Index: kernel/include/IMP/utility.h
===================================================================
--- kernel/include/IMP/utility.h (revision 354)
+++ kernel/include/IMP/utility.h (working copy)
@@ -8,303 +8,8 @@
#ifndef __IMP_UTILITY_H
#define __IMP_UTILITY_H
+#include "macros.h"
-//! Implement comparison in a class using field as the variable to compare
-/** The macro requires that This be defined as the type of the current class.
- */
-#define IMP_COMPARISONS_1(field) \
- /** */ bool operator==(const This &o) const { \
- return (field== o.field); \
- } \
- /** */ bool operator!=(const This &o) const { \
- return (field!= o.field); \
- } \
- /** */ bool operator<(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- return (field< o.field); \
- } \
- /** */ bool operator>(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- return (field> o.field); \
- } \
- /** */ bool operator>=(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- return (field>= o.field); \
- } \
- /** */ bool operator<=(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- return (field<= o.field); \
- }
-
-//! Implement comparison in a class using field as the variable to compare
-/** The macro requires that This be defined as the type of the current class.
- */
-#define IMP_COMPARISONS_2(f0, f1) \
- /** */ bool operator==(const This &o) const { \
- return (f0== o.f0 && f1==o.f1); \
- } \
- /** */ bool operator!=(const This &o) const { \
- return (f0!= o.f0 || f1 != o.f1); \
- } \
- /** */ bool operator<(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- if (f0< o.f0) return true; \
- else if (f0 > o.f0) return false; \
- else return f1 < o.f1; \
- } \
- /** */ bool operator>(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- if (f0 > o.f0) return true; \
- else if (f0 < o.f0) return false; \
- else return f1 > o.f1; \
- } \
- /** */ bool operator>=(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- return operator>(o) || operator==(o); \
- } \
- /** */ bool operator<=(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- return operator<(o) || operator==(o); \
- }
-
-//! Implement comparison in a class using field as the variable to compare
-/** The macro requires that This be defined as the type of the current class.
- */
-#define IMP_COMPARISONS_3(f0, f1, f2) \
- /** */ bool operator==(const This &o) const { \
- return (f0== o.f0 && f1==o.f1 && f2 == o.f2); \
- } \
- /** */ bool operator!=(const This &o) const { \
- return (f0!= o.f0 || f1 != o.f1 || f2 != o.f2); \
- } \
- /** */ bool operator<(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- if (f0< o.f0) return true; \
- else if (f0 > o.f0) return false; \
- if (f1< o.f1) return true; \
- else if (f1 > o.f1) return false; \
- else return f2 < o.f2; \
- } \
- /** */ bool operator>(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- if (f0 > o.f0) return true; \
- else if (f0 < o.f0) return false; \
- if (f1 > o.f1) return true; \
- else if (f1 < o.f1) return false; \
- else return f2 > o.f2; \
- } \
- /** */ bool operator>=(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- return operator>(o) || operator==(o); \
- } \
- /** */ bool operator<=(const This &o) const { \
- IMP_assert(!is_default() && !o.is_default(), \
- "Ordering with uninitialized index is undefined"); \
- return operator<(o) || operator==(o); \
- }
-
-//! Implement operator<< on class name, assuming it has one template argument
-/** class name should also define the method std::ostream &show(std::ostream&)
- */
-#define IMP_OUTPUT_OPERATOR_1(name) /** write to a stream*/ \
-template <class L> \
- inline std::ostream &operator<<(std::ostream &out, const name<L> &i) \
- { \
- return i.show(out); \
- }
-
-//! Implement operator<< on class name
-/** class name should also define the method std::ostream &show(std::ostream&)
- */
-#define IMP_OUTPUT_OPERATOR(name) /** write to a stream*/ \
- inline std::ostream &operator<<(std::ostream &out, const name &i) \
- { \
- i.show(out); \
- return out; \
- }
-
-//! Define the basic things you need for a Restraint.
-/** These are: show, evaluate, version, last_modified_by
- \param[in] version_string The version string.
- \param[in] lmb_string The name of the last modifier.
-*/
-#define IMP_RESTRAINT(version_string, lmb_string) \
- /** evaluate the restraint*/ \
- virtual Float evaluate(DerivativeAccumulator *accum); \
- /** write information about the restraint to the stream*/ \
- virtual void show(std::ostream &out=std::cout) const; \
- /** \return the current version*/ \
- virtual std::string version() const {return std::string(version_string);}\
- /** \return the last person to modify this restraint */ \
- virtual std::string last_modified_by() const {return std::string(lmb_string);}
-
-//! Define the basic things you need for an optimizer.
-/** These are: optimize, version, last_modified_by
- \param[in] version_string The version string.
- \param[in] lmb_string The name of the last modifier.
-*/
-#define IMP_OPTIMIZER(version_string, lmb_string) \
- /** \short Optimize the model.
- \param[in] max_steps The maximum number of steps to take.
- \return The final score.
- */ \
- virtual Float optimize(unsigned int max_steps); \
- /** \return the current version*/ \
- virtual std::string version() const {return std::string(version_string);}\
- /** \return the last person to modify this restraint */ \
- virtual std::string last_modified_by() const {return std::string(lmb_string);}
-
-
-//! Define the basics needed for an OptimizerState
-/**
- This macro declares the required functions
- - void update()
- - void show(std::ostream &out) const
- and defines the functions
- - version
- - last_modified_by
-
- \param[in] version_string The version.
- \param[in] lmb_string The person who last modified it.
-*/
-#define IMP_OPTIMIZER_STATE(version_string, lmb_string) \
- /** update the state*/ \
- virtual void update(); \
- /** write information about the state to the stream*/ \
- virtual void show(std::ostream &out=std::cout) const; \
- /** \return the current version*/ \
- virtual std::string version() const {return std::string(version_string);} \
- /** \return the last person to modify this restraint */ \
- virtual std::string last_modified_by() const {return std::string(lmb_string);}
-
-//! See IMP_OPTIMIZER_STATE
-#define IMP_SCORE_STATE(version_string, lmb_string)\
- IMP_OPTIMIZER_STATE(version_string, lmb_string)
-
-//! Use the swap_with member function to swap two objects
-#define IMP_SWAP(name) \
- inline void swap(name &a, name &b) { \
- a.swap_with(b); \
- }
-
-//! swap two member variables assuming the other object is called o
-#define IMP_SWAP_MEMBER(var_name) \
- std::swap(var_name, o.var_name);
-
-
-
-//! use a copy_from method to create a copy constructor and operator=
-#define IMP_COPY_CONSTRUCTOR(TC) TC(const TC &o){copy_from(o);} \
- TC& operator=(const TC &o) {copy_from(o); return *this;}
-
-
-
-
-//! Use this to add a container of IMP objects
-/**
- Such a container adds public methods add_foo, get_foo, 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.
-
- Eventually we can add removal and correctness checks.
- */
-#define IMP_CONTAINER(Ucname, lcname, IndexType) \
- public: \
- /** \short Add an object.
- \param[in] obj Pointer to the object
- \return index of object within the object
- */ \
- IndexType add_##lcname(Ucname *obj); \
- /** \short Get object refered to by the index
- \throws IndexException if the index is out of range
- */ \
- Ucname *get_##lcname(IndexType i) const ; \
- /** \short return the number of objects*/ \
- unsigned int number_of_##lcname##s() const { \
- return lcname##_vector_.size();} \
-/** \short Get a container of all the objects.
- This is for Python as the container can be used like a Python list*/\
-const std::vector<Ucname*> &get_##lcname##s() const { \
- return lcname##_vector_;} \
-/** \short An iterator through the objects.
- The value type is a pointer.*/ \
- typedef std::vector<Ucname*>::iterator Ucname##Iterator; \
-/** \short A const iterator through the objects.
- The value type is a pointer.*/ \
- typedef std::vector<Ucname*>::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: \
- std::vector<Ucname*> lcname##_vector_;
-
-
-
-//! 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.
- */
-#define IMP_CONTAINER_IMPL(Class, Ucname, lcname, IndexType, init) \
- IndexType Class::add_##lcname(Ucname *obj) { \
- IndexType index(lcname##_vector_.size()); \
- for (unsigned int i=0; i< lcname##_vector_.size(); ++i) { \
- IMP_assert(lcname##_vector_[i] != obj, #Ucname \
- " can only be added once to container"); \
- } \
- lcname##_vector_.push_back(obj); \
- init; \
- IMP_CHECK_OBJECT(obj); \
- return index; \
- } \
- Ucname *Class::get_##lcname(IndexType i) const { \
- IMP_check(i.get_index() < lcname##_vector_.size(), \
- "Index " << i << " out of range", \
- IndexException(#Ucname)); \
- Ucname *r= lcname##_vector_[i.get_index()]; \
- IMP_CHECK_OBJECT(r); \
- return r; \
- } \
-
-
-//! Destroy the things in the container
-/**
- Put this in the containing object desctructor when you use the
- IMP_CONTAINER macro.
- \param[in] Ucname the uppercase name
- \param[in] lcname the lower case name
- */
-#define IMP_CONTAINER_DELETE(Ucname, lcname) \
- for (Ucname##Iterator it= lcname##s_begin(); \
- it != lcname##s_end(); ++it) { \
- delete *it; \
- } \
- lcname##_vector_.clear();
-
-//! 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)
-
namespace IMP
{
Index: kernel/include/IMP/macros.h
===================================================================
--- kernel/include/IMP/macros.h (revision 0)
+++ kernel/include/IMP/macros.h (revision 0)
@@ -0,0 +1,402 @@
+/**
+ * \file IMP/macros.h \brief Various general useful macros for IMP.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef __IMP_MACROS_H
+#define __IMP_MACROS_H
+
+
+//! Implement comparison in a class using field as the variable to compare
+/** The macro requires that This be defined as the type of the current class.
+ */
+#define IMP_COMPARISONS_1(field) \
+ /** */ bool operator==(const This &o) const { \
+ return (field== o.field); \
+ } \
+ /** */ bool operator!=(const This &o) const { \
+ return (field!= o.field); \
+ } \
+ /** */ bool operator<(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ return (field< o.field); \
+ } \
+ /** */ bool operator>(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ return (field> o.field); \
+ } \
+ /** */ bool operator>=(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ return (field>= o.field); \
+ } \
+ /** */ bool operator<=(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ return (field<= o.field); \
+ }
+
+//! Implement comparison in a class using field as the variable to compare
+/** The macro requires that This be defined as the type of the current class.
+ */
+#define IMP_COMPARISONS_2(f0, f1) \
+ /** */ bool operator==(const This &o) const { \
+ return (f0== o.f0 && f1==o.f1); \
+ } \
+ /** */ bool operator!=(const This &o) const { \
+ return (f0!= o.f0 || f1 != o.f1); \
+ } \
+ /** */ bool operator<(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ if (f0< o.f0) return true; \
+ else if (f0 > o.f0) return false; \
+ else return f1 < o.f1; \
+ } \
+ /** */ bool operator>(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ if (f0 > o.f0) return true; \
+ else if (f0 < o.f0) return false; \
+ else return f1 > o.f1; \
+ } \
+ /** */ bool operator>=(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ return operator>(o) || operator==(o); \
+ } \
+ /** */ bool operator<=(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ return operator<(o) || operator==(o); \
+ }
+
+//! Implement comparison in a class using field as the variable to compare
+/** The macro requires that This be defined as the type of the current class.
+ */
+#define IMP_COMPARISONS_3(f0, f1, f2) \
+ /** */ bool operator==(const This &o) const { \
+ return (f0== o.f0 && f1==o.f1 && f2 == o.f2); \
+ } \
+ /** */ bool operator!=(const This &o) const { \
+ return (f0!= o.f0 || f1 != o.f1 || f2 != o.f2); \
+ } \
+ /** */ bool operator<(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ if (f0< o.f0) return true; \
+ else if (f0 > o.f0) return false; \
+ if (f1< o.f1) return true; \
+ else if (f1 > o.f1) return false; \
+ else return f2 < o.f2; \
+ } \
+ /** */ bool operator>(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ if (f0 > o.f0) return true; \
+ else if (f0 < o.f0) return false; \
+ if (f1 > o.f1) return true; \
+ else if (f1 < o.f1) return false; \
+ else return f2 > o.f2; \
+ } \
+ /** */ bool operator>=(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ return operator>(o) || operator==(o); \
+ } \
+ /** */ bool operator<=(const This &o) const { \
+ IMP_assert(!is_default() && !o.is_default(), \
+ "Ordering with uninitialized index is undefined"); \
+ return operator<(o) || operator==(o); \
+ }
+
+//! Implement operator<< on class name, assuming it has one template argument
+/** class name should also define the method std::ostream &show(std::ostream&)
+ */
+#define IMP_OUTPUT_OPERATOR_1(name) /** write to a stream*/ \
+template <class L> \
+ inline std::ostream& operator<<(std::ostream &out, const name<L> &i) \
+ { \
+ i.show(out); \
+ return out; \
+ }
+
+//! Implement operator<< on class name
+/** class name should also define the method std::ostream &show(std::ostream&)
+ */
+#define IMP_OUTPUT_OPERATOR(name) /** write to a stream*/ \
+ inline std::ostream &operator<<(std::ostream &out, const name &i) \
+ { \
+ i.show(out); \
+ return out; \
+ }
+
+//! Define the basic things you need for a Restraint.
+/** These are: show, evaluate, version, last_modified_by
+ \param[in] version_string The version string.
+ \param[in] lmb_string The name of the last modifier.
+*/
+#define IMP_RESTRAINT(version_string, lmb_string) \
+ /** evaluate the restraint*/ \
+ virtual Float evaluate(DerivativeAccumulator *accum); \
+ /** write information about the restraint to the stream*/ \
+ virtual void show(std::ostream &out=std::cout) const; \
+ /** \return the current version*/ \
+ virtual std::string version() const {return std::string(version_string);}\
+ /** \return the last person to modify this restraint */ \
+ virtual std::string last_modified_by() const {return std::string(lmb_string);}
+
+//! Define the basic things you need for an optimizer.
+/** These are: optimize, version, last_modified_by
+ \param[in] version_string The version string.
+ \param[in] lmb_string The name of the last modifier.
+*/
+#define IMP_OPTIMIZER(version_string, lmb_string) \
+ /** \short Optimize the model.
+ \param[in] max_steps The maximum number of steps to take.
+ \return The final score.
+ */ \
+ virtual Float optimize(unsigned int max_steps); \
+ /** \return the current version*/ \
+ virtual std::string version() const {return std::string(version_string);}\
+ /** \return the last person to modify this restraint */ \
+ virtual std::string last_modified_by() const {return std::string(lmb_string);}
+
+
+//! Define the basics needed for an OptimizerState
+/**
+ This macro declares the required functions
+ - void update()
+ - void show(std::ostream &out) const
+ and defines the functions
+ - version
+ - last_modified_by
+
+ \param[in] version_string The version.
+ \param[in] lmb_string The person who last modified it.
+*/
+#define IMP_OPTIMIZER_STATE(version_string, lmb_string) \
+ /** update the state*/ \
+ virtual void update(); \
+ /** write information about the state to the stream*/ \
+ virtual void show(std::ostream &out=std::cout) const; \
+ /** \return the current version*/ \
+ virtual std::string version() const {return std::string(version_string);} \
+ /** \return the last person to modify this restraint */ \
+ virtual std::string last_modified_by() const {return std::string(lmb_string);}
+
+//! See IMP_OPTIMIZER_STATE
+#define IMP_SCORE_STATE(version_string, lmb_string)\
+ IMP_OPTIMIZER_STATE(version_string, lmb_string)
+
+//! Use the swap_with member function to swap two objects
+#define IMP_SWAP(name) \
+ inline void swap(name &a, name &b) { \
+ a.swap_with(b); \
+ }
+
+//! swap two member variables assuming the other object is called o
+#define IMP_SWAP_MEMBER(var_name) \
+ std::swap(var_name, o.var_name);
+
+
+
+//! use a copy_from method to create a copy constructor and operator=
+#define IMP_COPY_CONSTRUCTOR(TC) TC(const TC &o){copy_from(o);} \
+ TC& operator=(const TC &o) {copy_from(o); return *this;}
+
+
+
+
+//! Use this to add a container of IMP objects
+/**
+ Such a container adds public methods add_foo, get_foo, 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.
+
+ Eventually we can add removal and correctness checks.
+ */
+#define IMP_CONTAINER(Ucname, lcname, IndexType) \
+ public: \
+ /** \short Add an object.
+ \param[in] obj Pointer to the object
+ \return index of object within the object
+ */ \
+ IndexType add_##lcname(Ucname *obj); \
+ /** \short Add several objects.
+ \param[in] obj a vector of pointers
+ */ \
+ void add_##lcname##s(const std::vector<Ucname*>& obj); \
+ /** \short Get object refered to by the index
+ \throws IndexException if the index is out of range
+ */ \
+ Ucname *get_##lcname(IndexType i) const ; \
+ /** \short return the number of objects*/ \
+ unsigned int number_of_##lcname##s() const { \
+ return lcname##_vector_.size();} \
+/** \short Get a container of all the objects.
+ This is for Python as the container can be used like a Python list*/\
+const std::vector<Ucname*> &get_##lcname##s() const { \
+ return lcname##_vector_;} \
+/** \short An iterator through the objects.
+ The value type is a pointer.*/ \
+ typedef std::vector<Ucname*>::iterator Ucname##Iterator; \
+/** \short A const iterator through the objects.
+ The value type is a pointer.*/ \
+ typedef std::vector<Ucname*>::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: \
+ std::vector<Ucname*> lcname##_vector_;
+
+
+
+//! 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.
+ */
+#define IMP_CONTAINER_IMPL(Class, Ucname, lcname, IndexType, init) \
+ IndexType Class::add_##lcname(Ucname *obj) { \
+ IndexType index(lcname##_vector_.size()); \
+ for (unsigned int i=0; i< lcname##_vector_.size(); ++i) { \
+ IMP_assert(lcname##_vector_[i] != obj, #Ucname \
+ " can only be added once to container"); \
+ } \
+ lcname##_vector_.push_back(obj); \
+ init; \
+ IMP_CHECK_OBJECT(obj); \
+ return index; \
+ } \
+ void Class::add_##lcname##s(const std::vector<Ucname*> &objs) { \
+ for (unsigned int i=0; i< objs.size(); ++i) { \
+ add_##lcname(objs[i]); \
+ } \
+ } \
+ Ucname *Class::get_##lcname(IndexType i) const { \
+ IMP_check(i.get_index() < lcname##_vector_.size(), \
+ "Index " << i << " out of range", \
+ IndexException(#Ucname)); \
+ Ucname *r= lcname##_vector_[i.get_index()]; \
+ IMP_CHECK_OBJECT(r); \
+ return r; \
+ } \
+
+
+//! Destroy the things in the container
+/**
+ Put this in the containing object desctructor when you use the
+ IMP_CONTAINER macro.
+ \param[in] Ucname the uppercase name
+ \param[in] lcname the lower case name
+ */
+#define IMP_CONTAINER_DELETE(Ucname, lcname) \
+ for (Ucname##Iterator it= lcname##s_begin(); \
+ it != lcname##s_end(); ++it) { \
+ delete *it; \
+ } \
+ lcname##_vector_.clear();
+
+
+//! Use this to add a set of IMP objects owned by the containing one
+/**
+ Such a container adds public methods add_foo, get_foo, 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.
+
+ Eventually we can add removal and correctness checks.
+ */
+#define IMP_CHILDREN(Ucname, lcname, IndexType) \
+ public: \
+ /** \short Add an object.
+ \param[in] obj Pointer to the object
+ \return index of object within the object
+ */ \
+ IndexType add_##lcname(Ucname *obj); \
+ /** \short Add several objects.
+ \param[in] obj a vector of pointers
+ */ \
+ void add_##lcname##s(const std::vector<Ucname*>& obj); \
+ /** \short Get object refered to by the index
+ \throws IndexException if the index is out of range
+ */ \
+ Ucname *get_##lcname(IndexType i) const ; \
+ /** \short return the number of objects*/ \
+ unsigned int number_of_##lcname##s() const { \
+ return lcname##_vector_.size();} \
+/** \short Get a container of all the objects.
+ This is for Python as the container can be used like a Python list*/\
+const std::vector<Ucname*> &get_##lcname##s() const { \
+ return lcname##_vector_;} \
+/** \short An iterator through the objects.
+ The value type is a pointer.*/ \
+typedef std::vector<Ucname*>::iterator Ucname##Iterator; \
+/** \short A const iterator through the objects.
+ The value type is a pointer.*/ \
+typedef std::vector<Ucname*>::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: \
+std::vector<std::auto_ptr<Ucname> > lcname##_vector_;
+
+
+
+//! 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.
+ */
+#define IMP_CHILDREN_IMPL(Class, Ucname, lcname, IndexType, init) \
+ IndexType Class::add_##lcname(Ucname *obj) { \
+ IndexType index(lcname##_vector_.size()); \
+ for (unsigned int i=0; i< lcname##_vector_.size(); ++i) { \
+ IMP_assert(lcname##_vector_[i] != obj, #Ucname \
+ " can only be added once to container"); \
+ } \
+ lcname##_vector_.push_back(obj); \
+ init; \
+ IMP_CHECK_OBJECT(obj); \
+ return index; \
+ } \
+ void Class::add_##lcname##s(const std::vector<Ucname*> &objs) { \
+ for (unsigned int i=0; i< objs.size(); ++i) { \
+ add_##lcname(objs[i]); \
+ } \
+ } \
+ Ucname *Class::get_##lcname(IndexType i) const { \
+ IMP_check(i.get_index() < lcname##_vector_.size(), \
+ "Index " << i << " out of range", \
+ IndexException(#Ucname)); \
+ Ucname *r= lcname##_vector_[i.get_index()]; \
+ IMP_CHECK_OBJECT(r); \
+ return r; \
+ } \
+
+
+//! 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_MACROS_H */
Index: kernel/include/IMP/decorators/utility.h
===================================================================
--- kernel/include/IMP/decorators/utility.h (revision 354)
+++ kernel/include/IMP/decorators/utility.h (working copy)
@@ -9,220 +9,6 @@
#ifndef __IMP_DECORATOR_UTILITY_H
#define __IMP_DECORATOR_UTILITY_H
+#include "macros.h"
-//! Define the basic things needed by a Decorator.
-/** The key things this defines are a default constructor, a static create
- function, a static cast function, a method get_particle(), a method
- get_model() and comparisons.
-
- \param[in] Name is the name of the decorator, such as NameDecorator
- \param[in] Parent The class name for the parent of this class,
- typically DecoratorBase
- \param[in] check_required is code which returns a bool which checks
- if a Particle *p has the required fields
- \param[in] add_required is code which adds the required fields
-
- It requires that the implementer of the Decorator implement the static
- method:
-
- - void initialize_static_data() which initializes static data such as
- AttributeKey instances. Ideally, this should internally make sure it
- is only done once.
- */
-#define IMP_DECORATOR(Name, Parent, check_required, add_required) \
- protected: \
- static bool decorator_keys_initialized_; \
- static void decorator_initialize_static_data(); \
- static bool has_required_attributes(::IMP::Particle *p) { \
- if (!Parent::has_required_attributes(p)) return false; \
- check_required; \
- } \
- static void add_required_attributes(::IMP::Particle *p) { \
- Parent::add_required_attributes(p); \
- add_required; \
- } \
- friend class DecoratorBase; \
- Name(::IMP::Particle* p): Parent(p) { \
- IMP_assert(has_required_attributes(p), \
- "This is not a particle of type " \
- << #Name << *p); \
- } \
-public: \
- typedef Name This; \
- /** The default constructor. This is used as a null value */ \
- Name(): Parent(){} \
- /** Add the necessary attributes to p and return a decorator. */ \
- static Name create(::IMP::Particle *p) { \
- return IMP::DecoratorBase::create<Name>(p); \
- } \
- /** Check that p has the necessary attributes and return a decorator. \
- \throws InvalidStateException if some required attributes are \
- missing \
- */ \
- static Name cast(::IMP::Particle *p) { \
- return IMP::DecoratorBase::cast<Name>(p); \
- } \
- /** Write information about this decorator to out. Each line should \
- prefixed by prefix*/ \
- void show(std::ostream &out=std::cout, \
- std::string prefix=std::string()) const;
-
-
-/**
- Put this macro in to the .cpp with code to initialize the keys
- used by the decorator. This will make sure that the keys are
- initialized before use and initialized exactly once.
- \param[in] Name the name of the decorate
- \param[in] Parent the name of the parent decorator to make sure its keys
- are initalized
- \param[in] work The list of statements to initialize the keys.
- this should probably look something like {a_key_=IntKey("Foo");...}
- */
-#define IMP_DECORATOR_INITIALIZE(Name, Parent, work)\
- bool Name::decorator_keys_initialized_=false; \
- void Name::decorator_initialize_static_data() { \
- if (decorator_keys_initialized_) return; \
- else { \
- Parent::decorator_initialize_static_data(); \
- work; \
- decorator_keys_initialized_=true; \
- } \
- }
-
-//! Perform actions dependent on whether a particle has an attribute.
-/** A common pattern is to check if a particle has a particular attribute,
- do one thing if it does and another if it does not. This macro implements
- that pattern. It requires that the method get_particle() return the
- particle being used.
-
- \param[in] AttributeKey The key for the attribute
- \param[in] Type The type for the attribute ("Int", "Float", "String")
- \param[in] has_action The action to take if the Particle has the attribute.
- The attribute value is stored in the variable VALUE.
- \param[in] not_has_action The action to take if the Particle does not have
- the attribute.
- */
-#define IMP_DECORATOR_GET(AttributeKey, Type, has_action, not_has_action) \
- if (get_particle()->has_attribute(AttributeKey)) { \
- Type VALUE = get_particle()->get_value(AttributeKey); \
- has_action; \
- } else { \
- not_has_action; \
- }
-
-
-//! Set an attribute, creating it if it does not already exist.
-/** Another commont pattern is to have an assumed value if the attribute
- is not there. Then, you sometimes need to set the value whether it
- is there or not.
- */
-#define IMP_DECORATOR_SET(AttributeKey, value) \
- if (get_particle()->has_attribute(AttributeKey)) { \
- get_particle()->set_value(AttributeKey, value) ; \
- } else { \
- get_particle()->add_attribute(AttributeKey, value); \
- }
-
-//! define methods for getting and setting a particular simple field
-/**
- This macros defines methods to get an set a particular attribute.
-
- \param[in] name The lower case name of the attribute
- \param[in] AttributeKey The AttributeKey object controlling
- the attribute.
- \param[in] Type The type of the attribute (upper case).
- \param[in] ReturnType The type to return from the get.
-*/
-#define IMP_DECORATOR_GET_SET(name, AttributeKey, Type, ReturnType) \
- /** \return the attribute value */ \
- ReturnType get_##name() const { \
- return static_cast<ReturnType>(get_particle()->get_value(AttributeKey)); \
- } \
- /** Set the attribute \param[in] t the value */ \
- void set_##name(ReturnType t) { \
- get_particle()->set_value(AttributeKey, t); \
- }
-
-//! Define methods for getting and setting an optional simple field.
-/**
- See IMP_DECORATOR_GET_SET.
-
- \param[in] name The lower case name of the attribute
- \param[in] AttributeKey The AttributeKey object controlling
- the attribute.
- \param[in] Type The type of the attribute (upper case).
- \param[in] ReturnType The type to return from the get.
- \param[in] default_value The value returned if the attribute is missing.
- */
-#define IMP_DECORATOR_GET_SET_OPT(name, AttributeKey, Type, \
- ReturnType, default_value) \
- /** \return the attribute value*/ \
- ReturnType get_##name() const { \
- IMP_DECORATOR_GET(AttributeKey, Type, \
- return static_cast<ReturnType>(VALUE), \
- return default_value); \
- } \
- /** \param[in] t the value to set the attribute to*/ \
- void set_##name(ReturnType t) { \
- IMP_DECORATOR_SET(AttributeKey, t); \
- }
-
-
-//! Define a set of attributes which form an array
-/**
- This macro should go in the header and IMP_DECORATOR_ARRAY_CPP into the .cpp
- and IMP_DECORATOR_ARRAY_INIT in the initialize_static_data function
-
- To use the array, use functions
-
- - Type internal_get_name(unsigned int i)
-
- - void internal_add_name(Type)
-
- - unsigned int internal_get_number_of_name() const
- */
-#define IMP_DECORATOR_ARRAY_DECL(name, Type) \
- protected: \
- static IntKey number_of_##name##_key_; \
- static std::vector<Type##Key> name##_keys_; \
- static void generate_##name##_keys(unsigned int i); \
- static const Type##Key get_##name##_key(unsigned int i) { \
- if (i >= name##_keys_.size()) generate_##name##_keys(i); \
- return name##_keys_[i]; \
- } \
- Type internal_get_##name(unsigned int i) const{ \
- IMP_DECORATOR_GET(get_##name##_key(i), Type, \
- return VALUE, \
- throw IndexException(); return Type()); \
- } \
- int internal_add_##name(Type t); \
- unsigned int internal_get_number_of_##name() const { \
- IMP_DECORATOR_GET(number_of_##name##_key_, \
- Int, return VALUE, return 0); \
- } \
-
-//! See IMP_DECORATOR_ARRAY_DECL
-#define IMP_DECORATOR_ARRAY_DEF(DecoratorType, name, Type) \
- IntKey DecoratorType##Decorator::number_of_##name##_key_; \
- std::vector<Type##Key> DecoratorType##Decorator::name##_keys_; \
- void DecoratorType##Decorator::generate_##name##_keys(unsigned int i) \
- { \
- while (!(i < name##_keys_.size())) { \
- std::ostringstream oss; \
- oss << #DecoratorType " " #name " " << name##_keys_.size(); \
- name##_keys_.push_back(Type##Key(oss.str().c_str())); \
- } \
- } \
- int DecoratorType##Decorator::internal_add_##name(Type t) { \
- int nc= internal_get_number_of_##name(); \
- get_particle()->add_attribute(get_##name##_key(nc), t); \
- IMP_DECORATOR_SET(number_of_##name##_key_, nc+1); \
- return nc; \
- }
-
-//! See IMP_DECORATOR_ARRAY_DECL
-#define IMP_DECORATOR_ARRAY_INIT(DecoratorType, name, Type) \
- number_of_##name##_key_= IntKey(#DecoratorType " num " #name);
-
-
#endif /* __IMP_DECORATOR_UTILITY_H */
Index: kernel/include/IMP/decorators/macros.h
===================================================================
--- kernel/include/IMP/decorators/macros.h (revision 0)
+++ kernel/include/IMP/decorators/macros.h (revision 0)
@@ -0,0 +1,230 @@
+/**
+ * \file decorators/macros.h \brief Various important macros
+ * for implementing decorators.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ *
+ */
+
+#ifndef __IMP_DECORATOR_MACROS_H
+#define __IMP_DECORATOR_MACROS_H
+
+
+//! Define the basic things needed by a Decorator.
+/** The key things this defines are a default constructor, a static create
+ function, a static cast function, a method get_particle(), a method
+ get_model() and comparisons.
+
+ \param[in] Name is the name of the decorator, such as NameDecorator
+ \param[in] Parent The class name for the parent of this class,
+ typically DecoratorBase
+ \param[in] check_required is code which returns a bool which checks
+ if a Particle *p has the required fields
+ \param[in] add_required is code which adds the required fields
+
+ It requires that the implementer of the Decorator implement the static
+ method:
+
+ - void initialize_static_data() which initializes static data such as
+ AttributeKey instances. Ideally, this should internally make sure it
+ is only done once.
+ */
+#define IMP_DECORATOR(Name, Parent, check_required, add_required) \
+ protected: \
+ static bool decorator_keys_initialized_; \
+ static void decorator_initialize_static_data(); \
+ static bool has_required_attributes(::IMP::Particle *p) { \
+ if (!Parent::has_required_attributes(p)) return false; \
+ check_required; \
+ } \
+ static void add_required_attributes(::IMP::Particle *p) { \
+ if (!Parent::has_required_attributes(p)) { \
+ Parent::add_required_attributes(p); \
+ } \
+ add_required; \
+ } \
+ friend class DecoratorBase; \
+ Name(::IMP::Particle* p): Parent(p) { \
+ IMP_assert(has_required_attributes(p), \
+ "This is not a particle of type " \
+ << #Name << *p); \
+ } \
+public: \
+ typedef Name This; \
+ /** The default constructor. This is used as a null value */ \
+ Name(): Parent(){} \
+ /** Add the necessary attributes to p and return a decorator. */ \
+ static Name create(::IMP::Particle *p) { \
+ return IMP::DecoratorBase::create<Name>(p); \
+ } \
+ /** Check that p has the necessary attributes and return a decorator. \
+ \throws InvalidStateException if some required attributes are \
+ missing \
+ */ \
+ static Name cast(::IMP::Particle *p) { \
+ return IMP::DecoratorBase::cast<Name>(p); \
+ } \
+ /** Write information about this decorator to out. Each line should \
+ prefixed by prefix*/ \
+ void show(std::ostream &out=std::cout, \
+ std::string prefix=std::string()) const;
+
+
+/**
+ Put this macro in to the .cpp with code to initialize the keys
+ used by the decorator. This will make sure that the keys are
+ initialized before use and initialized exactly once.
+ \param[in] Name the name of the decorate
+ \param[in] Parent the name of the parent decorator to make sure its keys
+ are initalized
+ \param[in] work The list of statements to initialize the keys.
+ this should probably look something like {a_key_=IntKey("Foo");...}
+ */
+#define IMP_DECORATOR_INITIALIZE(Name, Parent, work)\
+ bool Name::decorator_keys_initialized_=false; \
+ void Name::decorator_initialize_static_data() { \
+ if (decorator_keys_initialized_) return; \
+ else { \
+ Parent::decorator_initialize_static_data(); \
+ work; \
+ decorator_keys_initialized_=true; \
+ } \
+ }
+
+//! Perform actions dependent on whether a particle has an attribute.
+/** A common pattern is to check if a particle has a particular attribute,
+ do one thing if it does and another if it does not. This macro implements
+ that pattern. It requires that the method get_particle() return the
+ particle being used.
+
+ \param[in] AttributeKey The key for the attribute
+ \param[in] Type The type for the attribute ("Int", "Float", "String")
+ \param[in] has_action The action to take if the Particle has the attribute.
+ The attribute value is stored in the variable VALUE.
+ \param[in] not_has_action The action to take if the Particle does not have
+ the attribute.
+ */
+#define IMP_DECORATOR_GET(AttributeKey, Type, has_action, not_has_action) \
+ if (get_particle()->has_attribute(AttributeKey)) { \
+ Type VALUE = get_particle()->get_value(AttributeKey); \
+ has_action; \
+ } else { \
+ not_has_action; \
+ }
+
+
+//! Set an attribute, creating it if it does not already exist.
+/** Another commont pattern is to have an assumed value if the attribute
+ is not there. Then, you sometimes need to set the value whether it
+ is there or not.
+ */
+#define IMP_DECORATOR_SET(AttributeKey, value) \
+ if (get_particle()->has_attribute(AttributeKey)) { \
+ get_particle()->set_value(AttributeKey, value) ; \
+ } else { \
+ get_particle()->add_attribute(AttributeKey, value); \
+ }
+
+//! define methods for getting and setting a particular simple field
+/**
+ This macros defines methods to get an set a particular attribute.
+
+ \param[in] name The lower case name of the attribute
+ \param[in] AttributeKey The AttributeKey object controlling
+ the attribute.
+ \param[in] Type The type of the attribute (upper case).
+ \param[in] ReturnType The type to return from the get.
+*/
+#define IMP_DECORATOR_GET_SET(name, AttributeKey, Type, ReturnType) \
+ /** \return the attribute value */ \
+ ReturnType get_##name() const { \
+ return static_cast<ReturnType>(get_particle()->get_value(AttributeKey)); \
+ } \
+ /** Set the attribute \param[in] t the value */ \
+ void set_##name(ReturnType t) { \
+ get_particle()->set_value(AttributeKey, t); \
+ }
+
+//! Define methods for getting and setting an optional simple field.
+/**
+ See IMP_DECORATOR_GET_SET.
+
+ \param[in] name The lower case name of the attribute
+ \param[in] AttributeKey The AttributeKey object controlling
+ the attribute.
+ \param[in] Type The type of the attribute (upper case).
+ \param[in] ReturnType The type to return from the get.
+ \param[in] default_value The value returned if the attribute is missing.
+ */
+#define IMP_DECORATOR_GET_SET_OPT(name, AttributeKey, Type, \
+ ReturnType, default_value) \
+ /** \return the attribute value*/ \
+ ReturnType get_##name() const { \
+ IMP_DECORATOR_GET(AttributeKey, Type, \
+ return static_cast<ReturnType>(VALUE), \
+ return default_value); \
+ } \
+ /** \param[in] t the value to set the attribute to*/ \
+ void set_##name(ReturnType t) { \
+ IMP_DECORATOR_SET(AttributeKey, t); \
+ }
+
+
+//! Define a set of attributes which form an array
+/**
+ This macro should go in the header and IMP_DECORATOR_ARRAY_CPP into the .cpp
+ and IMP_DECORATOR_ARRAY_INIT in the initialize_static_data function
+
+ To use the array, use functions
+
+ - Type internal_get_name(unsigned int i)
+
+ - void internal_add_name(Type)
+
+ - unsigned int internal_get_number_of_name() const
+ */
+#define IMP_DECORATOR_ARRAY_DECL(name, Type) \
+ protected: \
+ static IntKey number_of_##name##_key_; \
+ static std::vector<Type##Key> name##_keys_; \
+ static void generate_##name##_keys(unsigned int i); \
+ static const Type##Key get_##name##_key(unsigned int i) { \
+ if (i >= name##_keys_.size()) generate_##name##_keys(i); \
+ return name##_keys_[i]; \
+ } \
+ Type internal_get_##name(unsigned int i) const{ \
+ IMP_DECORATOR_GET(get_##name##_key(i), Type, \
+ return VALUE, \
+ throw IndexException(); return Type()); \
+ } \
+ int internal_add_##name(Type t); \
+ unsigned int internal_get_number_of_##name() const { \
+ IMP_DECORATOR_GET(number_of_##name##_key_, \
+ Int, return VALUE, return 0); \
+ } \
+
+//! See IMP_DECORATOR_ARRAY_DECL
+#define IMP_DECORATOR_ARRAY_DEF(DecoratorType, name, Type) \
+ IntKey DecoratorType##Decorator::number_of_##name##_key_; \
+ std::vector<Type##Key> DecoratorType##Decorator::name##_keys_; \
+ void DecoratorType##Decorator::generate_##name##_keys(unsigned int i) \
+ { \
+ while (!(i < name##_keys_.size())) { \
+ std::ostringstream oss; \
+ oss << #DecoratorType " " #name " " << name##_keys_.size(); \
+ name##_keys_.push_back(Type##Key(oss.str().c_str())); \
+ } \
+ } \
+ int DecoratorType##Decorator::internal_add_##name(Type t) { \
+ int nc= internal_get_number_of_##name(); \
+ get_particle()->add_attribute(get_##name##_key(nc), t); \
+ IMP_DECORATOR_SET(number_of_##name##_key_, nc+1); \
+ return nc; \
+ }
+
+//! See IMP_DECORATOR_ARRAY_DECL
+#define IMP_DECORATOR_ARRAY_INIT(DecoratorType, name, Type) \
+ number_of_##name##_key_= IntKey(#DecoratorType " num " #name);
+
+
+#endif /* __IMP_DECORATOR_UTILITY_H */
Index: kernel/pyext/IMP_macros.i
===================================================================
--- kernel/pyext/IMP_macros.i (revision 354)
+++ kernel/pyext/IMP_macros.i (working copy)
@@ -1,46 +1,5 @@
-/* Ignore shared object import/export stuff */
#define IMPDLLEXPORT
#define IMPDLLLOCAL
-#define IMP_COMPARISONS_1(f) bool operator==(const This &o) const ; bool operator<(const This &o) const; bool operator>(const This &o) const; bool operator!=(const This &o) const; bool operator<=(const This &o) const; bool operator>=(const This &o) const;
-#define IMP_OUTPUT_OPERATOR_1(f)
-#define IMP_OUTPUT_OPERATOR(f)
-#define IMP_RESTRAINT(a,b) \
- virtual Float evaluate(DerivativeAccumulator *accum);\
- virtual void show(std::ostream &out=std::cout) const;\
- virtual std::string version() const {return std::string(a);}\
- virtual std::string last_modified_by() const {return std::string(b);}
-#define IMP_OPTIMIZER(a, b) \
- virtual Float optimize(unsigned int max_steps);\
- virtual std::string version() const {return std::string(a);};\
- virtual std::string last_modified_by() const {return std::string(b);};
-#define IMP_DECORATOR_GET(a,b,c,d)
-#define IMP_DECORATOR_GET_SET(n,a,t,r) r get_##n() const;\
- void set_##n(t);
-#define IMP_DECORATOR_GET_SET_OPT(n,a,t,r,d) r get_##n() const;\
- void set_##n(t);
-#define IMP_DECORATOR(Name, Parent, a,b) \
- public:\
- typedef Name This;\
- public: Name(); \
- static Name create(::IMP::Particle *p);\
- static Name cast(::IMP::Particle *p);\
- void show(std::ostream &out=std::cout, std::string pre="")
-#define IMP_DECORATOR_ARRAY_DECL(a, b)
-#define IMP_CONTAINER(Ucname, lcname, IndexType) \
- public: \
- IndexType add_##lcname(Ucname *obj); \
- Ucname *get_##lcname(IndexType i) const ; \
- unsigned int number_of_##lcname##s() const {return lcname##_vector_.size();} \
-const std::vector<Ucname*> &get_##lcname##s() const {\
- return lcname##_vector_;}\
-
- #define IMP_OPTIMIZER_STATE(version_string, lmb_string) \
- virtual void update(); \
- virtual void show(std::ostream &out=std::cout) const; \
- virtual std::string version() const {return std::string(version_string);} \
- virtual std::string last_modified_by() const {return std::string(lmb_string);}
-
-
-#define IMP_SCORE_STATE(version_string, lmb_string)\
- IMP_OPTIMIZER_STATE(version_string, lmb_string)
+%include "IMP/macros.h"
+%include "IMP/decorators/macros.h"