Index: kernel/include/base_types.h
===================================================================
--- kernel/include/base_types.h (revision 855)
+++ kernel/include/base_types.h (working copy)
@@ -49,27 +49,22 @@
struct ScoreStateTag {};
struct OptimizerStateTag {};
-typedef Index<ParticleTag> ParticleIndex;
typedef Index<RestraintTag> RestraintIndex;
typedef Index<ScoreStateTag> ScoreStateIndex;
typedef Index<OptimizerStateTag> OptimizerStateIndex;
+typedef Index<ParticleTag> ParticleIndex;
+typedef std::vector<ParticleIndex> ParticleIndexes;
+/* This needs to be here so that both Model and Particle can use Particles */
class Particle;
//! A class which is used for representing collections of particles
/**
- We need this to have a uniform return type for python.
- \todo It would be nice to use internal::Vector instead, but that
- is not as pretty for Python.
+ We need this to have a uniform return type for python.
+ \todo It would be nice to use internal::Vector instead, but that
+ is not as pretty for Python.
*/
typedef std::vector<Particle*> Particles;
-typedef std::pair<Particle*, Particle*> ParticlePair;
-typedef std::vector<ParticlePair> ParticlePairs;
-
-typedef std::vector<ParticleIndex> ParticleIndexes;
-
-class Particle;
-
//! The type used to identify float attributes in the Particles
IMP_DECLARE_KEY_TYPE(FloatKey, 0);
//! The type used to identify int attributes in the Particles
Index: kernel/include/Model.h
===================================================================
--- kernel/include/Model.h (revision 855)
+++ kernel/include/Model.h (working copy)
@@ -11,7 +11,9 @@
#include "IMP_config.h"
#include "Object.h"
+#include "Particle.h"
#include "internal/kernel_version_info.h"
+#include "container_macros.h"
#include "base_types.h"
#include "VersionInfo.h"
Index: kernel/include/SConscript
===================================================================
--- kernel/include/SConscript (revision 855)
+++ kernel/include/SConscript (working copy)
@@ -7,7 +7,8 @@
'DecoratorBase.h', 'Vector3D.h',
'UnaryFunction.h', 'PairScore.h', 'SingletonScore.h', 'macros.h',
'TripletScore.h', 'exception.h', 'VersionInfo.h',
- 'Object.h', 'Pointer.h', 'RefCountedObject.h', 'ParticleRefiner.h']
+ 'Object.h', 'Pointer.h', 'RefCountedObject.h', 'ParticleRefiner.h',
+ 'container_macros.h']
# Subdirectories
files = [File(f) for f in files] \
Index: kernel/include/Particle.h
===================================================================
--- kernel/include/Particle.h (revision 855)
+++ kernel/include/Particle.h (working copy)
@@ -629,6 +629,87 @@
particles_.remove(name);
}
+
+//! A class to store a pair of particles.
+/** \note These do not due ref counting currently. SWIG prevents
+ use of Pointer<Particle> as the storage type without some
+ gynmastics.
+ */
+class ParticlePair {
+ bool is_default() const {return false;}
+public:
+ typedef ParticlePair This;
+ Particle *first, *second;
+ ParticlePair(): first(NULL), second(NULL){}
+ ParticlePair(Particle *a, Particle *b):
+ first(a), second(b) {}
+ IMP_COMPARISONS_2(first, second)
+ Particle * operator[](unsigned int i) const {
+ switch (i) {
+ case 0:
+ return first;
+ case 1:
+ return second;
+ default:
+ throw IndexException("Invalid member of pair");
+ }
+ }
+ Particle *& operator[](unsigned int i) {
+ switch (i) {
+ case 0:
+ return first;
+ case 1:
+ return second;
+ default:
+ throw IndexException("Invalid member of pair");
+ }
+ }
+
+};
+
+typedef std::vector<ParticlePair> ParticlePairs;
+
+
+
+//! Store three particles
+class ParticleTriplet {
+ bool is_default() const {return false;}
+public:
+ typedef ParticleTriplet This;
+ Particle *first, *second, *third;
+ ParticleTriplet(): first(NULL), second(NULL), third(NULL){}
+ ParticleTriplet(Particle *a, Particle *b, Particle *c):
+ first(a), second(b), third(c) {}
+ IMP_COMPARISONS_3(first, second, third)
+ Particle *operator[](unsigned int i) const {
+ switch (i) {
+ case 0:
+ return first;
+ case 1:
+ return second;
+ case 2:
+ return third;
+ default:
+ throw IndexException("Invalid member of triplet");
+ };
+ }
+ Particle *&operator[](unsigned int i) {
+ switch (i) {
+ case 0:
+ return first;
+ case 1:
+ return second;
+ case 2:
+ return third;
+ default:
+ throw IndexException("Invalid member of triplet");
+ };
+ }
+
+};
+
+typedef std::vector<ParticleTriplet> ParticleTriplets;
+
IMP_END_NAMESPACE
#endif /* IMP_PARTICLE_H */
Index: kernel/include/Object.h
===================================================================
--- kernel/include/Object.h (revision 855)
+++ kernel/include/Object.h (working copy)
@@ -63,4 +63,11 @@
IMP_END_NAMESPACE
+//! Call the assert_is_valid method in the object base
+#define IMP_CHECK_OBJECT(obj) do { \
+IMP_assert(obj != NULL, "NULL object"); \
+(obj)->assert_is_valid(); \
+} while (false)
+
+
#endif /* IMP_OBJECT_H */
Index: kernel/include/Restraint.h
===================================================================
--- kernel/include/Restraint.h (revision 855)
+++ kernel/include/Restraint.h (working copy)
@@ -17,6 +17,7 @@
#include "Pointer.h"
#include "log.h"
#include "utility.h"
+#include "container_macros.h"
#include <vector>
#include <iostream>
Index: kernel/include/ParticleRefiner.h
===================================================================
--- kernel/include/ParticleRefiner.h (revision 855)
+++ kernel/include/ParticleRefiner.h (working copy)
@@ -9,6 +9,7 @@
#include "IMP_config.h"
#include "base_types.h"
+#include "Particle.h"
#include "VersionInfo.h"
#include "RefCountedObject.h"
Index: kernel/include/macros.h
===================================================================
--- kernel/include/macros.h (revision 855)
+++ kernel/include/macros.h (working copy)
@@ -247,194 +247,4 @@
#define IMP_COPY_CONSTRUCTOR(TC) TC(const TC &o){copy_from(o);} \
TC& operator=(const TC &o) {copy_from(o); return *this;}
-
-
-
-/** \internal
- */
-#define IMP_CONTAINER_CORE(protection, Ucname, lcname, Data, IndexType,\
- Container) \
- protection: \
- /** \short Add an object.
- \param[in] obj Pointer to the object
- \return index of object within the object
- */ \
- IndexType add_##lcname(Data obj); \
- /** \short Add several objects.
- \param[in] obj a vector of pointers
- */ \
- void add_##lcname##s(const std::vector<Data>& obj); \
- /** \short Clear the contents of the container */ \
- void clear_##lcname##s(); \
- /** \short return the number of objects*/ \
- unsigned int get_number_of_##lcname##s() const { \
- return lcname##_vector_.size();} \
- /** \short Get object refered to by the index
- \throws IndexException if the index is out of range
- */ \
- Data get_##lcname(IndexType i) const { \
- return lcname##_vector_[i]; \
- } \
- /** \short An iterator through the objects.
- The value type is a pointer.*/ \
- typedef Container::iterator Ucname##Iterator; \
- /** \short A const iterator through the objects.
- The value type is a pointer.*/ \
- typedef Container::const_iterator Ucname##ConstIterator; \
- Ucname##Iterator lcname##s_begin() {return lcname##_vector_.begin();} \
- Ucname##Iterator lcname##s_end() {return lcname##_vector_.end();} \
- Ucname##ConstIterator lcname##s_begin() const { \
- return lcname##_vector_.begin();} \
- Ucname##ConstIterator lcname##s_end() const { \
- return lcname##_vector_.end();} \
- private: \
- /** \internal */ \
- Container lcname##_vector_; \
- protection:
-
-/** \internal
- */
-#define IMP_CONTAINER_CORE_IMPL(Class, Ucname, lcname, Data, IndexType, \
- Init_obj, Onchanged) \
- IndexType Class::add_##lcname(Data obj) { \
- IndexType index= lcname##_vector_.push_back(obj); \
- Init_obj; \
- Onchanged; \
- if (false) {index=index; obj=obj;}; \
- return index; \
- } \
- void Class::add_##lcname##s(const std::vector<Data> &objs) { \
- unsigned int osz= lcname##_vector_.size(); \
- lcname##_vector_.insert(lcname##_vector_.end(), objs.begin(), \
- objs.end()); \
- for (unsigned int i=0; i< objs.size(); ++i) { \
- Data obj= lcname##_vector_[osz+i]; \
- IndexType index(osz+i); \
- Init_obj; \
- if (false) {obj=obj; index=index;} \
- } \
- Onchanged; \
- } \
- /** \short Clear the contents of the container */ \
- void Class::clear_##lcname##s(){ \
- lcname##_vector_.clear(); \
- Onchanged; \
- } \
-
-
-//! Use this to add a container of IMP objects
-/**
- Such a container adds public methods add_foo, get_foo, get_number_of_foo
- and a private type foo_iterator, with methods foo_begin, foo_end.
- \param[in] protection The level of protection for the container.
- \param[in] Ucname The name of the type in uppercase
- \param[in] lcname The name of the type in lower case
- \param[in] Data The type of the data to store.
-
- \note the type Ucnames must be declared and be a vector of
- Data.
- */
-#define IMP_LIST(protection, Ucname, lcname, Data) \
- protection: \
- /** \short Remove any occurences of d from the container */ \
- void erase_##lcname(Data d); \
- /** \short Get a container of all the objects.
- This is for Python as the container can be used like a Python list*/\
- const Ucname##s &get_##lcname##s() const { \
- return static_cast< const Ucname##s &>(lcname##_vector_); \
- } \
- void set_##lcname##s(const Ucname##s &ps) { \
- clear_##lcname##s(); \
- add_##lcname##s(ps); \
- } \
- IMP_CONTAINER_CORE(protection, Ucname, lcname, Data, unsigned int, \
- IMP::internal::Vector<Data>)
-
-
-
-//! Use this to add a container of IMP objects
-/**
- This code should go in a .cpp file. One macro for each IMP_CONTAINER.
- \param[in] init Code to modify the passed in object. The object is obj
- its index index.
- \param[in] OnChanged Code to get executed when the container changes.
- */
-#define IMP_LIST_IMPL(Class, Ucname, lcname, Data, init, OnChanged) \
- IMP_CONTAINER_CORE_IMPL(Class, Ucname, lcname, Data, unsigned int, \
- init, OnChanged) \
- /** \short Remove any occurences of d from the container */ \
- void Class::erase_##lcname(Data d) { \
- for (Ucname##Iterator it= lcname##s_begin(); \
- it != lcname##s_end(); ++it) { \
- if (*it == d) { \
- lcname##_vector_.erase(it); break; \
- } \
- } \
- OnChanged; \
- } \
-
-
-
-//! Use this to add a set of IMP objects owned by the containing one
-/**
- Such a container adds public methods add_foo, get_foo, get_number_of_foo
- and a private type foo_iterator, with methods foo_begin, foo_end.
- \param[in] Ucname The name of the type in uppercase
- \param[in] lcname The name of the type in lower case
- \param[in] IndexType The type to use for the index. This should be
- an instantiation of Index<T> or something similar.
-
- \note The type Ucnames must be declared and be a vector of
- Data.
- \note these containers are always public
-*/
-#define IMP_CONTAINER(Ucname, lcname, IndexType) \
- public: \
- void remove_##lcname(IndexType i) ; \
-private: \
-/** \internal
- This is an implementation detail.*/ \
-typedef IMP::internal::ObjectContainer<Ucname, IndexType> \
-Ucname##Container; \
-IMP_CONTAINER_CORE(public, Ucname, lcname, Ucname*, IndexType, \
- Ucname##Container)
-
-
-
-//! Use this to add a container of IMP objects
-/**
- This code should go in a .cpp file. One macro for each
- IMP_CONTAINER.
- \param[in] init Code to modify the passed in object. The object is obj
- its index index.
- \param[in] onchanged Code to execute when the container is changed.
- \param[in] onremove Code to execute when an object is removed. The object
- being removed is obj.
- */
-#define IMP_CONTAINER_IMPL(Class, Ucname, lcname, IndexType, init, \
-onchanged, onremove) \
- void Class::remove_##lcname(IndexType i) { \
- Ucname* obj= lcname##_vector_[i]; \
- onremove; \
- lcname##_vector_.remove(i); \
- if (false) std::cout << *obj; \
- } \
- IMP_CONTAINER_CORE_IMPL(Class, Ucname, lcname, Ucname*, IndexType, \
- init,onchanged)
-
-
-
-//! Call the assert_is_valid method in the object base
-#define IMP_CHECK_OBJECT(obj) do { \
- IMP_assert(obj != NULL, "NULL object"); \
- (obj)->assert_is_valid(); \
- } while (false)
-
-
-// They use IMP_CHECK_OBJECT and so must be included at the end
-
-#include "internal/Vector.h"
-#include "internal/ObjectContainer.h"
-
-
#endif /* IMP_MACROS_H */
Index: kernel/include/internal/ExponentialNumber.h
===================================================================
--- kernel/include/internal/ExponentialNumber.h (revision 855)
+++ kernel/include/internal/ExponentialNumber.h (working copy)
@@ -10,6 +10,7 @@
#define IMP_EXPONENTIAL_NUMBER_H
#include "../macros.h"
+#include "../base_types.h"
#include <iostream>
#include <cmath>
Index: kernel/include/container_macros.h
===================================================================
--- kernel/include/container_macros.h (revision 0)
+++ kernel/include/container_macros.h (revision 0)
@@ -0,0 +1,188 @@
+/*
+ * \file container_macros.h
+ * \brief Macros to define containers of objects
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef IMP_INTERNAL_CONTAINER_MACROS_H
+#define IMP_INTERNAL_CONTAINER_MACROS_H
+
+#include "internal/Vector.h"
+#include "internal/ObjectContainer.h"
+#include "macros.h"
+
+/** \internal
+ */
+#define IMP_CONTAINER_CORE(protection, Ucname, lcname, Data, IndexType,\
+Container) \
+protection: \
+/** \short Add an object.
+\param[in] obj Pointer to the object
+\return index of object within the object
+*/ \
+IndexType add_##lcname(Data obj); \
+/** \short Add several objects.
+\param[in] obj a vector of pointers
+*/ \
+void add_##lcname##s(const std::vector<Data>& obj); \
+/** \short Clear the contents of the container */ \
+void clear_##lcname##s(); \
+/** \short return the number of objects*/ \
+unsigned int get_number_of_##lcname##s() const { \
+return lcname##_vector_.size();} \
+/** \short Get object refered to by the index
+\throws IndexException if the index is out of range
+*/ \
+Data get_##lcname(IndexType i) const { \
+return lcname##_vector_[i]; \
+} \
+/** \short An iterator through the objects.
+The value type is a pointer.*/ \
+typedef Container::iterator Ucname##Iterator; \
+/** \short A const iterator through the objects.
+The value type is a pointer.*/ \
+typedef Container::const_iterator Ucname##ConstIterator; \
+Ucname##Iterator lcname##s_begin() {return lcname##_vector_.begin();} \
+Ucname##Iterator lcname##s_end() {return lcname##_vector_.end();} \
+Ucname##ConstIterator lcname##s_begin() const { \
+return lcname##_vector_.begin();} \
+Ucname##ConstIterator lcname##s_end() const { \
+return lcname##_vector_.end();} \
+private: \
+/** \internal */ \
+Container lcname##_vector_; \
+protection:
+
+/** \internal
+ */
+#define IMP_CONTAINER_CORE_IMPL(Class, Ucname, lcname, Data, IndexType, \
+Init_obj, Onchanged) \
+IndexType Class::add_##lcname(Data obj) { \
+IndexType index= lcname##_vector_.push_back(obj); \
+Init_obj; \
+Onchanged; \
+if (false) {index=index; obj=obj;}; \
+return index; \
+} \
+void Class::add_##lcname##s(const std::vector<Data> &objs) { \
+unsigned int osz= lcname##_vector_.size(); \
+lcname##_vector_.insert(lcname##_vector_.end(), objs.begin(), \
+objs.end()); \
+for (unsigned int i=0; i< objs.size(); ++i) { \
+Data obj= lcname##_vector_[osz+i]; \
+IndexType index(osz+i); \
+Init_obj; \
+if (false) {obj=obj; index=index;} \
+} \
+Onchanged; \
+} \
+/** \short Clear the contents of the container */ \
+void Class::clear_##lcname##s(){ \
+lcname##_vector_.clear(); \
+Onchanged; \
+} \
+
+
+//! Use this to add a container of IMP objects
+/**
+ Such a container adds public methods add_foo, get_foo, get_number_of_foo
+ and a private type foo_iterator, with methods foo_begin, foo_end.
+ \param[in] protection The level of protection for the container.
+ \param[in] Ucname The name of the type in uppercase
+ \param[in] lcname The name of the type in lower case
+ \param[in] Data The type of the data to store.
+
+ \note the type Ucnames must be declared and be a vector of
+ Data.
+ */
+#define IMP_LIST(protection, Ucname, lcname, Data) \
+protection: \
+/** \short Remove any occurences of d from the container */ \
+void erase_##lcname(Data d); \
+/** \short Get a container of all the objects.
+This is for Python as the container can be used like a Python list*/\
+const Ucname##s &get_##lcname##s() const { \
+return static_cast< const Ucname##s &>(lcname##_vector_); \
+} \
+void set_##lcname##s(const Ucname##s &ps) { \
+clear_##lcname##s(); \
+add_##lcname##s(ps); \
+} \
+IMP_CONTAINER_CORE(protection, Ucname, lcname, Data, unsigned int, \
+IMP::internal::Vector<Data>)
+
+
+
+//! Use this to add a container of IMP objects
+/**
+ This code should go in a .cpp file. One macro for each IMP_CONTAINER.
+ \param[in] init Code to modify the passed in object. The object is obj
+ its index index.
+ \param[in] OnChanged Code to get executed when the container changes.
+ */
+#define IMP_LIST_IMPL(Class, Ucname, lcname, Data, init, OnChanged) \
+IMP_CONTAINER_CORE_IMPL(Class, Ucname, lcname, Data, unsigned int, \
+init, OnChanged) \
+/** \short Remove any occurences of d from the container */ \
+void Class::erase_##lcname(Data d) { \
+for (Ucname##Iterator it= lcname##s_begin(); \
+it != lcname##s_end(); ++it) { \
+if (*it == d) { \
+lcname##_vector_.erase(it); break; \
+} \
+} \
+OnChanged; \
+} \
+
+
+
+//! Use this to add a set of IMP objects owned by the containing one
+/**
+ Such a container adds public methods add_foo, get_foo, get_number_of_foo
+ and a private type foo_iterator, with methods foo_begin, foo_end.
+ \param[in] Ucname The name of the type in uppercase
+ \param[in] lcname The name of the type in lower case
+ \param[in] IndexType The type to use for the index. This should be
+ an instantiation of Index<T> or something similar.
+
+ \note The type Ucnames must be declared and be a vector of
+ Data.
+ \note these containers are always public
+ */
+#define IMP_CONTAINER(Ucname, lcname, IndexType) \
+public: \
+void remove_##lcname(IndexType i) ; \
+private: \
+/** \internal
+This is an implementation detail.*/ \
+typedef IMP::internal::ObjectContainer<Ucname, IndexType> \
+Ucname##Container; \
+IMP_CONTAINER_CORE(public, Ucname, lcname, Ucname*, IndexType, \
+Ucname##Container)
+
+
+
+//! Use this to add a container of IMP objects
+/**
+ This code should go in a .cpp file. One macro for each
+ IMP_CONTAINER.
+ \param[in] init Code to modify the passed in object. The object is obj
+ its index index.
+ \param[in] onchanged Code to execute when the container is changed.
+ \param[in] onremove Code to execute when an object is removed. The object
+ being removed is obj.
+ */
+#define IMP_CONTAINER_IMPL(Class, Ucname, lcname, IndexType, init, \
+onchanged, onremove) \
+void Class::remove_##lcname(IndexType i) { \
+Ucname* obj= lcname##_vector_[i]; \
+onremove; \
+lcname##_vector_.remove(i); \
+if (false) std::cout << *obj; \
+} \
+IMP_CONTAINER_CORE_IMPL(Class, Ucname, lcname, Ucname*, IndexType, \
+init,onchanged)
+
+#endif
Property changes on: kernel/include/container_macros.h
___________________________________________________________________
Added: svn:mergeinfo
Index: kernel/pyext/IMP_macros.i
===================================================================
--- kernel/pyext/IMP_macros.i (revision 855)
+++ kernel/pyext/IMP_macros.i (working copy)
@@ -53,3 +53,4 @@
%enddef
%include "IMP/macros.h"
+%include "IMP/container_macros.h"
Index: kernel/pyext/IMP.i
===================================================================
--- kernel/pyext/IMP.i (revision 855)
+++ kernel/pyext/IMP.i (working copy)
@@ -15,6 +15,31 @@
%include "typemaps.i"
+%ignore IMP::ParticlePair::operator[];
+%ignore IMP::ParticleTriplet::operator[];
+%extend IMP::ParticlePair {
+ Particle* __getitem__(unsigned int index) const {
+ return self->operator[](index);
+ }
+ void __setitem__(unsigned int index, Particle* val) {
+ self->operator[](index) = val;
+ }
+ int __len__() const {
+ return 2;
+ }
+}
+%extend IMP::ParticleTriplet {
+ Particle* __getitem__(unsigned int index) const {
+ return self->operator[](index);
+ }
+ void __setitem__(unsigned int index, Particle* val) {
+ self->operator[](index) = val;
+ }
+ int __len__() const {
+ return 3;
+ }
+}
+
namespace IMP {
%typemap(out) std::pair<Float,Float> {
PyObject *tup= PyTuple_New(2);
@@ -124,8 +149,8 @@
%template(OptimizerStateIndex) Index<OptimizerStateTag>;
%template(Particles) ::std::vector<Particle*>;
%template(ParticlesList) ::std::vector<Particles>;
- %template(ParticlePair) ::std::pair<IMP::Particle*, IMP::Particle*>;
%template(ParticlePairs) ::std::vector<ParticlePair>;
+ %template(ParticleTriplets) ::std::vector<ParticleTriplet>;
%template(Restraints) ::std::vector<IMP::Restraint*>;
%template(ScoreStates) ::std::vector<ScoreState*>;
%template(OptimizerStates) ::std::vector<OptimizerState*>;