<Kmer, int>, int> {
 public:
  KmerIterator() : s_(NULL), p_(), invalid_(true) {}
  KmerIterator(const char *s) : s_(s), p_(), invalid_(false) { find_next(-1,-1,false);}
  KmerIterator(const KmerIterator& o) : s_(o.s_), p_(o.p_), invalid_(o.invalid_) {}

  KmerIterator& operator++();
  KmerIterator operator++(int);
  void raise(Kmer& km, Kmer& rep);

  bool operator==(const KmerIterator& o);
  bool operator!=(const KmerIterator& o) { return !this->operator==(o);}

  std::pair<Kmer, int>& operator*();
  std::pair<Kmer, int> *operator->();

 private:
  void find_next(size_t i, size_t j, bool last_valid);

  const char *s_;
  std::pair<Kmer, int> p_;
  bool invalid_;
};

#endif // BFG_KMER_ITERATOR_HPP