alg/sequence_location.hpp

   1 #ifndef _SEQUENCE_LOCATION_H_
   2 #define _SEQUENCE_LOCATION_H_
   3
   4 #include <boost/shared_ptr.hpp>
   5 #include "alg/sequence.hpp"
   6
   7 // FIXME: Deprecate! SeqSpan and/or Sequence should replace sequence location
   8 //! convenience structure for holding selected track segments
   9 class SequenceLocation {
  10   public:
  11     typedef size_t size_type;
  12
  13     SequenceLocation(boost::shared_ptr<Sequence> s, int l, int r);
  14     SequenceLocation(const Sequence& s, int l, int r);
  15     SequenceLocation(const SequenceLocation& );
  16     SequenceLocation& operator=(const SequenceLocation&);
  17
  18     //! get the sequence we're selecting from
  19     const Sequence& getSequence() const;
  20     //! return the selected subsequence
  21     Sequence getSelectedSequence() const;
  22     void setLeft(int l);
  23     int getLeft() const;
  24     void setCount(size_type c);
  25     size_type getCount() const;
  26     //! set one past the right-most base
  27     void setRight(int r);
  28     int getRight() const;
  29
  30     //! return total length of region (alias for getCount())
  31     size_type size() const;
  32   private:
  33     boost::shared_ptr<Sequence> sequence;
  34     int left;
  35     int right;
  36   };
  37 #endif