Index: kernel/include/Vector3D.h
===================================================================
--- kernel/include/Vector3D.h (revision 975)
+++ 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 975)
+++ kernel/include/base_types.h (working copy)
@@ -17,13 +17,11 @@
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.
+/**
+ \namespace IMP \brief The IMP kernel.
*/
+
/** \internal \namespace IMP::internal Implementation details.
*/
Index: kernel/include/SingletonScore.h
===================================================================
--- kernel/include/SingletonScore.h (revision 975)
+++ 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.
@@ -33,6 +27,7 @@
//! Compute the score for the particle and the derivative if needed.
virtual Float evaluate(Particle *a,
DerivativeAccumulator *da) const = 0;
+ //!
virtual void show(std::ostream &out=std::cout) const = 0;
IMP_REF_COUNTED_DESTRUCTOR(SingletonScore)
};
Index: kernel/include/exception.h
===================================================================
--- kernel/include/exception.h (revision 975)
+++ kernel/include/exception.h (working copy)
@@ -139,7 +139,11 @@
IMPDLLEXPORT CheckLevel get_check_level();
-
+//! Execute the code block if a certain level checks are on
+/**
+ The next code block (delimited by { }) is executed if
+ get_check_level() <= level.
+ */
#define IMP_IF_CHECK(level)\
if (level <= ::IMP::get_check_level())
Index: kernel/include/Model.h
===================================================================
--- kernel/include/Model.h (revision 975)
+++ kernel/include/Model.h (working copy)
@@ -26,7 +26,6 @@
//! 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
{
@@ -34,7 +33,9 @@
friend class Restraint;
unsigned int iteration_;
public:
+ //!
Model();
+ //!
~Model();
IMP_CONTAINER(Particle, particle, ParticleIndex);
Index: kernel/include/VersionInfo.h
===================================================================
--- kernel/include/VersionInfo.h (revision 975)
+++ 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 975)
+++ kernel/include/DerivativeAccumulator.h (working copy)
@@ -19,9 +19,11 @@
class IMPDLLEXPORT DerivativeAccumulator
{
public:
+ //!
DerivativeAccumulator(Float weight=1.0)
: weight_(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 975)
+++ kernel/include/Particle.h (working copy)
@@ -59,8 +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 975)
+++ 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
{
@@ -34,12 +32,11 @@
//! Calculate score and derivative with respect to the given feature.
/** \param[in] feature Value of feature being tested.
- \param[out] deriv Partial derivative of the score with respect to the
- given feaure.
- \return Score
+ \return a pair containting the score and the derivative
*/
virtual FloatPair evaluate_with_derivative(Float feature) const = 0;
+ //!
virtual void show(std::ostream &out=std::cout) const = 0;
IMP_REF_COUNTED_DESTRUCTOR(UnaryFunction)
Index: kernel/include/VectorD.h
===================================================================
--- kernel/include/VectorD.h (revision 975)
+++ kernel/include/VectorD.h (working copy)
@@ -1,5 +1,5 @@
/**
- * \File VectorD.h \brief Simple D vector class.
+ * \file VectorD.h \brief Simple D vector class.
*
* Copyright 2007-8 Sali Lab. All rights reserved.
*
@@ -22,8 +22,6 @@
IMP_BEGIN_NAMESPACE
//! Simple D vector class
-/** \ingroup helper
- */
template <unsigned int D>
class VectorD
{
@@ -89,8 +87,6 @@
}
//! \return the scalar product of two vectors.
- /** \param[in] vec2 The other vector to use in the product.
- */
Float scalar_product(const This &o) const {
Float ret=0;
for (unsigned int i=0; i< D; ++i) {
@@ -132,8 +128,6 @@
}
//! \return the vector product of two vectors.
- /** \param[in] vec2 The other vector to use in the product.
- */
VectorD vector_product(const VectorD &vec2) const {
BOOST_STATIC_ASSERT(D==3);
return VectorD(vec_[1] * vec2.vec_[2] - vec_[2] * vec2.vec_[1],
Index: kernel/include/Index.h
===================================================================
--- kernel/include/Index.h (revision 975)
+++ 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/Restraint.h
===================================================================
--- kernel/include/Restraint.h (revision 975)
+++ 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();
~Restraint();
Index: kernel/include/DecoratorBase.h
===================================================================
--- kernel/include/DecoratorBase.h (revision 975)
+++ 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 975)
+++ kernel/include/ParticleRefiner.h (working copy)
@@ -42,6 +42,7 @@
*/
virtual void cleanup_refined(Particle *a, Particles &b,
DerivativeAccumulator *da=0) const {}
+ //!
virtual void show(std::ostream &out=std::cout) const {
out << "ParticleRefiner base" << std::endl;
};
Index: kernel/include/TripletScore.h
===================================================================
--- kernel/include/TripletScore.h (revision 975)
+++ 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.
Index: kernel/include/Pointer.h
===================================================================
--- kernel/include/Pointer.h (revision 975)
+++ kernel/include/Pointer.h (working copy)
@@ -65,7 +65,9 @@
set_pointer(o.o_);
return *this;
}
+ //! create a null pointer
Pointer(): o_(NULL) {}
+ //! create a Pointer from a raw pointer
explicit Pointer(O* o): o_(NULL) {
IMP_assert(o, "Can't initialize with NULL pointer");
set_pointer(o);
@@ -73,22 +75,29 @@
~Pointer(){
set_pointer(NULL);
}
+ /** Yup, its a pointer.*/
const O& operator*() const {
audit();
return *o_;
}
+ /** Yup, its a pointer.*/
O& operator*() {
audit();
return *o_;
}
+ /** Yup, its a pointer.*/
const O* operator->() const {
audit();
return o_;
}
+ /** Yup, its a pointer.*/
O* operator->() {
audit();
return o_;
}
+ //! return the raw pointer.
+ /** \assert if NULL
+ */
O* get() const {
audit();
return o_;
@@ -96,12 +105,15 @@
void operator=(O* o) {
set_pointer(o);
}
+
IMP_COMPARISONS_1(o_);
+ //! return true if non-null
bool operator!() const {
return !o_;
}
+ //! convert to a raw pointer
operator O*() const {
return o_;
}
Index: kernel/include/Optimizer.h
===================================================================
--- kernel/include/Optimizer.h (revision 975)
+++ 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.
Index: kernel/include/macros.h
===================================================================
--- kernel/include/macros.h (revision 975)
+++ kernel/include/macros.h (working copy)
@@ -388,6 +388,10 @@
//! 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] Class The name of the class containing 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 data type to store in the list
\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.
@@ -438,6 +442,11 @@
/**
This code should go in a .cpp file. One macro for each
IMP_CONTAINER.
+ \param[in] Class The name of the class containing 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] IndexType The type to use for the index. This should be
+ an instantiation of Index<T> or something similar.
\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.
Index: kernel/include/RefCountedObject.h
===================================================================
--- kernel/include/RefCountedObject.h (revision 975)
+++ kernel/include/RefCountedObject.h (working copy)
@@ -41,6 +41,7 @@
// never hold pointers to it directly
virtual ~RefCountedObject() {
IMP_assert(!get_has_ref(), "Deleting object which still has references");
+ IMP_LOG(VERBOSE, "Deleting ref counted object " << this << std::endl);
--live_objects_;
}
Index: kernel/include/internal/ref_counting.h
===================================================================
--- kernel/include/internal/ref_counting.h (revision 975)
+++ kernel/include/internal/ref_counting.h (working copy)
@@ -15,11 +15,8 @@
#include <boost/static_assert.hpp>
#include <boost/type_traits.hpp>
-IMP_BEGIN_NAMESPACE
+IMP_BEGIN_INTERNAL_NAMESPACE
-namespace internal
-{
-
template <bool REF>
struct Ref
{
@@ -35,7 +32,7 @@
{
template <class O>
static void eval(O* o) {
- IMP_LOG(VERBOSE, "Refing particle " << o->get_index()
+ IMP_LOG(VERBOSE, "Refing object with count "
<< o->get_ref_count() << std::endl);
o->assert_is_valid();
o->ref();
@@ -57,8 +54,8 @@
{
template <class O>
static void eval(O *o) {
- IMP_LOG(VERBOSE, "Unrefing particle " << o->get_index()
- << " " << o->get_ref_count() << std::endl);
+ IMP_LOG(VERBOSE, "Unrefing object with count "
+ << o->get_ref_count() << std::endl);
o->assert_is_valid();
o->unref();
if (!o->get_has_ref()) {
@@ -132,8 +129,6 @@
}
-} // namespace internal
+IMP_END_INTERNAL_NAMESPACE
-IMP_END_NAMESPACE
-
#endif /* IMP_REF_COUNTING_H */
Index: kernel/include/PairScore.h
===================================================================
--- kernel/include/PairScore.h (revision 975)
+++ 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.
Index: kernel/include/Key.h
===================================================================
--- kernel/include/Key.h (revision 975)
+++ kernel/include/Key.h (working copy)
@@ -95,7 +95,7 @@
return get_map().find(sc)->second;
}
}
-protected:
+private:
bool is_default() const;
public:
static const std::string get_string(int i)
Index: doc/internal/doxygen.conf
===================================================================
--- doc/internal/doxygen.conf (revision 975)
+++ doc/internal/doxygen.conf (working copy)
@@ -1,4 +1,4 @@
-# Doxyfile 1.5.7.1
+# Doxyfile 1.5.7
# This file describes the settings to be used by the documentation system
# doxygen (www.doxygen.org) for a project
@@ -99,7 +99,7 @@
# members were ordinary class members. Constructors, destructors and assignment
# operators of the base classes will not be shown.
-INLINE_INHERITED_MEMB = NO
+INLINE_INHERITED_MEMB = YES
# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
# path before files name in the file list and in the header files. If set
@@ -179,7 +179,8 @@
# will result in a user-defined paragraph with heading "Side Effects:".
# You can put \n's in the value part of an alias to insert newlines.
-ALIASES =
+ALIASES = "command{1}=\code \1 \endcode" \
+ "imp=\p IMP"
# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
# sources only. Doxygen will then generate output that is more tailored for C.
@@ -325,21 +326,21 @@
# various overviews, but no documentation section is generated.
# This option has no effect if EXTRACT_ALL is enabled.
-HIDE_UNDOC_MEMBERS = NO
+HIDE_UNDOC_MEMBERS = YES
# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
# undocumented classes that are normally visible in the class hierarchy.
# If set to NO (the default) these classes will be included in the various
# overviews. This option has no effect if EXTRACT_ALL is enabled.
-HIDE_UNDOC_CLASSES = NO
+HIDE_UNDOC_CLASSES = YES
# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
# friend (class|struct|union) declarations.
# If set to NO (the default) these declarations will be included in the
# documentation.
-HIDE_FRIEND_COMPOUNDS = NO
+HIDE_FRIEND_COMPOUNDS = YES
# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
# documentation blocks found inside the body of a function.
@@ -373,7 +374,7 @@
# will put a list of the files that are included by a file in the documentation
# of that file.
-SHOW_INCLUDE_FILES = YES
+SHOW_INCLUDE_FILES = NO
# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
# is inserted in the documentation for inline members.
@@ -414,7 +415,7 @@
# disable (NO) the todo list. This list is created by putting \todo
# commands in the documentation.
-GENERATE_TODOLIST = YES
+GENERATE_TODOLIST = NO
# The GENERATE_TESTLIST tag can be used to enable (YES) or
# disable (NO) the test list. This list is created by putting \test
@@ -426,7 +427,7 @@
# disable (NO) the bug list. This list is created by putting \bug
# commands in the documentation.
-GENERATE_BUGLIST = YES
+GENERATE_BUGLIST = NO
# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
# disable (NO) the deprecated list. This list is created by putting
@@ -465,7 +466,7 @@
# This will remove the Files entry from the Quick Index and from the
# Folder Tree View (if specified). The default is YES.
-SHOW_FILES = YES
+SHOW_FILES = NO
# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
# Namespaces page. This will remove the Namespaces entry from the Quick Index
@@ -552,14 +553,10 @@
# directories like "/usr/src/myproject". Separate the files or directories
# with spaces.
-INPUT = ../../kernel/src \
+INPUT = ../../build/include \
../../kernel/doc \
- ../../modules/domino/src \
- ../../modules/em/src \
- ../../modules/misc/src \
- ../../modules/core/src \
- ../../build/include \
- ../../doc/internal
+ ../../modules/core/doc \
+ ../../modules/misc/doc
# This tag can be used to specify the character encoding of the source files
# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
@@ -592,7 +589,7 @@
# excluded from the INPUT source files. This way you can easily exclude a
# subdirectory from a directory tree whose root is specified with the INPUT tag.
-EXCLUDE =
+EXCLUDE =
# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
# directories that are symbolic links (a Unix filesystem feature) are excluded
@@ -608,10 +605,10 @@
EXCLUDE_PATTERNS = */tests/* \
*/imp_wrap.* \
- */internal/* \
*/imp2.py \
*/.svn \
- ._*
+ ._* \
+ */internal/*
# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
# (namespaces, classes, functions, etc.) that should be excluded from the
@@ -632,7 +629,7 @@
# and *.h) to filter out the source-files in the directories. If left
# blank all files are included.
-EXAMPLE_PATTERNS =
+EXAMPLE_PATTERNS = *.py
# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
# searched for input files to be used with the \include or \dontinclude
@@ -775,13 +772,13 @@
# each generated HTML page. If it is left blank doxygen will generate a
# standard header.
-HTML_HEADER =
+HTML_HEADER = ../../kernel/doc/header.html
# The HTML_FOOTER tag can be used to specify a personal HTML footer for
# each generated HTML page. If it is left blank doxygen will generate a
# standard footer.
-HTML_FOOTER =
+HTML_FOOTER = ../../kernel/doc/footer.html
# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
# style sheet that is used by each HTML page. It can be used to
@@ -804,7 +801,7 @@
# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
-HTML_DYNAMIC_SECTIONS = NO
+HTML_DYNAMIC_SECTIONS = YES
# If the GENERATE_DOCSET tag is set to YES, additional index files
# will be generated that can be used as input for Apple's Xcode 3
@@ -816,21 +813,21 @@
# it at startup.
# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information.
-GENERATE_DOCSET = NO
+GENERATE_DOCSET = YES
# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
# feed. A documentation feed provides an umbrella under which multiple
# documentation sets from a single provider (such as a company or product suite)
# can be grouped.
-DOCSET_FEEDNAME = "Doxygen generated docs"
+DOCSET_FEEDNAME = IMP
# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
# should uniquely identify the documentation set bundle. This should be a
# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
# will append .docset to the name.
-DOCSET_BUNDLE_ID = org.doxygen.Project
+DOCSET_BUNDLE_ID = org.salilab.imp
# If the GENERATE_HTMLHELP tag is set to YES, additional index files
# will be generated that can be used as input for tools like the
@@ -1215,7 +1212,7 @@
# directories. If left blank, the patterns specified with FILE_PATTERNS will
# be used.
-INCLUDE_FILE_PATTERNS = *.py
+INCLUDE_FILE_PATTERNS = *.h
# The PREDEFINED tag can be used to specify one or more macro names that
# are defined before the preprocessor is started (similar to the -D option of
@@ -1331,11 +1328,6 @@
DOT_FONTNAME = FreeSans
-# The DOT_FONTSIZE tag can be used to set the size of the font of dot graphs.
-# The default size is 10pt.
-
-DOT_FONTSIZE = 10
-
# By default doxygen will tell dot to use the output directory to look for the
# FreeSans.ttf font (which doxygen will put there itself). If you specify a
# different font using DOT_FONTNAME you can set the path where dot
@@ -1371,7 +1363,7 @@
# If set to YES, the inheritance and collaboration graphs will show the
# relations between templates and their instances.
-TEMPLATE_RELATIONS = NO
+TEMPLATE_RELATIONS = YES
# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
# tags are set to YES then doxygen will generate a graph for each documented
@@ -1413,7 +1405,7 @@
# in a graphical way. The dependency relations are determined by the #include
# relations between the files in the directories.
-DIRECTORY_GRAPH = YES
+DIRECTORY_GRAPH = NO
# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
# generated by dot. Possible values are png, jpg, or gif
@@ -1450,7 +1442,7 @@
# code bases. Also note that the size of a graph can be further restricted by
# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
-MAX_DOT_GRAPH_DEPTH = 0
+MAX_DOT_GRAPH_DEPTH = 1000
# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
# background. This is disabled by default, because dot on Windows does not
@@ -1458,14 +1450,14 @@
# enabling this option may lead to badly anti-aliased labels on the edges of
# a graph (i.e. they become hard to read).
-DOT_TRANSPARENT = NO
+DOT_TRANSPARENT = YES
# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
# files in one run (i.e. multiple -o and -T options on the command line). This
# makes dot run faster, but since only newer versions of dot (>1.8.10)
# support this, this feature is disabled by default.
-DOT_MULTI_TARGETS = NO
+DOT_MULTI_TARGETS = YES
# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
# generate a legend page explaining the meaning of the various boxes and