Index: kernel/include/IMP/singleton_scores/DistanceToSingletonScore.h
===================================================================
--- kernel/include/IMP/singleton_scores/DistanceToSingletonScore.h (revision 619)
+++ kernel/include/IMP/singleton_scores/DistanceToSingletonScore.h (working copy)
@@ -10,7 +10,7 @@
#include "../SingletonScore.h"
#include "../Vector3D.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../UnaryFunction.h"
namespace IMP
@@ -21,7 +21,7 @@
*/
class IMPDLLEXPORT DistanceToSingletonScore : public SingletonScore
{
- internal::ObjectPointer<UnaryFunction, true> f_;
+ Pointer<UnaryFunction> f_;
Vector3D pt_;
public:
DistanceToSingletonScore(UnaryFunction *f, const Vector3D& pt);
Index: kernel/include/IMP/singleton_scores/AttributeSingletonScore.h
===================================================================
--- kernel/include/IMP/singleton_scores/AttributeSingletonScore.h (revision 619)
+++ kernel/include/IMP/singleton_scores/AttributeSingletonScore.h (working copy)
@@ -9,7 +9,7 @@
#define __IMP_ATTRIBUTE_SINGLETON_SCORE_H
#include "../SingletonScore.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../UnaryFunction.h"
namespace IMP
@@ -20,7 +20,7 @@
*/
class IMPDLLEXPORT AttributeSingletonScore : public SingletonScore
{
- internal::ObjectPointer<UnaryFunction, true> f_;
+ Pointer<UnaryFunction> f_;
FloatKey k_;
public:
AttributeSingletonScore(UnaryFunction *f, FloatKey k);
Index: kernel/include/IMP/SingletonScore.h
===================================================================
--- kernel/include/IMP/SingletonScore.h (revision 619)
+++ kernel/include/IMP/SingletonScore.h (working copy)
@@ -9,7 +9,7 @@
#include "IMP_config.h"
#include "base_types.h"
-#include "internal/RefCountedObject.h"
+#include "RefCountedObject.h"
#include "DerivativeAccumulator.h"
namespace IMP
@@ -27,7 +27,7 @@
/** SingletonScores should take a UnaryFunction as their first
argument if such is needed.
*/
-class IMPDLLEXPORT SingletonScore : public internal::RefCountedObject
+class IMPDLLEXPORT SingletonScore : public RefCountedObject
{
public:
SingletonScore() {}
Index: kernel/include/IMP/Model.h
===================================================================
--- kernel/include/IMP/Model.h (revision 619)
+++ kernel/include/IMP/Model.h (working copy)
@@ -10,7 +10,7 @@
#define __IMP_MODEL_H
#include "IMP_config.h"
-#include "internal/Object.h"
+#include "Object.h"
#include "internal/kernel_version_info.h"
#include "base_types.h"
#include "VersionInfo.h"
@@ -30,7 +30,7 @@
Currently no suport for constraints (e.g. rigid bodies).
\ingroup kernel
*/
-class IMPDLLEXPORT Model: public internal::Object
+class IMPDLLEXPORT Model: public Object
{
friend class Restraint;
unsigned int iteration_;
Index: kernel/include/IMP/UnaryFunction.h
===================================================================
--- kernel/include/IMP/UnaryFunction.h (revision 619)
+++ kernel/include/IMP/UnaryFunction.h (working copy)
@@ -9,7 +9,7 @@
#include "IMP_config.h"
#include "base_types.h"
-#include "internal/RefCountedObject.h"
+#include "RefCountedObject.h"
namespace IMP
{
@@ -18,7 +18,7 @@
/** These functors take a single feature value, and return a corresponding
score (and optionally also the first derivative).
*/
-class IMPDLLEXPORT UnaryFunction : public internal::RefCountedObject
+class IMPDLLEXPORT UnaryFunction : public RefCountedObject
{
public:
UnaryFunction() {}
Index: kernel/include/IMP/score_states/CoverBondsScoreState.h
===================================================================
--- kernel/include/IMP/score_states/CoverBondsScoreState.h (revision 619)
+++ kernel/include/IMP/score_states/CoverBondsScoreState.h (working copy)
@@ -11,7 +11,7 @@
#include "../ScoreState.h"
#include "BondDecoratorListScoreState.h"
#include "../internal/kernel_version_info.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
namespace IMP
{
@@ -30,7 +30,7 @@
*/
class IMPDLLEXPORT CoverBondsScoreState: public ScoreState
{
- internal::ObjectPointer<BondDecoratorListScoreState, true> bl_;
+ Pointer<BondDecoratorListScoreState> bl_;
FloatKey rk_;
public:
/** Get the list of bonds from the BondDecoratorListScoreState. This list is
Index: kernel/include/IMP/score_states/BipartiteNonbondedListScoreState.h
===================================================================
--- kernel/include/IMP/score_states/BipartiteNonbondedListScoreState.h (revision 619)
+++ kernel/include/IMP/score_states/BipartiteNonbondedListScoreState.h (working copy)
@@ -43,7 +43,7 @@
};
protected:
Algorithm a_;
- internal::ObjectPointer<MaxChangeScoreState, true> mc0_, mc1_, mcr_;
+ Pointer<MaxChangeScoreState> mc0_, mc1_, mcr_;
void process_sets(const Particles &p0,
const Particles &p1);
Index: kernel/include/IMP/score_states/AllNonbondedListScoreState.h
===================================================================
--- kernel/include/IMP/score_states/AllNonbondedListScoreState.h (revision 619)
+++ kernel/include/IMP/score_states/AllNonbondedListScoreState.h (working copy)
@@ -50,7 +50,7 @@
};
protected:
Algorithm a_;
- internal::ObjectPointer<MaxChangeScoreState, true> mc_, mcr_;
+ Pointer<MaxChangeScoreState> mc_, mcr_;
void check_nbl() const;
Index: kernel/include/IMP/restraints/ConnectivityRestraint.h
===================================================================
--- kernel/include/IMP/restraints/ConnectivityRestraint.h (revision 619)
+++ kernel/include/IMP/restraints/ConnectivityRestraint.h (working copy)
@@ -50,7 +50,7 @@
protected:
- internal::ObjectPointer<PairScore, true> ps_;
+ Pointer<PairScore> ps_;
//! The indices for the first particle in each set
/** set_offset_[i] is the first index of set i and set_offset_[i+1] is
Index: kernel/include/IMP/restraints/SingletonListRestraint.h
===================================================================
--- kernel/include/IMP/restraints/SingletonListRestraint.h (revision 619)
+++ kernel/include/IMP/restraints/SingletonListRestraint.h (working copy)
@@ -12,7 +12,7 @@
#include "../IMP_config.h"
#include "../Restraint.h"
#include "../internal/kernel_version_info.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../SingletonScore.h"
#include <iostream>
@@ -40,7 +40,7 @@
using Restraint::set_particles;
protected:
- internal::ObjectPointer<SingletonScore, true> ss_;
+ Pointer<SingletonScore> ss_;
};
} // namespace IMP
Index: kernel/include/IMP/restraints/PairChainRestraint.h
===================================================================
--- kernel/include/IMP/restraints/PairChainRestraint.h (revision 619)
+++ kernel/include/IMP/restraints/PairChainRestraint.h (working copy)
@@ -12,7 +12,7 @@
#include "../IMP_config.h"
#include "../Restraint.h"
#include "../internal/kernel_version_info.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../PairScore.h"
#include <vector>
@@ -43,7 +43,7 @@
void clear_chains();
protected:
- internal::ObjectPointer<PairScore, true> ts_;
+ Pointer<PairScore> ts_;
std::vector<unsigned int> chain_splits_;
};
Index: kernel/include/IMP/restraints/BondDecoratorRestraint.h
===================================================================
--- kernel/include/IMP/restraints/BondDecoratorRestraint.h (revision 619)
+++ kernel/include/IMP/restraints/BondDecoratorRestraint.h (working copy)
@@ -14,7 +14,7 @@
#include "../IMP_config.h"
#include "../Restraint.h"
#include "../internal/kernel_version_info.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../UnaryFunction.h"
namespace IMP
@@ -49,7 +49,7 @@
protected:
BondDecoratorListScoreState *bl_;
- internal::ObjectPointer<UnaryFunction, true> f_;
+ Pointer<UnaryFunction> f_;
};
} // namespace IMP
Index: kernel/include/IMP/restraints/TunnelRestraint.h
===================================================================
--- kernel/include/IMP/restraints/TunnelRestraint.h (revision 619)
+++ kernel/include/IMP/restraints/TunnelRestraint.h (working copy)
@@ -39,7 +39,7 @@
Vector3D center_;
Float height_;
Float radius_;
- internal::ObjectPointer<UnaryFunction, true> f_;
+ Pointer<UnaryFunction> f_;
FloatKey rk_;
public:
TunnelRestraint(UnaryFunction* f, FloatKey rk);
Index: kernel/include/IMP/restraints/AngleRestraint.h
===================================================================
--- kernel/include/IMP/restraints/AngleRestraint.h (revision 619)
+++ kernel/include/IMP/restraints/AngleRestraint.h (working copy)
@@ -11,7 +11,7 @@
#include "../IMP_config.h"
#include "../Restraint.h"
#include "../internal/kernel_version_info.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../triplet_scores/AngleTripletScore.h"
namespace IMP
@@ -35,7 +35,7 @@
IMP_RESTRAINT(internal::kernel_version_info)
protected:
- internal::ObjectPointer<AngleTripletScore, true> sf_;
+ Pointer<AngleTripletScore> sf_;
};
} // namespace IMP
Index: kernel/include/IMP/restraints/NonbondedRestraint.h
===================================================================
--- kernel/include/IMP/restraints/NonbondedRestraint.h (revision 619)
+++ kernel/include/IMP/restraints/NonbondedRestraint.h (working copy)
@@ -14,7 +14,7 @@
#include "../IMP_config.h"
#include "../Restraint.h"
#include "../internal/kernel_version_info.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../score_states/NonbondedListScoreState.h"
namespace IMP
@@ -41,8 +41,8 @@
IMP_RESTRAINT(internal::kernel_version_info)
protected:
- internal::ObjectPointer<NonbondedListScoreState, true> nbl_;
- internal::ObjectPointer<PairScore, true> sf_;
+ Pointer<NonbondedListScoreState> nbl_;
+ Pointer<PairScore> sf_;
};
} // namespace IMP
Index: kernel/include/IMP/restraints/TripletChainRestraint.h
===================================================================
--- kernel/include/IMP/restraints/TripletChainRestraint.h (revision 619)
+++ kernel/include/IMP/restraints/TripletChainRestraint.h (working copy)
@@ -12,7 +12,7 @@
#include "../IMP_config.h"
#include "../Restraint.h"
#include "../internal/kernel_version_info.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../TripletScore.h"
#include <vector>
@@ -43,7 +43,7 @@
void clear_chains();
protected:
- internal::ObjectPointer<TripletScore, true> ts_;
+ Pointer<TripletScore> ts_;
std::vector<unsigned int> chain_splits_;
};
Index: kernel/include/IMP/restraints/PairListRestraint.h
===================================================================
--- kernel/include/IMP/restraints/PairListRestraint.h (revision 619)
+++ kernel/include/IMP/restraints/PairListRestraint.h (working copy)
@@ -13,7 +13,7 @@
#include "../Restraint.h"
#include "../Particle.h"
#include "../internal/kernel_version_info.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../PairScore.h"
#include <iostream>
@@ -41,7 +41,7 @@
void add_particle_pairs(const ParticlePairs &ps);
protected:
- internal::ObjectPointer<PairScore, true> ss_;
+ Pointer<PairScore> ss_;
};
} // namespace IMP
Index: kernel/include/IMP/Restraint.h
===================================================================
--- kernel/include/IMP/Restraint.h (revision 619)
+++ kernel/include/IMP/Restraint.h (working copy)
@@ -13,8 +13,8 @@
#include "Model.h"
#include "Particle.h"
#include "VersionInfo.h"
-#include "internal/Object.h"
-#include "internal/ObjectPointer.h"
+#include "Object.h"
+#include "Pointer.h"
#include "log.h"
#include "utility.h"
@@ -52,7 +52,7 @@
\note Physical restraints should use the units of kcal/mol for restraint
values and kcal/mol/A for derivatives.
*/
-class IMPDLLEXPORT Restraint : public internal::RefCountedObject
+class IMPDLLEXPORT Restraint : public RefCountedObject
{
public:
//! Initialize the Restraint
@@ -100,7 +100,7 @@
IMP_LIST(protected, Particle, particle, Particle*)
private:
- internal::ObjectPointer<Model, false> model_;
+ Pointer<Model> model_;
/* True if restraint has not been deactivated.
If it is not active, evaluate should not be called
Index: kernel/include/IMP/DecoratorBase.h
===================================================================
--- kernel/include/IMP/DecoratorBase.h (revision 619)
+++ kernel/include/IMP/DecoratorBase.h (working copy)
@@ -8,8 +8,8 @@
#ifndef __IMP_DECORATOR_BASE_H
#define __IMP_DECORATOR_BASE_H
-#include "internal/Object.h"
-#include "internal/ObjectPointer.h"
+#include "Object.h"
+#include "Pointer.h"
#include "Particle.h"
namespace IMP
@@ -21,7 +21,7 @@
class IMPDLLEXPORT DecoratorBase
{
protected:
- internal::ObjectPointer<Particle, true> particle_;
+ Pointer<Particle> particle_;
DecoratorBase(Particle *p): particle_(p) {}
bool is_default() const {
return !particle_;
Index: kernel/include/IMP/ParticleRefiner.h
===================================================================
--- kernel/include/IMP/ParticleRefiner.h (revision 619)
+++ kernel/include/IMP/ParticleRefiner.h (working copy)
@@ -10,7 +10,7 @@
#include "IMP_config.h"
#include "base_types.h"
#include "VersionInfo.h"
-#include "internal/RefCountedObject.h"
+#include "RefCountedObject.h"
namespace IMP
{
@@ -22,7 +22,7 @@
/** The job of this class is to take a single particle and, if
appropriate, return a list of particles.
*/
-class IMPDLLEXPORT ParticleRefiner : public internal::RefCountedObject
+class IMPDLLEXPORT ParticleRefiner : public RefCountedObject
{
public:
ParticleRefiner() {}
Index: kernel/include/IMP/optimizers/MonteCarlo.h
===================================================================
--- kernel/include/IMP/optimizers/MonteCarlo.h (revision 619)
+++ kernel/include/IMP/optimizers/MonteCarlo.h (working copy)
@@ -97,7 +97,7 @@
Float prior_energy_;
Float stop_energy_;
Float probability_;
- internal::ObjectPointer<Optimizer, true> cg_;
+ Pointer<Optimizer> cg_;
unsigned int num_local_steps_;
unsigned int stat_forward_steps_taken_;
unsigned int stat_upward_steps_taken_;
Index: kernel/include/IMP/optimizers/Mover.h
===================================================================
--- kernel/include/IMP/optimizers/Mover.h (revision 619)
+++ kernel/include/IMP/optimizers/Mover.h (working copy)
@@ -10,8 +10,8 @@
#include "../IMP_config.h"
#include "../base_types.h"
-#include "../internal/Object.h"
-#include "../internal/ObjectPointer.h"
+#include "../Object.h"
+#include "../Pointer.h"
#include "../Optimizer.h"
#include <vector>
@@ -32,7 +32,7 @@
//! A class to make a monte carlo move.
/** You probably want to use MoverBase if you are implementing a Mover.
*/
-class IMPDLLEXPORT Mover: public internal::Object
+class IMPDLLEXPORT Mover: public Object
{
friend class MonteCarlo;
void set_optimizer(Optimizer *c, MoverIndex i) {
@@ -40,7 +40,7 @@
index_=i;
}
- internal::ObjectPointer<Optimizer, false> opt_;
+ Pointer<Optimizer> opt_;
MoverIndex index_;
public:
Mover();
Index: kernel/include/IMP/OptimizerState.h
===================================================================
--- kernel/include/IMP/OptimizerState.h (revision 619)
+++ kernel/include/IMP/OptimizerState.h (working copy)
@@ -10,8 +10,8 @@
#include "IMP_config.h"
#include "VersionInfo.h"
-#include "internal/RefCountedObject.h"
-#include "internal/ObjectPointer.h"
+#include "RefCountedObject.h"
+#include "Pointer.h"
#include "Optimizer.h"
#include <iostream>
@@ -33,7 +33,7 @@
logging is TERSE the restraint should print out only a constant number
of lines per update call.
*/
-class IMPDLLEXPORT OptimizerState : public internal::Object
+class IMPDLLEXPORT OptimizerState : public Object
{
friend class Optimizer;
void set_optimizer(Optimizer* optimizer);
@@ -64,7 +64,7 @@
}
protected:
//! Stored optimizer
- internal::ObjectPointer<Optimizer, false> optimizer_;
+ Pointer<Optimizer> optimizer_;
};
IMP_OUTPUT_OPERATOR(OptimizerState);
Index: kernel/include/IMP/pair_scores/SphereDistancePairScore.h
===================================================================
--- kernel/include/IMP/pair_scores/SphereDistancePairScore.h (revision 619)
+++ kernel/include/IMP/pair_scores/SphereDistancePairScore.h (working copy)
@@ -9,7 +9,7 @@
#define __IMP_SPHERE_DISTANCE_PAIR_SCORE_H
#include "../PairScore.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
#include "../UnaryFunction.h"
namespace IMP
@@ -20,7 +20,7 @@
*/
class IMPDLLEXPORT SphereDistancePairScore : public PairScore
{
- internal::ObjectPointer<UnaryFunction, true> f_;
+ Pointer<UnaryFunction> f_;
FloatKey radius_;
public:
SphereDistancePairScore(UnaryFunction *f,
Index: kernel/include/IMP/pair_scores/TypedPairScore.h
===================================================================
--- kernel/include/IMP/pair_scores/TypedPairScore.h (revision 619)
+++ kernel/include/IMP/pair_scores/TypedPairScore.h (working copy)
@@ -58,14 +58,14 @@
void set_pair_score(PairScore *ps, Int atype, Int btype) {
score_map_[std::pair<Int,Int>(std::min(atype, btype),
std::max(atype, btype))]
- = internal::ObjectPointer<PairScore, true>(ps);
+ = Pointer<PairScore>(ps);
}
protected:
//! The key used for the particle types.
IntKey typekey_;
typedef std::map<std::pair<Int,Int>,
- internal::ObjectPointer<PairScore, true> > ScoreMap;
+ Pointer<PairScore> > ScoreMap;
//! Mapping from particle types to PairScores.
ScoreMap score_map_;
//! Whether to throw an exception for invalid particle types.
Index: kernel/include/IMP/pair_scores/DistancePairScore.h
===================================================================
--- kernel/include/IMP/pair_scores/DistancePairScore.h (revision 619)
+++ kernel/include/IMP/pair_scores/DistancePairScore.h (working copy)
@@ -10,7 +10,7 @@
#include "../PairScore.h"
#include "../UnaryFunction.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
namespace IMP
{
@@ -20,7 +20,7 @@
*/
class IMPDLLEXPORT DistancePairScore : public PairScore
{
- internal::ObjectPointer<UnaryFunction, true> f_;
+ Pointer<UnaryFunction> f_;
public:
DistancePairScore(UnaryFunction *f);
virtual ~DistancePairScore(){}
Index: kernel/include/IMP/pair_scores/RefineOncePairScore.h
===================================================================
--- kernel/include/IMP/pair_scores/RefineOncePairScore.h (revision 619)
+++ kernel/include/IMP/pair_scores/RefineOncePairScore.h (working copy)
@@ -11,7 +11,7 @@
#include "../PairScore.h"
#include "../UnaryFunction.h"
#include "../ParticleRefiner.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
namespace IMP
{
@@ -24,8 +24,8 @@
*/
class IMPDLLEXPORT RefineOncePairScore : public PairScore
{
- internal::ObjectPointer<ParticleRefiner, true> r_;
- internal::ObjectPointer<PairScore, true> f_;
+ Pointer<ParticleRefiner> r_;
+ Pointer<PairScore> f_;
public:
/** \param[in] r The ParticleRefiner to call on each particle
Index: kernel/include/IMP/RefCountedObject.h
===================================================================
--- kernel/include/IMP/RefCountedObject.h (revision 619)
+++ kernel/include/IMP/RefCountedObject.h (working copy)
@@ -17,9 +17,6 @@
namespace IMP
{
-namespace internal
-{
-
//! Common base class for ref counted objects.
/** This class acts as a tag rather than providing any functionality.
@@ -48,125 +45,6 @@
}
};
-
-
-template <bool REF>
-struct Ref
-{
- template <class O>
- static void eval(O* o) {
- BOOST_STATIC_ASSERT((!boost::is_base_of<RefCountedObject, O >::value));
- IMP_LOG(VERBOSE, "Not refing particle " << o << std::endl);
- }
-};
-
-template <>
-struct Ref<true>
-{
- template <class O>
- static void eval(O* o) {
- IMP_LOG(VERBOSE, "Refing particle " << o->get_index()
- << o->get_ref_count() << std::endl);
- o->assert_is_valid();
- o->ref();
- }
-};
-
-template <bool REF>
-struct UnRef
-{
- template <class O>
- static void eval(O* o) {
- BOOST_STATIC_ASSERT((!boost::is_base_of<RefCountedObject, O >::value));
- IMP_LOG(VERBOSE, "Not Unrefing object " << o << std::endl);
- }
-};
-
-template <>
-struct UnRef<true>
-{
- template <class O>
- static void eval(O *o) {
- IMP_LOG(VERBOSE, "Unrefing particle " << o->get_index()
- << " " << o->get_ref_count() << std::endl);
- o->assert_is_valid();
- o->unref();
- if (!o->get_has_ref()) {
- delete o;
- }
- }
- };
-
-
-//! Can be called on any object and will only unref it if appropriate
-template <class O>
-void unref(O o)
-{
- BOOST_STATIC_ASSERT(!boost::is_pointer<O>::value);
-}
-
-
-//! Can be called on any object and will only ref it if appropriate
-template <class O>
-void ref(O o)
-{
- BOOST_STATIC_ASSERT(!boost::is_pointer<O>::value);
-}
-
-//! Can be called on any object and will only unref it if appropriate
-template <class O>
-void unref(O* o)
-{
- UnRef<(boost::is_base_of<RefCountedObject, O >::value)>::eval(o);
-}
-
-
-//! Can be called on any object and will only ref it if appropriate
-template <class O>
-void ref(O* o)
-{
- Ref<(boost::is_base_of<RefCountedObject, O >::value)>::eval(o);
-}
-
-
-//! Can be called on any object and will only unref it if appropriate
-template <class O>
-void disown(O* o)
-{
- /*IMP_LOG(VERBOSE, "Disown called with "
- << (boost::is_base_of<RefCountedObject, O >::value)
- << " for " << o << " " << o->get_ref_count() << std::endl);*/
- o->unref();
- if (!o->get_has_ref()) {
- delete o;
- }
-}
-
-
-//! Can be called on any object and will only ref it if appropriate
-template <class O>
-void own(O* o)
-{
- /*IMP_LOG(VERBOSE, "Own called with "
- << (boost::is_base_of<RefCountedObject, O >::value)
- << " for " << o
- << " " << o->get_ref_count() << std::endl);*/
- if (boost::is_base_of<RefCountedObject, O >::value) {
- // no checks
- } else {
- IMP_check(!o->get_has_ref(), "Trying to own already owned but "
- << "non-reference-counted object: " << *o,
- ValueException);
- }
- o->ref();
-}
-
-
-
-
-
-} // namespace internal
-
} // namespace IMP
#endif /* __IMP_REF_COUNTED_OBJECT_H */
Index: kernel/include/IMP/internal/SConscript
===================================================================
--- kernel/include/IMP/internal/SConscript (revision 619)
+++ kernel/include/IMP/internal/SConscript (working copy)
@@ -2,9 +2,9 @@
Import('env')
files = ['AttributeTable.h', 'graph_base.h', 'Grid3D.h', 'Vector.h',
- 'Object.h', 'ObjectPointer.h', 'ObjectContainer.h', 'ParticleGrid.h',
+ 'ref_counting.h', 'ObjectContainer.h', 'ParticleGrid.h',
'kernel_version_info.h', 'constants.h', 'units.h',
- 'RefCountedObject.h', 'utility.h', 'bbox_nbl_helpers.h',
+ 'utility.h', 'bbox_nbl_helpers.h',
'ArrayOnAttributesHelper.h', 'Unit.h', 'ExponentialNumber.h']
# Install the include files:
Index: kernel/include/IMP/internal/Vector.h
===================================================================
--- kernel/include/IMP/internal/Vector.h (revision 619)
+++ kernel/include/IMP/internal/Vector.h (working copy)
@@ -9,8 +9,9 @@
#define __IMP_VECTOR_H
#include "../exception.h"
-#include "Object.h"
-#include "RefCountedObject.h"
+#include "../Object.h"
+#include "../RefCountedObject.h"
+#include "ref_counting.h"
#include <vector>
Index: kernel/include/IMP/internal/units.h
===================================================================
--- kernel/include/IMP/internal/units.h (revision 619)
+++ kernel/include/IMP/internal/units.h (working copy)
@@ -119,6 +119,8 @@
typedef Multiply<Multiply<Centimeter, Centimeter>::type,
Centimeter>::type CubicCentimeter;
typedef Divide<Gram, CubicCentimeter>::type GramPerCubicCentimeter;
+typedef Shift<Second, -9>::type NanoSecond;
+typedef Shift<Second, -15>::type FemtoSecond;
Index: kernel/include/IMP/internal/Object.h
===================================================================
--- kernel/include/IMP/internal/Object.h (revision 619)
+++ kernel/include/IMP/internal/Object.h (working copy)
@@ -1,72 +0,0 @@
-/**
- * \file Object.h
- * \brief A shared base class to help in debugging and things.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_OBJECT_H
-#define __IMP_OBJECT_H
-
-#include "../exception.h"
-
-namespace IMP
-{
-
-namespace internal
-{
-
-//! Common base class for IMP objects.
-/** Currently this just makes the object noncopyable and adds heuristic checks
- to make sure the memory has not been freed.
-
- \note Do not use NDEBUG to remove check_value_ as that changes the memory
- layout and causes bad things to happen. It should get wrapped in some
- sort of macro later.
-
- \note This has ref and unref methods to simplifity ObjectContainer.
- For Object, the reference count can be at most 1.
-
- \internal
- */
-class IMPDLLEXPORT Object
-{
-protected:
- Object();
- ~Object();
-
-public:
- //! Throw an assertion if the object has been freed
- void assert_is_valid() const;
-
- bool get_has_ref() const {return count_ != 0;}
-
- void ref() {
- assert_is_valid();
- ++count_;
- }
-
- void unref() {
- assert_is_valid();
- IMP_assert(count_ !=0, "Too many unrefs on object");
- --count_;
- }
-
- unsigned int get_ref_count() const {
- return count_;
- }
-
-private:
- Object(const Object &o){}
- const internal::Object& operator=(const Object &o) {return *this;}
-
- int count_;
- double check_value_;
-};
-
-} // namespace internal
-
-} // namespace IMP
-
-#endif /* __IMP_OBJECT_H */
Index: kernel/include/IMP/internal/ObjectPointer.h
===================================================================
--- kernel/include/IMP/internal/ObjectPointer.h (revision 619)
+++ kernel/include/IMP/internal/ObjectPointer.h (working copy)
@@ -1,116 +0,0 @@
-/**
- * \file ObjectPointer.h
- * \brief A NULL-initialized pointer to an IMP Object.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_OBJECT_POINTER_H
-#define __IMP_OBJECT_POINTER_H
-
-#include "../log.h"
-#include "Object.h"
-#include "RefCountedObject.h"
-#include "../macros.h"
-#include "../exception.h"
-
-#include <boost/static_assert.hpp>
-#include <boost/type_traits.hpp>
-
-namespace IMP
-{
-
-namespace internal
-{
-
-//! A pointer to an IMP::Object
-/** The pointer is NULL initialized and checks accesses to throw an exception
- rather than core dump on an invalid access.
- \param[in] O The type of IMP::Object-derived object to point to
- \param[in] RC If true, the pointer is refcounted.
- */
-template <class O, bool RC>
-class ObjectPointer
-{
- typedef ObjectPointer<O, RC> This;
- O* o_;
-
- void set_pointer(O* p) {
- if (RC) {
- if (o_) disown(o_);
- if (p) own(p);
- o_=p;
- } else {
- o_=p;
- }
- }
-
- // Enforce that ref counted objects are ref counted
- BOOST_STATIC_ASSERT((RC || !boost::is_base_of<RefCountedObject, O>::value));
-
- void audit() const {
- IMP_assert(o_ != NULL, "Pointer is NULL");
- IMP_CHECK_OBJECT(o_);
- }
-
- bool is_default() const {
- return o_==NULL;
- }
- typedef bool (This::*unspecified_bool)() const;
-
-public:
- ObjectPointer(const ObjectPointer &o): o_(NULL) {
- set_pointer(o.o_);
- }
- ObjectPointer& operator=(const ObjectPointer &o){
- set_pointer(o.o_);
- return *this;
- }
- ObjectPointer(): o_(NULL) {}
- explicit ObjectPointer(O* o): o_(NULL) {
- IMP_assert(o, "Can't initialize with NULL pointer");
- set_pointer(o);
- }
- ~ObjectPointer(){
- set_pointer(NULL);
- }
- const O& operator*() const {
- audit();
- return *o_;
- }
- O& operator*() {
- audit();
- return *o_;
- }
- const O* operator->() const {
- audit();
- return o_;
- }
- O* operator->() {
- audit();
- return o_;
- }
- O* get() const {
- audit();
- return o_;
- }
- void operator=(O* o) {
- set_pointer(o);
- }
- IMP_COMPARISONS_1(o_);
-
- bool operator!() const {
- return !o_;
- }
-
- operator unspecified_bool() const {
- return o_ ? &This::operator! : 0;
- }
-};
-
-} // namespace internal
-
-} // namespace IMP
-
-#endif /* __IMP_OBJECT_POINTER_H */
Index: kernel/include/IMP/internal/ObjectContainer.h
===================================================================
--- kernel/include/IMP/internal/ObjectContainer.h (revision 619)
+++ kernel/include/IMP/internal/ObjectContainer.h (working copy)
@@ -8,8 +8,9 @@
#ifndef __IMP_OBJECT_CONTAINER_H
#define __IMP_OBJECT_CONTAINER_H
-#include "Object.h"
-#include "RefCountedObject.h"
+#include "../Object.h"
+#include "../RefCountedObject.h"
+#include "ref_counting.h"
#include <boost/iterator/filter_iterator.hpp>
Index: kernel/include/IMP/internal/ParticleGrid.h
===================================================================
--- kernel/include/IMP/internal/ParticleGrid.h (revision 619)
+++ kernel/include/IMP/internal/ParticleGrid.h (working copy)
@@ -11,7 +11,7 @@
#include "Grid3D.h"
#include "../score_states/MaxChangeScoreState.h"
#include "../base_types.h"
-#include "ObjectPointer.h"
+#include "../Pointer.h"
namespace IMP
{
@@ -20,7 +20,7 @@
{
/** \internal */
-class ParticleGrid: public internal::Object
+class ParticleGrid: public Object
{
// don't need ref counting since mc_ has the same set of points
typedef internal::Grid3D<Particles> Grid;
Index: kernel/include/IMP/internal/AttributeTable.h
===================================================================
--- kernel/include/IMP/internal/AttributeTable.h (revision 619)
+++ kernel/include/IMP/internal/AttributeTable.h (working copy)
@@ -11,7 +11,7 @@
#include "../base_types.h"
#include "../utility.h"
#include "../log.h"
-#include "ObjectPointer.h"
+#include "../Pointer.h"
#include <boost/iterator/filter_iterator.hpp>
#include <boost/iterator/counting_iterator.hpp>
Index: kernel/include/IMP/internal/ref_counting.h
===================================================================
--- kernel/include/IMP/internal/ref_counting.h (revision 0)
+++ kernel/include/IMP/internal/ref_counting.h (revision 0)
@@ -0,0 +1,143 @@
+/**
+ * \file ref_counting.h
+ * \brief Helpers to handle reference counting.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef __IMP_REF_COUNTING_H
+#define __IMP_REF_COUNTING_H
+
+#include "../Object.h"
+#include "../RefCountedObject.h"
+
+#include <boost/static_assert.hpp>
+#include <boost/type_traits.hpp>
+
+namespace IMP
+{
+
+namespace internal
+{
+
+template <bool REF>
+struct Ref
+{
+ template <class O>
+ static void eval(O* o) {
+ BOOST_STATIC_ASSERT((!boost::is_base_of<RefCountedObject, O >::value));
+ IMP_LOG(VERBOSE, "Not refing particle " << o << std::endl);
+ }
+};
+
+template <>
+struct Ref<true>
+{
+ template <class O>
+ static void eval(O* o) {
+ IMP_LOG(VERBOSE, "Refing particle " << o->get_index()
+ << o->get_ref_count() << std::endl);
+ o->assert_is_valid();
+ o->ref();
+ }
+};
+
+template <bool REF>
+struct UnRef
+{
+ template <class O>
+ static void eval(O* o) {
+ BOOST_STATIC_ASSERT((!boost::is_base_of<RefCountedObject, O >::value));
+ IMP_LOG(VERBOSE, "Not Unrefing object " << o << std::endl);
+ }
+};
+
+template <>
+struct UnRef<true>
+{
+ template <class O>
+ static void eval(O *o) {
+ IMP_LOG(VERBOSE, "Unrefing particle " << o->get_index()
+ << " " << o->get_ref_count() << std::endl);
+ o->assert_is_valid();
+ o->unref();
+ if (!o->get_has_ref()) {
+ delete o;
+ }
+ }
+ };
+
+
+//! Can be called on any object and will only unref it if appropriate
+template <class O>
+void unref(O o)
+{
+ BOOST_STATIC_ASSERT(!boost::is_pointer<O>::value);
+}
+
+
+//! Can be called on any object and will only ref it if appropriate
+template <class O>
+void ref(O o)
+{
+ BOOST_STATIC_ASSERT(!boost::is_pointer<O>::value);
+}
+
+//! Can be called on any object and will only unref it if appropriate
+template <class O>
+void unref(O* o)
+{
+ UnRef<(boost::is_base_of<RefCountedObject, O >::value)>::eval(o);
+}
+
+
+//! Can be called on any object and will only ref it if appropriate
+template <class O>
+void ref(O* o)
+{
+ Ref<(boost::is_base_of<RefCountedObject, O >::value)>::eval(o);
+}
+
+
+//! Can be called on any object and will only unref it if appropriate
+template <class O>
+void disown(O* o)
+{
+ /*IMP_LOG(VERBOSE, "Disown called with "
+ << (boost::is_base_of<RefCountedObject, O >::value)
+ << " for " << o << " " << o->get_ref_count() << std::endl);*/
+ o->unref();
+ if (!o->get_has_ref()) {
+ delete o;
+ }
+}
+
+
+//! Can be called on any object and will only ref it if appropriate
+template <class O>
+void own(O* o)
+{
+ /*IMP_LOG(VERBOSE, "Own called with "
+ << (boost::is_base_of<RefCountedObject, O >::value)
+ << " for " << o
+ << " " << o->get_ref_count() << std::endl);*/
+ if (boost::is_base_of<RefCountedObject, O >::value) {
+ // no checks
+ } else {
+ IMP_check(!o->get_has_ref(), "Trying to own already owned but "
+ << "non-reference-counted object: " << *o,
+ ValueException);
+ }
+ o->ref();
+}
+
+
+
+
+
+} // namespace internal
+
+} // namespace IMP
+
+#endif /* __IMP_REF_COUNTING_H */
Index: kernel/include/IMP/internal/RefCountedObject.h
===================================================================
--- kernel/include/IMP/internal/RefCountedObject.h (revision 619)
+++ kernel/include/IMP/internal/RefCountedObject.h (working copy)
@@ -1,172 +0,0 @@
-/**
- * \file RefCountedObject.h
- * \brief A common base class for ref counted objects.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#ifndef __IMP_REF_COUNTED_OBJECT_H
-#define __IMP_REF_COUNTED_OBJECT_H
-
-#include "Object.h"
-
-#include <boost/static_assert.hpp>
-#include <boost/type_traits.hpp>
-
-namespace IMP
-{
-
-namespace internal
-{
-
-//! Common base class for ref counted objects.
-/** This class acts as a tag rather than providing any functionality.
-
- \internal
- */
-class IMPDLLEXPORT RefCountedObject: public Object
-{
- typedef Object P;
- typedef RefCountedObject This;
- static unsigned int live_objects_;
-protected:
- RefCountedObject() {
- ++live_objects_;
- }
-
-public:
-
- virtual ~RefCountedObject() {
- IMP_assert(!get_has_ref(), "Deleting object which still has references");
- --live_objects_;
- }
-
- static unsigned int get_number_of_live_objects() {
- // for debugging purposes only
- return live_objects_;
- }
-};
-
-
-
-template <bool REF>
-struct Ref
-{
- template <class O>
- static void eval(O* o) {
- BOOST_STATIC_ASSERT((!boost::is_base_of<RefCountedObject, O >::value));
- IMP_LOG(VERBOSE, "Not refing particle " << o << std::endl);
- }
-};
-
-template <>
-struct Ref<true>
-{
- template <class O>
- static void eval(O* o) {
- IMP_LOG(VERBOSE, "Refing particle " << o->get_index()
- << o->get_ref_count() << std::endl);
- o->assert_is_valid();
- o->ref();
- }
-};
-
-template <bool REF>
-struct UnRef
-{
- template <class O>
- static void eval(O* o) {
- BOOST_STATIC_ASSERT((!boost::is_base_of<RefCountedObject, O >::value));
- IMP_LOG(VERBOSE, "Not Unrefing object " << o << std::endl);
- }
-};
-
-template <>
-struct UnRef<true>
-{
- template <class O>
- static void eval(O *o) {
- IMP_LOG(VERBOSE, "Unrefing particle " << o->get_index()
- << " " << o->get_ref_count() << std::endl);
- o->assert_is_valid();
- o->unref();
- if (!o->get_has_ref()) {
- delete o;
- }
- }
- };
-
-
-//! Can be called on any object and will only unref it if appropriate
-template <class O>
-void unref(O o)
-{
- BOOST_STATIC_ASSERT(!boost::is_pointer<O>::value);
-}
-
-
-//! Can be called on any object and will only ref it if appropriate
-template <class O>
-void ref(O o)
-{
- BOOST_STATIC_ASSERT(!boost::is_pointer<O>::value);
-}
-
-//! Can be called on any object and will only unref it if appropriate
-template <class O>
-void unref(O* o)
-{
- UnRef<(boost::is_base_of<RefCountedObject, O >::value)>::eval(o);
-}
-
-
-//! Can be called on any object and will only ref it if appropriate
-template <class O>
-void ref(O* o)
-{
- Ref<(boost::is_base_of<RefCountedObject, O >::value)>::eval(o);
-}
-
-
-//! Can be called on any object and will only unref it if appropriate
-template <class O>
-void disown(O* o)
-{
- /*IMP_LOG(VERBOSE, "Disown called with "
- << (boost::is_base_of<RefCountedObject, O >::value)
- << " for " << o << " " << o->get_ref_count() << std::endl);*/
- o->unref();
- if (!o->get_has_ref()) {
- delete o;
- }
-}
-
-
-//! Can be called on any object and will only ref it if appropriate
-template <class O>
-void own(O* o)
-{
- /*IMP_LOG(VERBOSE, "Own called with "
- << (boost::is_base_of<RefCountedObject, O >::value)
- << " for " << o
- << " " << o->get_ref_count() << std::endl);*/
- if (boost::is_base_of<RefCountedObject, O >::value) {
- // no checks
- } else {
- IMP_check(!o->get_has_ref(), "Trying to own already owned but "
- << "non-reference-counted object: " << *o,
- ValueException);
- }
- o->ref();
-}
-
-
-
-
-
-} // namespace internal
-
-} // namespace IMP
-
-#endif /* __IMP_REF_COUNTED_OBJECT_H */
Index: kernel/include/IMP/PairScore.h
===================================================================
--- kernel/include/IMP/PairScore.h (revision 619)
+++ kernel/include/IMP/PairScore.h (working copy)
@@ -9,7 +9,7 @@
#include "IMP_config.h"
#include "base_types.h"
-#include "internal/RefCountedObject.h"
+#include "RefCountedObject.h"
#include "Particle.h"
#include "DerivativeAccumulator.h"
@@ -25,7 +25,7 @@
/** PairScores should take a UnaryFunction as their first
argument if such is needed.
*/
-class IMPDLLEXPORT PairScore : public internal::RefCountedObject
+class IMPDLLEXPORT PairScore : public RefCountedObject
{
public:
PairScore() {}
Index: kernel/include/IMP/SConscript
===================================================================
--- kernel/include/IMP/SConscript (revision 619)
+++ kernel/include/IMP/SConscript (working copy)
@@ -7,7 +7,8 @@
'Key.h', 'utility.h', 'Restraint.h', 'Optimizer.h',
'DecoratorBase.h', 'Vector3D.h',
'UnaryFunction.h', 'PairScore.h', 'SingletonScore.h', 'macros.h',
- 'TripletScore.h', 'exception.h', 'VersionInfo.h']
+ 'TripletScore.h', 'exception.h', 'VersionInfo.h',
+ 'Object.h', 'Pointer.h', 'RefCountedObject.h']
# Install the include files:
includedir = os.path.join(env['includedir'], 'IMP')
Index: kernel/include/IMP/Particle.h
===================================================================
--- kernel/include/IMP/Particle.h (revision 619)
+++ kernel/include/IMP/Particle.h (working copy)
@@ -11,12 +11,12 @@
#include "IMP_config.h"
#include "base_types.h"
#include "Model.h"
-#include "internal/Object.h"
+#include "Object.h"
#include "utility.h"
#include "Key.h"
#include "internal/AttributeTable.h"
#include "DerivativeAccumulator.h"
-#include "internal/ObjectPointer.h"
+#include "Pointer.h"
#include <limits>
@@ -49,17 +49,17 @@
\ingroup kernel
*/
-class IMPDLLEXPORT Particle : public internal::RefCountedObject
+class IMPDLLEXPORT Particle : public RefCountedObject
{
friend class Model;
/* This has to be declared here since boost 1.35 wants the full
- definition of Particle to be available when the ObjectPointer
+ definition of Particle to be available when the Pointer
is declared.
*/
struct ParticleAttributeTableTraits
{
- typedef internal::ObjectPointer<Particle, true> Value;
+ typedef Pointer<Particle> Value;
typedef KeyBase<Particle*> Key;
static Value get_invalid() {
return Value();
@@ -369,7 +369,7 @@
// Set pointer to model particle data.
void set_model(Model *md, ParticleIndex pi);
- internal::ObjectPointer<Model, false> model_;
+ Pointer<Model> model_;
// true if particle is active
bool is_active_;
@@ -526,7 +526,7 @@
{
IMP_check(get_is_active(), "Do not touch inactive particles",
InactiveParticleException);
- particles_.set_value(name, internal::ObjectPointer<Particle, true>(value));
+ particles_.set_value(name, Pointer<Particle>(value));
}
@@ -580,7 +580,7 @@
IMP_assert(model_,
"Particle must be added to Model before attributes are added");
particles_.insert(name,
- internal::ObjectPointer<Particle, true>(value));
+ Pointer<Particle>(value));
}
Index: kernel/include/IMP/Object.h
===================================================================
--- kernel/include/IMP/Object.h (revision 619)
+++ kernel/include/IMP/Object.h (working copy)
@@ -9,14 +9,11 @@
#ifndef __IMP_OBJECT_H
#define __IMP_OBJECT_H
-#include "../exception.h"
+#include "exception.h"
namespace IMP
{
-namespace internal
-{
-
//! Common base class for IMP objects.
/** Currently this just makes the object noncopyable and adds heuristic checks
to make sure the memory has not been freed.
@@ -59,14 +56,12 @@
private:
Object(const Object &o){}
- const internal::Object& operator=(const Object &o) {return *this;}
+ const Object& operator=(const Object &o) {return *this;}
int count_;
double check_value_;
};
-} // namespace internal
-
} // namespace IMP
#endif /* __IMP_OBJECT_H */
Index: kernel/include/IMP/triplet_scores/AngleTripletScore.h
===================================================================
--- kernel/include/IMP/triplet_scores/AngleTripletScore.h (revision 619)
+++ kernel/include/IMP/triplet_scores/AngleTripletScore.h (working copy)
@@ -10,7 +10,7 @@
#include "../TripletScore.h"
#include "../UnaryFunction.h"
-#include "../internal/ObjectPointer.h"
+#include "../Pointer.h"
namespace IMP
{
@@ -21,7 +21,7 @@
*/
class IMPDLLEXPORT AngleTripletScore : public TripletScore
{
- internal::ObjectPointer<UnaryFunction, true> f_;
+ Pointer<UnaryFunction> f_;
public:
AngleTripletScore(UnaryFunction *f);
virtual ~AngleTripletScore(){}
Index: kernel/include/IMP/ScoreState.h
===================================================================
--- kernel/include/IMP/ScoreState.h (revision 619)
+++ kernel/include/IMP/ScoreState.h (working copy)
@@ -9,8 +9,8 @@
#define __IMP_SCORE_STATE_H
#include "IMP_config.h"
-#include "internal/RefCountedObject.h"
-#include "internal/ObjectPointer.h"
+#include "RefCountedObject.h"
+#include "Pointer.h"
#include "Model.h"
#include "DerivativeAccumulator.h"
#include "VersionInfo.h"
@@ -37,7 +37,7 @@
of lines per update call.
*/
-class IMPDLLEXPORT ScoreState : public internal::RefCountedObject
+class IMPDLLEXPORT ScoreState : public RefCountedObject
{
friend class Model;
void set_model(Model* model);
@@ -121,7 +121,7 @@
unsigned int update_iteration_;
unsigned int after_iteration_;
// all of the particle data
- internal::ObjectPointer<Model, false> model_;
+ Pointer<Model> model_;
std::string name_;
};
Index: kernel/include/IMP/TripletScore.h
===================================================================
--- kernel/include/IMP/TripletScore.h (revision 619)
+++ kernel/include/IMP/TripletScore.h (working copy)
@@ -9,7 +9,7 @@
#include "IMP_config.h"
#include "base_types.h"
-#include "internal/RefCountedObject.h"
+#include "RefCountedObject.h"
#include "Particle.h"
#include "DerivativeAccumulator.h"
@@ -26,7 +26,7 @@
/** TripletScores should take a UnaryFunction as their first
argument if such is needed.
*/
-class IMPDLLEXPORT TripletScore : public internal::RefCountedObject
+class IMPDLLEXPORT TripletScore : public RefCountedObject
{
public:
TripletScore() {}
Index: kernel/include/IMP/Pointer.h
===================================================================
--- kernel/include/IMP/Pointer.h (revision 0)
+++ kernel/include/IMP/Pointer.h (revision 0)
@@ -0,0 +1,113 @@
+/**
+ * \file Pointer.h
+ * \brief A NULL-initialized pointer to an IMP Object.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef __IMP_POINTER_H
+#define __IMP_POINTER_H
+
+#include "log.h"
+#include "Object.h"
+#include "RefCountedObject.h"
+#include "internal/ref_counting.h"
+#include "macros.h"
+#include "exception.h"
+
+#include <boost/static_assert.hpp>
+#include <boost/type_traits.hpp>
+
+namespace IMP
+{
+
+//! A pointer to an IMP::Object
+/** The pointer is NULL initialized and checks accesses to throw an exception
+ rather than core dump on an invalid access. These should be used to hold
+ all pointers to IMP objects in C++ code.
+
+ The pointer will be ref counted if the object is one which should be ref
+ counted (that is, if the object inherits from RefCountedObject).
+
+ \param[in] O The type of IMP::Object-derived object to point to
+ */
+template <class O>
+class Pointer
+{
+ typedef Pointer<O> This;
+ O* o_;
+
+ void set_pointer(O* p) {
+ if (boost::is_base_of<RefCountedObject, O>::value) {
+ if (o_) internal::disown(o_);
+ if (p) internal::own(p);
+ o_=p;
+ } else {
+ o_=p;
+ }
+ }
+
+ void audit() const {
+ IMP_assert(o_ != NULL, "Pointer is NULL");
+ IMP_CHECK_OBJECT(o_);
+ }
+
+ bool is_default() const {
+ return o_==NULL;
+ }
+ typedef bool (This::*unspecified_bool)() const;
+
+public:
+ Pointer(const Pointer &o): o_(NULL) {
+ set_pointer(o.o_);
+ }
+ Pointer& operator=(const Pointer &o){
+ set_pointer(o.o_);
+ return *this;
+ }
+ Pointer(): o_(NULL) {}
+ explicit Pointer(O* o): o_(NULL) {
+ IMP_assert(o, "Can't initialize with NULL pointer");
+ set_pointer(o);
+ }
+ ~Pointer(){
+ set_pointer(NULL);
+ }
+ const O& operator*() const {
+ audit();
+ return *o_;
+ }
+ O& operator*() {
+ audit();
+ return *o_;
+ }
+ const O* operator->() const {
+ audit();
+ return o_;
+ }
+ O* operator->() {
+ audit();
+ return o_;
+ }
+ O* get() const {
+ audit();
+ return o_;
+ }
+ void operator=(O* o) {
+ set_pointer(o);
+ }
+ IMP_COMPARISONS_1(o_);
+
+ bool operator!() const {
+ return !o_;
+ }
+
+ operator unspecified_bool() const {
+ return o_ ? &This::operator! : 0;
+ }
+};
+
+} // namespace IMP
+
+#endif /* __IMP_OBJECT_POINTER_H */
Index: kernel/include/IMP/Optimizer.h
===================================================================
--- kernel/include/IMP/Optimizer.h (revision 619)
+++ kernel/include/IMP/Optimizer.h (working copy)
@@ -11,11 +11,11 @@
#include "IMP_config.h"
#include "base_types.h"
#include "VersionInfo.h"
-#include "internal/Object.h"
+#include "Object.h"
#include "utility.h"
#include "Model.h"
#include "Particle.h"
-#include "internal/ObjectPointer.h"
+#include "Pointer.h"
#include <limits>
@@ -34,7 +34,7 @@
/** \note There is currently no optimizer support for constraints
(e.g. rigid bodies).
*/
-class IMPDLLEXPORT Optimizer: public internal::Object
+class IMPDLLEXPORT Optimizer: public Object
{
public:
Optimizer();
@@ -198,7 +198,7 @@
typedef std::vector<FloatIndex> FloatIndexes;
private:
- internal::ObjectPointer<Model, false> model_;
+ Pointer<Model> model_;
};
IMP_OUTPUT_OPERATOR(Optimizer);
Index: kernel/src/Object.cpp
===================================================================
--- kernel/src/Object.cpp (revision 619)
+++ kernel/src/Object.cpp (working copy)
@@ -6,15 +6,12 @@
*
*/
-#include "IMP/internal/Object.h"
-#include "IMP/internal/RefCountedObject.h"
+#include "IMP/Object.h"
+#include "IMP/RefCountedObject.h"
namespace IMP
{
-namespace internal
-{
-
unsigned int RefCountedObject::live_objects_=0;
Object::Object()
@@ -35,6 +32,4 @@
"Previously freed object is not valid: " << this);
}
-} //namespace internal
-
} // namespace IMP
Index: kernel/src/SConscript
===================================================================
--- kernel/src/SConscript (revision 619)
+++ kernel/src/SConscript (working copy)
@@ -20,7 +20,7 @@
# Source files
files = ['base_types.cpp', 'Model.cpp',
- 'Particle.cpp', 'ScoreState.cpp',
+ 'Particle.cpp', 'ScoreState.cpp', 'Object.cpp',
'OptimizerState.cpp', 'Log.cpp', 'Restraint.cpp', 'Optimizer.cpp',
'random.cpp', 'Key.cpp', 'exception.cpp', 'ParticleRefiner.cpp'
] + decorators_files + restraints_files + optimizers_files \
Index: kernel/src/internal/Object.cpp
===================================================================
--- kernel/src/internal/Object.cpp (revision 619)
+++ kernel/src/internal/Object.cpp (working copy)
@@ -1,40 +0,0 @@
-/**
- * \file Object.cpp
- * \brief A shared base class to help in debugging and things.
- *
- * Copyright 2007-8 Sali Lab. All rights reserved.
- *
- */
-
-#include "IMP/internal/Object.h"
-#include "IMP/internal/RefCountedObject.h"
-
-namespace IMP
-{
-
-namespace internal
-{
-
-unsigned int RefCountedObject::live_objects_=0;
-
-Object::Object()
-{
- check_value_=111111111;
- count_=0;
-}
-
-Object::~Object()
-{
- assert_is_valid();
- check_value_=666666666;
-}
-
-void Object::assert_is_valid() const
-{
- IMP_assert(check_value_==111111111,
- "Previously freed object is not valid: " << this);
-}
-
-} //namespace internal
-
-} // namespace IMP
Index: kernel/src/internal/SConscript
===================================================================
--- kernel/src/internal/SConscript (revision 619)
+++ kernel/src/internal/SConscript (working copy)
@@ -1,6 +1,6 @@
Import('env')
-files = ['graph_base.cpp', 'ParticleGrid.cpp', 'Object.cpp',
+files = ['graph_base.cpp', 'ParticleGrid.cpp',
'kernel_version_info.cpp', 'constants.cpp', 'bbox_nbl_helpers.cpp']
files = [File(x) for x in files]
Index: kernel/pyext/IMP.i
===================================================================
--- kernel/pyext/IMP.i (revision 619)
+++ kernel/pyext/IMP.i (working copy)
@@ -162,8 +162,8 @@
%feature("director") IMP::ParticleRefiner;
%include "IMP/Key.h"
-%include "IMP/internal/Object.h"
-%include "IMP/internal/RefCountedObject.h"
+%include "IMP/Object.h"
+%include "IMP/RefCountedObject.h"
%include "IMP/Index.h"
%include "IMP/base_types.h"
%include "IMP/VersionInfo.h"