%include "IMP/core/core_macros.h"


/* Add additional IMPCORE_CONTAINER methods for scripting languages
   when the plural container is in the core namespace. */
%define IMPCORE_CONTAINER_SWIG(type, Ucname, lcname)
%extend type {
  IMP::core::Ucname##s get_##lcname##s() const {
    IMP::core::Ucname##s ret(self->lcname##s_begin(), self->lcname##s_end());
    return ret;
  }
}
%enddef


namespace IMP {
  namespace core {
    IMPCORE_CONTAINER_SWIG(MonteCarlo, Mover, mover)
    //IMP_CONTAINER_SWIG(FilteredListSingletonContainer, Particle, singleton)
    //IMP_CONTAINER_SWIG(ListSingletonContainer, Particle, singleton)
  }
}


IMP_REFCOUNT_RETURN_SINGLE(IMP::core::Mover)

/* Don't wrap internal classes */
%ignore IMP::core::internal::ChildArrayTraits;

/* Wrap our own base classes */
%include "IMP/core/ClosePairsFinder.h"
%include "IMP/core/Mover.h"
%include "IMP/core/MoverBase.h"

%include "IMP/core/XYZ.h"
%include "IMP/core/XYZR.h"


/* Wrap the final classes */
%include "IMP/core/AngleTripletScore.h"
%include "IMP/core/AttributeSingletonScore.h"
%include "IMP/core/BallMover.h"
%include "IMP/core/IncrementalBallMover.h"
%include "IMP/core/BoxSweepClosePairsFinder.h"
%include "IMP/core/CentroidOfRefined.h"
%include "IMP/core/ChecksScoreState.h"
%include "IMP/core/ChildrenRefiner.h"
%include "IMP/core/ClosedCubicSpline.h"
%include "IMP/core/ClosePairsPairScore.h"
%include "IMP/core/ConjugateGradients.h"
%include "IMP/core/ConnectivityRestraint.h"
%include "IMP/core/ConstantRestraint.h"
%include "IMP/core/Cosine.h"
%include "IMP/core/CoverRefined.h"
%include "IMP/core/DerivativesFromRefined.h"
%include "IMP/core/DerivativesToRefined.h"
%include "IMP/core/DiameterRestraint.h"
%include "IMP/core/Transform.h"
%include "IMP/core/DihedralRestraint.h"
%include "IMP/core/DistancePairScore.h"
%include "IMP/core/DistanceRestraint.h"
%include "IMP/core/DistanceToSingletonScore.h"
%include "IMP/core/ExcludedVolumeRestraint.h"
%include "IMP/core/BoundingBox3DSingletonScore.h"
%include "IMP/core/FixedRefiner.h"
%include "IMP/core/GridClosePairsFinder.h"
%include "IMP/core/Harmonic.h"
%include "IMP/core/HarmonicLowerBound.h"
%include "IMP/core/HarmonicUpperBound.h"
%include "IMP/core/Hierarchy.h"
%inline %{
namespace IMP {
namespace core {
void breadth_first_traversal(Hierarchy d, HierarchyVisitor *f)
{
  std::deque<Hierarchy> stack;
  stack.push_back(d);
  //d.show(std::cerr);
  do {
    Hierarchy cur= stack.front();
    stack.pop_front();
    if (f->operator()(cur)) {
      //std::cerr << "Visiting particle " << cur.get_particle() << std::endl;
      for (int i=cur.get_number_of_children()-1; i>=0; --i) {
        stack.push_back(cur.get_child(i));
      }
    }
  } while (!stack.empty());
}

void depth_first_traversal(Hierarchy d, HierarchyVisitor *f)
{
  std::vector<Hierarchy> stack;
  stack.push_back(d);
  do {
    Hierarchy cur= stack.back();
    stack.pop_back();
    if (f->operator()(cur)) {
      for (int i=cur.get_number_of_children()-1; i>=0; --i) {
        stack.push_back(cur.get_child(i));
      }
    }
  } while (!stack.empty());
}
}
}

%}
%include "IMP/core/LeavesRefiner.h"
%include "IMP/core/Linear.h"
%include "IMP/core/MonteCarlo.h"
%include "IMP/core/NormalMover.h"
%include "IMP/core/OpenCubicSpline.h"
%include "IMP/core/QuadraticClosePairsFinder.h"
%include "IMP/core/RefinedPairsPairScore.h"
%include "IMP/core/rigid_bodies.h"
%include "IMP/core/RigidClosePairsFinder.h"
%include "IMP/core/SphereDistancePairScore.h"
%include "IMP/core/SteepestDescent.h"
%include "IMP/core/TransformedDistancePairScore.h"
%include "IMP/core/TypedPairScore.h"
%include "IMP/core/RigidBodyDistancePairScore.h"
%include "IMP/core/TableRefiner.h"
%include "IMP/core/TruncatedHarmonic.h"
%include "IMP/core/MCCGSampler.h"

%include "IMP/core/PairRestraint.h"
%include "IMP/core/SingletonRestraint.h"
%include "IMP/core/TripletRestraint.h"
%include "IMP/core/QuadRestraint.h"

%include "IMP/core/SingletonConstraint.h"
%include "IMP/core/PairConstraint.h"
%include "IMP/core/TripletConstraint.h"
%include "IMP/core/QuadConstraint.h"

%include "IMP/core/AngleRestraint.h"
%include "IMP/core/RigidBodyMover.h"
%include "IMP/core/VolumeRestraint.h"
%include "IMP/core/utility.h"



namespace IMP {
  namespace core {
    %template(Movers) ::IMP::VectorOfRefCounted< IMP::core::Mover*, IMP::RefCounted::Policy >;
    %template(MoversTemp) ::std::vector<IMP::core::Mover*>;
    %implicitconv Mover ;
    %template(TruncatedHarmonicLowerBound) ::IMP::core::TruncatedHarmonic<LOWER>;
    %template(TruncatedHarmonicUpperBound) ::IMP::core::TruncatedHarmonic<UPPER>;
    %template(TruncatedHarmonicBound) ::IMP::core::TruncatedHarmonic<BOTH>;
    IMP_SWIG_DECORATORS(XYZ, XYZs, Particles)
    IMP_SWIG_DECORATORS(XYZR, XYZRs, XYZs)
    IMP_SWIG_DECORATORS(RigidBody, RigidBodies, XYZs)
    IMP_SWIG_DECORATORS(RigidMember, RigidMembers, XYZs)
    /* Swig bitches about it having "the same name" as IMP.atom.Hierarchies
       even though it doesn't. */
    %template(GenericHierarchies) ::IMP::DecoratorsWithTraits<IMP::core::Hierarchy,
                                                       IMP::Particles,
                                                       IMP::core::HierarchyTraits>;
    %template(GenericHierarchiesTemp) ::IMP::DecoratorsWithTraits<IMP::core::Hierarchy, IMP::ParticlesTemp, IMP::core::HierarchyTraits>;
    // swig screws up on scopes, I can't be bothered to fix it
    //%template(show_named_hierarchy) show<::IMP::core::Name>;
  }
  namespace algebra {
    %template(get_transformation_aligning_first_to_second) get_transformation_aligning_first_to_second<core::XYZsTemp, std::vector<algebra::VectorD<3> > >;
    %template(get_transformation_aligning_first_to_second) get_transformation_aligning_first_to_second<core::XYZsTemp, core::XYZsTemp>;
    %template(get_transformation_aligning_first_to_second) get_transformation_aligning_first_to_second< std::vector<algebra::VectorD<3> >, core::XYZsTemp>;
  }
}