Index: kernel/include/Vector3D.h
===================================================================
--- kernel/include/Vector3D.h (revision 916)
+++ kernel/include/Vector3D.h (working copy)
@@ -17,6 +17,7 @@
IMP_BEGIN_NAMESPACE
+//! A location in 3D
typedef VectorD<3> Vector3D;
IMP_END_NAMESPACE
Index: kernel/include/base_types.h
===================================================================
--- kernel/include/base_types.h (revision 916)
+++ kernel/include/base_types.h (working copy)
@@ -17,13 +17,6 @@
IMP_BEGIN_NAMESPACE
-/** \defgroup kernel IMP Kernel
- The core IMP types
-
- \defgroup helper Miscellaneous helpers
- Classes and functions which are there to make your life easier.
- */
-
/** \internal \namespace IMP::internal Implementation details.
*/
@@ -37,9 +30,11 @@
typedef std::string String;
-
+//! Standard way to pass a bunch of Float values
typedef std::vector<Float> Floats;
+//! Standard way to pass a bunch of Int values
typedef std::vector<Int> Ints;
+//! Standard way to pass a bunch of String values
typedef std::vector<String> Strings;
@@ -49,9 +44,13 @@
struct ScoreStateTag {};
struct OptimizerStateTag {};
+//! Index to access a Particle in a container in an object
typedef Index<ParticleTag> ParticleIndex;
+//! Index to access a Restraint in a container in an object
typedef Index<RestraintTag> RestraintIndex;
+//! Index to access a ScoreState in a container in an object
typedef Index<ScoreStateTag> ScoreStateIndex;
+//! Index to access a OptimizerState in a container in an object
typedef Index<OptimizerStateTag> OptimizerStateIndex;
class Particle;
@@ -62,10 +61,12 @@
is not as pretty for Python.
*/
typedef std::vector<Particle*> Particles;
+//! The standard way of storing a pair of Particles
typedef std::pair<Particle*, Particle*> ParticlePair;
+//! A collection of ParticlePair
typedef std::vector<ParticlePair> ParticlePairs;
-
+//! A collection of ParticleIndex
typedef std::vector<ParticleIndex> ParticleIndexes;
class Particle;
Index: kernel/include/SingletonScore.h
===================================================================
--- kernel/include/SingletonScore.h (revision 916)
+++ kernel/include/SingletonScore.h (working copy)
@@ -16,12 +16,6 @@
class Particle;
-/** \ingroup restraint
- \addtogroup singleton Score functions on one particle
- Score functions to be applied to a single particle. These can be
- used to make more flexible restraints.
- */
-
//! Abstract score function for a single particle.
/** SingletonScores should take a UnaryFunction as their first
argument if such is needed.
@@ -34,6 +28,9 @@
//! Compute the score for the particle and the derivative if needed.
virtual Float evaluate(Particle *a,
DerivativeAccumulator *da) const = 0;
+ //! Print information about the SingletonScore to a stream.
+ /** Should end in a newline.
+ */
virtual void show(std::ostream &out=std::cout) const = 0;
};
Index: kernel/include/exception.h
===================================================================
--- kernel/include/exception.h (revision 916)
+++ kernel/include/exception.h (working copy)
@@ -143,9 +143,6 @@
#define IMP_IF_CHECK(level)\
if (level <= ::IMP::get_check_level())
-namespace internal
-{
-
//! This is just here so you can catch errors more easily in the debugger
/** Break on exception.cpp:31 to catch assertion failures.
\ingroup assert
@@ -158,8 +155,6 @@
*/
IMPDLLEXPORT void check_fail(const char *msg);
-} // namespace internal
-
#ifndef NDEBUG
//! An assertion for IMP. An IMP::ErrorException will be thrown.
@@ -178,7 +173,7 @@
oss << message << std::endl \
<< " File \"" << __FILE__ << "\", line " << __LINE__ \
<< std::endl; \
- IMP::internal::assert_fail(oss.str().c_str()); \
+ IMP::assert_fail(oss.str().c_str()); \
} \
} while(false)
#else
@@ -197,7 +192,7 @@
if (IMP::get_check_level() >= IMP::CHEAP && !(expr)) { \
std::ostringstream oss; \
oss << message << std::endl; \
- IMP::internal::check_fail(oss.str().c_str()); \
+ IMP::check_fail(oss.str().c_str()); \
throw ExceptionType(oss.str().c_str()); \
} \
} while (false)
@@ -211,7 +206,7 @@
#define IMP_failure(message, ExceptionType) { \
std::ostringstream oss; \
oss << message << std::endl; \
- IMP::internal::check_fail(oss.str().c_str()); \
+ IMP::check_fail(oss.str().c_str()); \
throw ExceptionType(oss.str().c_str());}
IMP_END_NAMESPACE
Index: kernel/include/Model.h
===================================================================
--- kernel/include/Model.h (revision 916)
+++ kernel/include/Model.h (working copy)
@@ -26,15 +26,16 @@
//! Class for storing model, its restraints, and particles.
/** The Model maintains a standard IMP container for each of Particle,
ScoreState and Restraint object types.
- \ingroup kernel
*/
class IMPDLLEXPORT Model: public Object
{
- private:
+private:
friend class Restraint;
unsigned int iteration_;
public:
+ //!
Model();
+ //!
~Model();
IMP_CONTAINER(Particle, particle, ParticleIndex);
Index: kernel/include/VersionInfo.h
===================================================================
--- kernel/include/VersionInfo.h (revision 916)
+++ kernel/include/VersionInfo.h (working copy)
@@ -22,7 +22,6 @@
VersionInfo(std::string author, std::string version) : author_(author),
version_(version) {}
- //! Default constructor
VersionInfo() : author_("unknown"), version_("unknown") {}
//! \return author of this object.
@@ -37,7 +36,7 @@
out << "author: " << author_ << std::endl;
}
-protected:
+private:
std::string author_, version_;
};
Index: kernel/include/DerivativeAccumulator.h
===================================================================
--- kernel/include/DerivativeAccumulator.h (revision 916)
+++ kernel/include/DerivativeAccumulator.h (working copy)
@@ -19,9 +19,11 @@
class IMPDLLEXPORT DerivativeAccumulator
{
public:
+ //! the weight is one by default
DerivativeAccumulator(Float weight=1.0)
: weight_(weight) {}
+ //! The weight is multiplied by the new weight
DerivativeAccumulator(const DerivativeAccumulator ©, Float weight=1.0)
: weight_(copy.weight_ * weight) {}
@@ -34,7 +36,7 @@
return value * weight_;
}
-protected:
+private:
Float weight_;
};
Index: kernel/include/Particle.h
===================================================================
--- kernel/include/Particle.h (revision 916)
+++ kernel/include/Particle.h (working copy)
@@ -22,20 +22,6 @@
IMP_BEGIN_NAMESPACE
-namespace internal
-{
-
-template <class It>
-void check_particles_active(It b, It e, std::string msg)
-{
- for (It c= b; c != e; ++c) {
- IMP_check((*c)->get_is_active(), msg,
- InactiveParticleException);
- }
-}
-
-} // namespace internal
-
class Model;
//! Class to handle individual model particles.
@@ -73,8 +59,6 @@
\note In general, Particles should only be used through
\ref decorators "Decorators" as these provide a nice and more reliable
interface.
-
- \ingroup kernel
*/
class IMPDLLEXPORT Particle : public RefCountedObject
{
Index: kernel/include/UnaryFunction.h
===================================================================
--- kernel/include/UnaryFunction.h (revision 916)
+++ kernel/include/UnaryFunction.h (working copy)
@@ -18,8 +18,6 @@
//! Abstract single variable functor class for score functions.
/** These functors take a single feature value, and return a corresponding
score (and optionally also the first derivative).
-
- \ingroup kernel
*/
class IMPDLLEXPORT UnaryFunction : public RefCountedObject
{
@@ -41,6 +39,9 @@
*/
virtual FloatPair evaluate_with_derivative(Float feature) const = 0;
+ //! Print information about the UnaryFunction to a stream.
+ /** Should end in a newline.
+ */
virtual void show(std::ostream &out=std::cout) const = 0;
};
Index: kernel/include/VectorD.h
===================================================================
--- kernel/include/VectorD.h (revision 916)
+++ kernel/include/VectorD.h (working copy)
@@ -22,8 +22,6 @@
IMP_BEGIN_NAMESPACE
//! Simple D vector class
-/** \ingroup helper
- */
template <unsigned int D>
class IMPDLLEXPORT VectorD
{
Index: kernel/include/Index.h
===================================================================
--- kernel/include/Index.h (revision 916)
+++ kernel/include/Index.h (working copy)
@@ -38,6 +38,7 @@
ValueException);
return i_;
}
+ //!
void show(std::ostream &out) const {
if (!is_default()) {
out << "(" << i_ << ")";
@@ -57,7 +58,7 @@
++i_;
}
#endif
-protected:
+private:
bool is_default() const {
return i_==-1;
}
Index: kernel/include/IMP_config.h
===================================================================
--- kernel/include/IMP_config.h (revision 916)
+++ kernel/include/IMP_config.h (working copy)
@@ -34,4 +34,14 @@
#define IMP_END_NAMESPACE \
} /* namespace IMP */
+#define IMP_BEGIN_INTERNAL_NAMESPACE \
+IMP_BEGIN_NAMESPACE \
+namespace internal \
+{
+
+#define IMP_END_INTERNAL_NAMESPACE \
+} /* namespace internal */ \
+IMP_END_NAMESPACE
+
+
#endif /* IMP_CONFIG_H */
Index: kernel/include/Restraint.h
===================================================================
--- kernel/include/Restraint.h (revision 916)
+++ kernel/include/Restraint.h (working copy)
@@ -27,17 +27,7 @@
typedef std::vector<Particles> ParticlesList;
class Model;
-/** \defgroup restraint General purpose restraints
- Classes to define and help in defining restraints. The restraints
- typically involve a Restraint which defines the set of tuples of Particles
- and then various functions which are applied to the tuples.
- */
-/** \defgroup exp_restraint Experimental restraints
- These are restraints which directly use various types of experimental
- data.
- */
-
//! Abstract class for representing restraints
/** Restraints should take their score function or UnaryFunction
as the first argument. Restraints which act on large numbers of
@@ -60,13 +50,10 @@
without ever having been added to a model as this is an easy mistake
to make. To disable this warning for a particular restraint, call
set_was_owned(true).
-
- \ingroup kernel
*/
class IMPDLLEXPORT Restraint : public RefCountedObject
{
public:
- //! Initialize the Restraint
Restraint();
virtual ~Restraint();
Index: kernel/include/DecoratorBase.h
===================================================================
--- kernel/include/DecoratorBase.h (revision 916)
+++ kernel/include/DecoratorBase.h (working copy)
@@ -14,50 +14,6 @@
IMP_BEGIN_NAMESPACE
-/** \defgroup decorators Decorators
-
-Decorators wrap particles
-- maintain invariants: e.g. any the particles have all of x,y,z coordinates
-- add functionality: e.g. you can get the coordinates as an IMP::Vector3D
-- provide uniform names for attributes: so you don't use "x" some places
-and "X" other places
-- cache keys since those can be expensive to create
-
-\note In general, you should not access particle attributes except
-through decorators
-
-
-The general usage of the decorators is quite simple
-- Create a decorator around a particle which does not have the needed
-attributes. This adds the attributes.
-\verbatim
-d= IMP.core.MyDecorator.create(p)
-\endverbatim
-- Cast a particle which has the required attributes to a decorator,
-checking that it has the attributes
-\verbatim
-d= IMP.core.MyDecorator.cast(p)
-\endverbatim
-- Wrap a particle which is known to have the required attributes in a
-decorator. No checks are necessarily made
-\verbatim
-d= IMP.core.MyDecorator(p)
-\endverbatim
-- Access and manipulate attributes or groups of attributes through
-methods like
-\verbatim
-x=d.get_foo()
-d.set_foo(1.0)
-\endverbatim
-- When needed, access the keys used by the decorator through methods like
-\verbatim
-d.get_foo_key()
-\endverbatim
-
- */
-
-
-
/** A base class for decorators. Implementers of decorators should
just inherit from this and then use the IMP_DECORATOR macro
*/
Index: kernel/include/ParticleRefiner.h
===================================================================
--- kernel/include/ParticleRefiner.h (revision 916)
+++ kernel/include/ParticleRefiner.h (working copy)
@@ -43,6 +43,8 @@
*/
virtual void cleanup_refined(Particle *a, Particles &b,
DerivativeAccumulator *da=0) const {}
+ //! Print information about the refiner
+ /** It should end in a new line. */
virtual void show(std::ostream &out=std::cout) const {
out << "ParticleRefiner base" << std::endl;
};
Index: kernel/include/TripletScore.h
===================================================================
--- kernel/include/TripletScore.h (revision 916)
+++ kernel/include/TripletScore.h (working copy)
@@ -15,13 +15,6 @@
IMP_BEGIN_NAMESPACE
-/**
- \ingroup restraint
- \addtogroup tripletscore Score functions on three particles
- Score functions to by applied to a triplet of particles. These can be
- used to make more flexible restraints.
- */
-
//! Abstract score function for a triplet of particles.
/** TripletScores should take a UnaryFunction as their first
argument if such is needed.
@@ -34,6 +27,9 @@
//! Compute the score for the triplet and the derivative if needed.
virtual Float evaluate(Particle *a, Particle *b, Particle *c,
DerivativeAccumulator *da) const = 0;
+ //! Print information about the TripletScore to a stream.
+ /** Should end in a newline.
+ */
virtual void show(std::ostream &out=std::cout) const = 0;
};
Index: kernel/include/Pointer.h
===================================================================
--- kernel/include/Pointer.h (revision 916)
+++ kernel/include/Pointer.h (working copy)
@@ -58,50 +58,64 @@
typedef bool (This::*unspecified_bool)() const;
public:
+ /** copy constructor */
Pointer(const Pointer &o): o_(NULL) {
set_pointer(o.o_);
}
+ /** copy from another */
Pointer& operator=(const Pointer &o){
set_pointer(o.o_);
return *this;
}
+ //! initialize to NULL
Pointer(): o_(NULL) {}
+ /** initialize from a pointer */
explicit Pointer(O* o): o_(NULL) {
IMP_assert(o, "Can't initialize with NULL pointer");
set_pointer(o);
}
+ /** drop control of the object */
~Pointer(){
set_pointer(NULL);
}
+ /** it's a pointer */
const O& operator*() const {
audit();
return *o_;
}
+ /** it's a pointer */
O& operator*() {
audit();
return *o_;
}
+ /** it's a pointer */
const O* operator->() const {
audit();
return o_;
}
+ /** it's a pointer */
O* operator->() {
audit();
return o_;
}
+ //! get the raw pointer
O* get() const {
audit();
return o_;
}
+ //! Set it from a possibly NULL pointer.
void operator=(O* o) {
set_pointer(o);
}
+
IMP_COMPARISONS_1(o_);
+ //! Return true if the pointer is not NULL
bool operator!() const {
return !o_;
}
+ //! convert to the raw pointer
operator O*() const {
return o_;
}
Index: kernel/include/Optimizer.h
===================================================================
--- kernel/include/Optimizer.h (revision 916)
+++ kernel/include/Optimizer.h (working copy)
@@ -25,10 +25,6 @@
typedef std::vector<OptimizerState*> OptimizerStates;
-/** \defgroup optimizer Optimizers
- Optimizers of various sorts.
- */
-
//! Base class for all optimizers.
/** The Optimizer maintains a list of OptimizerStates which are
updated each time the conformation is changed.
@@ -66,6 +62,8 @@
*/
void set_model(Model *m) {model_=m;}
+ //! Print info about the optimizer state
+ /** It should end in a newline */
virtual void show(std::ostream &out= std::cout) const {
out << "Some optimizer" << std::endl;
}
Index: kernel/include/internal/key_helpers.h
===================================================================
--- kernel/include/internal/key_helpers.h (revision 0)
+++ kernel/include/internal/key_helpers.h (revision 0)
@@ -0,0 +1,45 @@
+/**
+ * \file key_helpers.h \brief helpers for declaring keys.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef IMP_INTERNAL_KEY_HELPERS_H
+#define IMP_INTERNAL_KEY_HELPERS_H
+
+#include "../IMP_config.h"
+#include <map>
+
+IMP_BEGIN_INTERNAL_NAMESPACE
+/** \internal The data concerning keys.
+ */
+struct IMPDLLEXPORT KeyData
+{
+ typedef std::map<std::string, int> Map;
+ typedef std::vector<std::string> RMap;
+
+ void show(std::ostream &out= std::cout) const;
+ KeyData();
+ void assert_is_initialized() const;
+ unsigned int add_key(std::string str) {
+ unsigned int i= map_.size();
+ map_[str]=i;
+ rmap_.push_back(str);
+ return i;
+ }
+
+ const Map &get_map() const {return map_;}
+ const RMap &get_rmap() const {return rmap_;}
+
+private:
+ double heuristic_;
+ Map map_;
+ RMap rmap_;
+};
+
+IMPDLLEXPORT extern std::map<unsigned int, KeyData> key_data;
+
+IMP_END_INTERNAL_NAMESPACE
+
+#endif /* IMP_INTERNAL_KEY_HELPERS_H */
\ No newline at end of file
Index: kernel/include/internal/SConscript
===================================================================
--- kernel/include/internal/SConscript (revision 916)
+++ kernel/include/internal/SConscript (working copy)
@@ -1,7 +1,7 @@
files = ['AttributeTable.h', 'Vector.h',
'ref_counting.h', 'ObjectContainer.h',
'kernel_version_info.h', 'constants.h', 'units.h',
- 'utility.h', 'Unit.h', 'ExponentialNumber.h']
+ 'utility.h', 'Unit.h', 'ExponentialNumber.h', 'key_helpers.h']
files = [File(f) for f in files]
Return('files')
Index: kernel/include/PairScore.h
===================================================================
--- kernel/include/PairScore.h (revision 916)
+++ kernel/include/PairScore.h (working copy)
@@ -15,12 +15,6 @@
IMP_BEGIN_NAMESPACE
-/** \ingroup restraint
- \addtogroup pairscore Score functions on two particles
- Score functions to by applied to a pair of particles. These can be
- used to make more flexible restraints.
- */
-
//! Abstract score function for a pair of particles.
/** PairScores should take a UnaryFunction as their first
argument if such is needed.
@@ -33,6 +27,8 @@
//! Compute the score for the pair and the derivative if needed.
virtual Float evaluate(Particle *a, Particle *b,
DerivativeAccumulator *da) const = 0;
+ //! Print information for the PairScore.
+ /** Should end in a newline. */
virtual void show(std::ostream &out=std::cout) const = 0;
};
Index: kernel/include/Key.h
===================================================================
--- kernel/include/Key.h (revision 916)
+++ kernel/include/Key.h (working copy)
@@ -10,6 +10,7 @@
#include "macros.h"
#include "exception.h"
+#include "internal/key_helpers.h"
#include <map>
#include <vector>
@@ -63,42 +64,7 @@
}; \
typedef std::vector<Name> Name##s
-namespace internal
-{
-
-/** \internal The data concerning keys.
- */
-struct IMPDLLEXPORT KeyData
-{
- typedef std::map<std::string, int> Map;
- typedef std::vector<std::string> RMap;
-
- void show(std::ostream &out= std::cout) const;
- KeyData();
- void assert_is_initialized() const;
- unsigned int add_key(std::string str) {
- unsigned int i= map_.size();
- map_[str]=i;
- rmap_.push_back(str);
- return i;
- }
-
- const Map &get_map() const {return map_;}
- const RMap &get_rmap() const {return rmap_;}
-
-private:
- double heuristic_;
- Map map_;
- RMap rmap_;
-};
-
-IMPDLLEXPORT extern std::map<unsigned int, KeyData> key_data;
-
-} // namespace internal
-
-
-
//! A base class for Keys
/** This class does internal caching of the strings to accelerate the
name lookup. It is better to create an Key and reuse it
@@ -129,7 +95,7 @@
return get_map().find(sc)->second;
}
}
-protected:
+private:
bool is_default() const;
public:
static const std::string get_string(int i)
Index: kernel/src/exception.cpp
===================================================================
--- kernel/src/exception.cpp (revision 916)
+++ kernel/src/exception.cpp (working copy)
@@ -51,12 +51,15 @@
{
}
-namespace internal
+namespace
{
// The error message is already in the exception
bool print_exceptions=false;
+
+}
+
void assert_fail(const char *msg)
{
if (print_exceptions) {
@@ -72,6 +75,4 @@
}
}
-} // namespace internal
-
IMP_END_NAMESPACE