/**
 *  \file IMP/atom/Fragment.h
 *  \brief A decorator for associating a Hierachy piece
 *
 *  Copyright 2007-2013 IMP Inventors. All rights reserved.
 */

#ifndef IMPATOM_FRAGMENT_H
#define IMPATOM_FRAGMENT_H

#include <IMP/atom/atom_config.h>
#include "Hierarchy.h"
#include <IMP/Decorator.h>

IMPATOM_BEGIN_NAMESPACE

//! A decorator to associate a particle with a part of a protein/DNA/RNA
/** The decorator stores an optional list of resdiue indexes.
 */
class IMPATOMEXPORT Fragment: public Hierarchy
{
  static IntsKey get_begins_key();
  static IntsKey get_ends_key();
  static void set_residue_indexes(Particle*p, Ints ris);
  static void set_residue_indexes(Particle*p, const IntPairs& ris);
  static IntKey get_marker_key();
public:
  static Fragment setup_particle(Particle *p, const Ints &ris=Ints()) {
    if (!Hierarchy::particle_is_instance(p)) {
      Hierarchy::setup_particle(p);
    }
    set_residue_indexes(p, ris);
    p->add_attribute(get_marker_key(), 1);
    return Fragment(p);
  }

  //! Create a domain by copying from o
  static Fragment setup_particle(Particle *p, Fragment o) {
    if (!Hierarchy::particle_is_instance(p)) {
      Hierarchy::setup_particle(p);
    }
    IntPairs ris= o.get_residue_index_ranges();
    set_residue_indexes(p, ris);
    p->add_attribute(get_marker_key(), 1);
    return Fragment(p);
  }

  virtual ~Fragment();

  static bool particle_is_instance(Particle *p) {
    return Hierarchy::particle_is_instance(p)
      && p->has_attribute(get_marker_key());
  }


  //! Add the residues whose indexes are listed in the passed vector
  void set_residue_indexes( Ints o) {
    set_residue_indexes(get_particle(), o);
  }

  Ints get_residue_indexes() const;

  IntPairs get_residue_index_ranges() const;

  //! Return true if this fragment contains a given residue
  /** This could be made more efficient. */
  bool get_contains_residue(int rindex) const;

  IMP_DECORATOR(Fragment, Hierarchy);
};

IMP_DECORATORS(Fragment,Fragments, Hierarchies);

IMPATOM_END_NAMESPACE

#endif  /* IMPATOM_FRAGMENT_H */