mutator.h

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#ifndef BALL_STRUCTURE_MUTATOR_H
#define BALL_STRUCTURE_MUTATOR_H

#include <BALL/COMMON/debug.h>
#include <BALL/COMMON/global.h>

namespace BALL
{
  class String;
  class FragmentDB;

  class BALL_EXPORT Mutator
  {
    public:
      enum MutatorOptions { NONE = 0, OPTIMIZE = 1 };

      Mutator(FragmentDB* db = 0);
      virtual ~Mutator();

      /*
       * Set a new FragmentDB instance that shall be used to obtain
       * the new bases. If 0 is passed, a default instance will be automatically
       * created when calling DNAMutator::mutate(). The passed instance will
       * <b>not</b> be deleted upon destruction.
       */
      void setFragmentDB(FragmentDB* db);

      virtual void setup();

      virtual void addMutation(Index i, const String& new_frag_name) = 0;

      virtual void clearMutations() = 0;

      void mutate(MutatorOptions opts = NONE);

      virtual bool optimize() = 0;

    protected:
      FragmentDB* db_;

      virtual void mutate_impl_(MutatorOptions opts) = 0;

    private:
      bool keep_db_;
      void freeDB_();
  };

#ifndef BALL_DEBUG
# include <BALL/STRUCTURE/mutator.iC>
#endif

}

#endif //BALL_STRUCTURE_MUTATOR_H