This change defines a few groups in the modules tab in the doxygen doc
and fixes various printed messages and such minor things. Doxygen now
excludes the scons generated temp files.
Index: kernel/include/IMP/base_types.h
===================================================================
--- kernel/include/IMP/base_types.h (revision 363)
+++ kernel/include/IMP/base_types.h (working copy)
@@ -1,5 +1,5 @@
/**
- * \file Base_Types.h \brief Basic types used by IMP.
+ * \file base_types.h \brief Basic types used by IMP.
*
* Copyright 2007-8 Sali Lab. All rights reserved.
*
@@ -18,6 +18,15 @@
namespace IMP
{
+
+/**
+ \defgroup kernel IMP Kernel
+ The core IMP types
+
+ \defgroup helper Miscellaneous helpers
+ Classes and functions which are there to make your life easier.
+ */
+
//! Basic floating-point value (could be float, double...)
typedef float Float;
Index: kernel/include/IMP/Model.h
===================================================================
--- kernel/include/IMP/Model.h (revision 363)
+++ kernel/include/IMP/Model.h (working copy)
@@ -24,6 +24,7 @@
//! Class for storing model, its restraints, constraints, and particles.
/** All attribute data for particles is stored through indexing in the
model_data_ structure.
+ \ingroup kernel
*/
class IMPDLLEXPORT Model: public Object
{
Index: kernel/include/IMP/restraints/RestraintSet.h
===================================================================
--- kernel/include/IMP/restraints/RestraintSet.h (revision 363)
+++ kernel/include/IMP/restraints/RestraintSet.h (working copy)
@@ -17,6 +17,9 @@
{
//! Used to hold a set of related restraints
+/**
+ \ingroup restraint
+ */
class IMPDLLEXPORT RestraintSet : public Restraint
{
public:
Index: kernel/include/IMP/AttributeTable.h
===================================================================
--- kernel/include/IMP/AttributeTable.h (revision 363)
+++ kernel/include/IMP/AttributeTable.h (working copy)
@@ -47,8 +47,8 @@
return k.get_index() < map_.size()
&& map_[k.get_index()] != Value();
}
- std::ostream &show(std::ostream &out, const char *prefix="",
- ModelData* md=NULL) const;
+ void show(std::ostream &out, const char *prefix="",
+ ModelData* md=NULL) const;
std::vector<Key> get_keys() const;
};
@@ -80,21 +80,19 @@
template <class T>
-inline std::ostream &AttributeTable<T>::show(std::ostream &out,
+inline void AttributeTable<T>::show(std::ostream &out,
const char *prefix,
ModelData *md) const
{
for (unsigned int i=0; i< map_.size(); ++i) {
if (map_[i] != Value()) {
- out << prefix
- << Key(i) << ": index = " << map_[i];
+ out << prefix;
if (md != NULL) {
- out << ", value= " << md->get_value(map_[i]);
+ out << md->get_value(map_[i]);
}
out << std::endl;
}
}
- return out;
}
Index: kernel/include/IMP/Restraint.h
===================================================================
--- kernel/include/IMP/Restraint.h (revision 363)
+++ kernel/include/IMP/Restraint.h (working copy)
@@ -23,6 +23,12 @@
{
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 restraint General purpose restraints
Classes to define and help in defining restraints. The restraints
@@ -31,6 +37,8 @@
*/
//! Abstract class for representing restraints
+/**
+ */
class IMPDLLEXPORT Restraint : public Object
{
public:
Index: kernel/include/IMP/decorators/XYZDecorator.h
===================================================================
--- kernel/include/IMP/decorators/XYZDecorator.h (revision 363)
+++ kernel/include/IMP/decorators/XYZDecorator.h (working copy)
@@ -22,6 +22,8 @@
{
//! A a decorator for a particle with x,y,z coordinates.
+/** \ingroup helper
+ */
class IMPDLLEXPORT XYZDecorator: public DecoratorBase
{
IMP_DECORATOR(XYZDecorator, DecoratorBase,
@@ -90,6 +92,8 @@
IMP_OUTPUT_OPERATOR(XYZDecorator);
//! Compute the distance between a pair of particles
+/** \ingroup helper
+ */
IMPDLLEXPORT Float distance(XYZDecorator a, XYZDecorator b);
} // namespace IMP
Index: kernel/include/IMP/decorators/AtomDecorator.h
===================================================================
--- kernel/include/IMP/decorators/AtomDecorator.h (revision 363)
+++ kernel/include/IMP/decorators/AtomDecorator.h (working copy)
@@ -27,6 +27,7 @@
mechanism for the types. This could be done by having an
add_type(string) method which adds a string name and assigns it to the
next unused type int available.
+ \ingroup hierarchy
*/
class IMPDLLEXPORT AtomDecorator: public XYZDecorator
{
Index: kernel/include/IMP/decorators/ResidueDecorator.h
===================================================================
--- kernel/include/IMP/decorators/ResidueDecorator.h (revision 363)
+++ kernel/include/IMP/decorators/ResidueDecorator.h (working copy)
@@ -22,6 +22,7 @@
As with the AtomDecorator, the types of residues may been to be expanded
dynamically. This can be easily done in an analogous manner when we
need it.
+ \ingroup hierarchy
*/
class IMPDLLEXPORT ResidueDecorator: public DecoratorBase
{
Index: kernel/include/IMP/decorators/bond_decorators.h
===================================================================
--- kernel/include/IMP/decorators/bond_decorators.h (revision 363)
+++ kernel/include/IMP/decorators/bond_decorators.h (working copy)
@@ -20,9 +20,10 @@
class BondDecorator;
class BondedDecorator;
+/** \defgroup bond Creating and restraining bonds
+ A set of classes and functions for manipulating bonds.
+ */
-
-
namespace internal
{
@@ -39,6 +40,8 @@
/**
As with AtomDecorator, the types of bonds will eventually be run-time
expandible.
+
+ \ingroup bond Bonds
*/
class IMPDLLEXPORT BondDecorator: public DecoratorBase
{
@@ -76,6 +79,8 @@
//! A decorator for a particle which has bonds.
+/** \ingroup bond
+ */
class IMPDLLEXPORT BondedDecorator: public DecoratorBase
{
IMP_DECORATOR(BondedDecorator, DecoratorBase, return true, );
@@ -133,6 +138,8 @@
\param[in] b The second Particle as a BondedDecorator
\param[in] t The type to use for the bond
\return BondDecorator of the bond Particle.
+
+ \ingroup bond
*/
IMPDLLEXPORT
BondDecorator bond(BondedDecorator a, BondedDecorator b, Int t);
@@ -144,6 +151,8 @@
\param[in] length The length of the bond.
\param[in] stiffness The stiffness of the bond.
\return BondDecorator of the bond Particle.
+
+ \ingroup bond
*/
IMPDLLEXPORT
inline BondDecorator custom_bond(BondedDecorator a, BondedDecorator b,
@@ -158,6 +167,7 @@
//! Destroy the bond connecting to particles.
/** \param[in] b The bond.
+ \ingroup bond
*/
IMPDLLEXPORT
void unbond(BondDecorator b);
@@ -165,6 +175,7 @@
//! Get the bond between two particles.
/**
BondDecorator() is returned if the particles are not bonded.
+ \ingroup bond
*/
IMPDLLEXPORT
BondDecorator get_bond(BondedDecorator a, BondedDecorator b);
Index: kernel/include/IMP/optimizers/MolecularDynamics.h
===================================================================
--- kernel/include/IMP/optimizers/MolecularDynamics.h (revision 363)
+++ kernel/include/IMP/optimizers/MolecularDynamics.h (working copy)
@@ -19,6 +19,7 @@
/** The particles to be optimized must be xyz particles; this optimizer
assumes the score to be energy in kcal/mol, and the xyz coordinates to
be in angstroms.
+ \ingroup optimizer
*/
class IMPDLLEXPORT MolecularDynamics : public Optimizer
{
Index: kernel/include/IMP/optimizers/ConjugateGradients.h
===================================================================
--- kernel/include/IMP/optimizers/ConjugateGradients.h (revision 363)
+++ kernel/include/IMP/optimizers/ConjugateGradients.h (working copy)
@@ -17,6 +17,7 @@
//! Simple conjugate gradients optimizer.
/** Algorithm is as per Shanno and Phua, ACM Transactions On Mathematical
Software 6 (December 1980), 618-622
+ \ingroup optimizer
*/
class IMPDLLEXPORT ConjugateGradients : public Optimizer
{
Index: kernel/include/IMP/optimizers/SteepestDescent.h
===================================================================
--- kernel/include/IMP/optimizers/SteepestDescent.h (revision 363)
+++ kernel/include/IMP/optimizers/SteepestDescent.h (working copy)
@@ -16,9 +16,10 @@
//! A simple steepest descent optimizer
/** Follow the gradient based on the partial derivatives. Multiply by the
- current step size. If the score gets worse, reduce the step size.
- If the score gets better, increase the step size if we are sufficiently
- far from a score of zero. If the score reaches the threshold, quit.
+ current step size. If the score gets worse, reduce the step size.
+ If the score gets better, increase the step size if we are sufficiently
+ far from a score of zero. If the score reaches the threshold, quit.
+ \ingroup optimizer
*/
class IMPDLLEXPORT SteepestDescent : public Optimizer
{
Index: kernel/include/IMP/pair_scores/SphereDistancePairScore.h
===================================================================
--- kernel/include/IMP/pair_scores/SphereDistancePairScore.h (revision 363)
+++ kernel/include/IMP/pair_scores/SphereDistancePairScore.h (working copy)
@@ -15,6 +15,8 @@
class UnaryFunction;
//! A score on the distance between the surfaces of two spheres.
+/** \ingroup pairscore
+ */
class IMPDLLEXPORT SphereDistancePairScore : public PairScore
{
std::auto_ptr<UnaryFunction> f_;
Index: kernel/include/IMP/pair_scores/DistancePairScore.h
===================================================================
--- kernel/include/IMP/pair_scores/DistancePairScore.h (revision 363)
+++ kernel/include/IMP/pair_scores/DistancePairScore.h (working copy)
@@ -15,6 +15,8 @@
{
//! Apply a function to the distance between two particles.
+/** \ingroup pairscore
+ */
class IMPDLLEXPORT DistancePairScore : public PairScore
{
std::auto_ptr<UnaryFunction> f_;
Index: kernel/include/IMP/PairScore.h
===================================================================
--- kernel/include/IMP/PairScore.h (revision 363)
+++ kernel/include/IMP/PairScore.h (working copy)
@@ -15,6 +15,12 @@
namespace IMP
{
+/**
+ \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.
class IMPDLLEXPORT PairScore : public Object
Index: kernel/include/IMP/Key.h
===================================================================
--- kernel/include/IMP/Key.h (revision 363)
+++ kernel/include/IMP/Key.h (working copy)
@@ -116,8 +116,8 @@
IMP_COMPARISONS_1(str_)
- std::ostream &show(std::ostream &out) const {
- return out << "\"" << get_string() << "\"";
+ void show(std::ostream &out = std::cout) const {
+ out << "\"" << get_string() << "\"";
}
unsigned int get_index() const {
Index: kernel/include/IMP/unary_functions/Harmonic.h
===================================================================
--- kernel/include/IMP/unary_functions/Harmonic.h (revision 363)
+++ kernel/include/IMP/unary_functions/Harmonic.h (working copy)
@@ -12,7 +12,16 @@
namespace IMP
{
+/**
+ \ingroup restraint
+ \addtogroup unaryf Unary Functions
+ Functions of a single variable. These are used by scoring
+ functions.
+ */
+
//! Harmonic function (symmetric about the mean)
+/** \ingroup unaryf
+ */
class IMPDLLEXPORT Harmonic : public UnaryFunction
{
public:
Index: kernel/include/IMP/unary_functions/Cosine.h
===================================================================
--- kernel/include/IMP/unary_functions/Cosine.h (revision 363)
+++ kernel/include/IMP/unary_functions/Cosine.h (working copy)
@@ -18,6 +18,8 @@
where k is a force constant, n the periodicity, a the phase, and f the
input value. This is most commonly used for dihedral angle restraints,
e.g. in the CHARMM force field.
+
+ \ingroup unaryf
*/
class IMPDLLEXPORT Cosine : public UnaryFunction
{
Index: kernel/include/IMP/unary_functions/HarmonicLowerBound.h
===================================================================
--- kernel/include/IMP/unary_functions/HarmonicLowerBound.h (revision 363)
+++ kernel/include/IMP/unary_functions/HarmonicLowerBound.h (working copy)
@@ -13,6 +13,8 @@
{
//! Lower bound harmonic function (non-zero when feature < mean)
+/** \ingroup unaryf
+ */
class IMPDLLEXPORT HarmonicLowerBound : public Harmonic
{
public:
Index: kernel/include/IMP/unary_functions/HarmonicUpperBound.h
===================================================================
--- kernel/include/IMP/unary_functions/HarmonicUpperBound.h (revision 363)
+++ kernel/include/IMP/unary_functions/HarmonicUpperBound.h (working copy)
@@ -13,6 +13,8 @@
{
//! Upper bound harmonic function (non-zero when feature > mean)
+/** \ingroup unaryf
+ */
class IMPDLLEXPORT HarmonicUpperBound : public Harmonic
{
public:
Index: kernel/include/IMP/Particle.h
===================================================================
--- kernel/include/IMP/Particle.h (revision 363)
+++ kernel/include/IMP/Particle.h (working copy)
@@ -30,6 +30,7 @@
Particles can be deactivated so that they no longer play a role in model
optimization. Removing particles and their attributes would cause
problems in the way attribute values are indexed and should not be done.
+ \ingroup kernel
*/
class IMPDLLEXPORT Particle : public Object
{
@@ -174,7 +175,7 @@
//! Show the particle
/** \param[in] out Stream to write particle description to.
*/
- std::ostream& show(std::ostream& out = std::cout) const;
+ void show(std::ostream& out = std::cout) const;
//! Return a vector containing all the FloatKeys for the Particle
@@ -213,23 +214,23 @@
model_->get_model_data()->set_value(k, v);
}
- //! Set pointer to model particle data.
- /** This is called by the Model after the particle is added.
+ // Set pointer to model particle data.
+ /* This is called by the Model after the particle is added.
\param[in] md Pointer to a ModelData object.
*/
void set_model(Model *md, ParticleIndex pi);
- //! all of the particle data
+ // all of the particle data
Model* model_;
- //! true if particle is active
+ // true if particle is active
bool is_active_;
- //! float attributes associated with the particle
+ // float attributes associated with the particle
internal::AttributeTable<Float> float_indexes_;
- //! int attributes associated with the particle
+ // int attributes associated with the particle
internal::AttributeTable<Int> int_indexes_;
- //! string attributes associated with the particle
+ // string attributes associated with the particle
internal::AttributeTable<String> string_indexes_;
ParticleIndex pi_;
@@ -278,7 +279,7 @@
const DerivativeAccumulator &da)
{
return model_->get_model_data()->add_to_deriv(float_indexes_.get_value(name),
- da(value));
+ da(value));
}
inline bool Particle::has_attribute(IntKey name) const
Index: kernel/include/IMP/Index.h
===================================================================
--- kernel/include/IMP/Index.h (revision 363)
+++ kernel/include/IMP/Index.h (working copy)
@@ -33,13 +33,12 @@
ErrorException());
return i_;
}
- std::ostream &show(std::ostream &out) const {
+ void show(std::ostream &out) const {
if (!is_default()) {
out << "(" << i_ << ")";
} else {
out << "(Invalid)";
}
- return out;
}
IMP_COMPARISONS_1(i_)
Index: kernel/include/IMP/log.h
===================================================================
--- kernel/include/IMP/log.h (revision 363)
+++ kernel/include/IMP/log.h (working copy)
@@ -91,12 +91,16 @@
static Log *logpt_;
};
-//! A general exception for an error in IMP
+//! A general exception for an error in IMP.
+/** \ingroup assert
+ */
class IMPDLLEXPORT ErrorException: public std::exception
{
};
//! An exception for an invalid model state
+/** \ingroup assert
+ */
class IMPDLLEXPORT InvalidStateException : public std::exception
{
public:
@@ -107,6 +111,8 @@
};
//! An exception for a request for an invalid member of a container
+/** \ingroup assert
+ */
class IMPDLLEXPORT IndexException: public std::exception
{
public:
Index: kernel/include/IMP/Optimizer.h
===================================================================
--- kernel/include/IMP/Optimizer.h (revision 363)
+++ kernel/include/IMP/Optimizer.h (working copy)
@@ -21,6 +21,10 @@
class Model;
+/** \defgroup optimizer Optimizers
+ Optimizers of various sorts.
+ */
+
//! Base class for all optimizers
class IMPDLLEXPORT Optimizer: public Object
{
Index: kernel/doc/internal/doxygen.conf
===================================================================
--- kernel/doc/internal/doxygen.conf (revision 363)
+++ kernel/doc/internal/doxygen.conf (working copy)
@@ -1,1259 +1,241 @@
-# Doxyfile 1.5.2
+# Doxyfile 1.5.4
-# This file describes the settings to be used by the documentation system
-# doxygen (www.doxygen.org) for a project
-#
-# All text after a hash (#) is considered a comment and will be ignored
-# The format is:
-# TAG = value [value, ...]
-# For lists items can also be appended using:
-# TAG += value [value, ...]
-# Values that contain spaces should be placed between quotes (" ")
-
#---------------------------------------------------------------------------
# Project related configuration options
#---------------------------------------------------------------------------
-
-# This tag specifies the encoding used for all characters in the config file that
-# follow. The default is UTF-8 which is also the encoding used for all text before
-# the first occurrence of this tag. Doxygen uses libiconv (or the iconv built into
-# libc) for the transcoding. See http://www.gnu.org/software/libiconv for the list of
-# possible encodings.
-
DOXYFILE_ENCODING = UTF-8
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
-# by quotes) that should identify the project.
-
PROJECT_NAME = IMP
-
-# The PROJECT_NUMBER tag can be used to enter a project or revision number.
-# This could be handy for archiving the generated documentation or
-# if some version control system is used.
-
PROJECT_NUMBER =
-
-# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
-# base path where the generated documentation will be put.
-# If a relative path is entered, it will be relative to the location
-# where doxygen was started. If left blank the current directory will be used.
-
OUTPUT_DIRECTORY = .
-
-# If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
-# 4096 sub-directories (in 2 levels) under the output directory of each output
-# format and will distribute the generated files over these directories.
-# Enabling this option can be useful when feeding doxygen a huge amount of
-# source files, where putting all generated files in the same directory would
-# otherwise cause performance problems for the file system.
-
CREATE_SUBDIRS = NO
-
-# The OUTPUT_LANGUAGE tag is used to specify the language in which all
-# documentation generated by doxygen is written. Doxygen will use this
-# information to generate all constant output in the proper language.
-# The default language is English, other supported languages are:
-# Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
-# Croatian, Czech, Danish, Dutch, Finnish, French, German, Greek, Hungarian,
-# Italian, Japanese, Japanese-en (Japanese with English messages), Korean,
-# Korean-en, Lithuanian, Norwegian, Polish, Portuguese, Romanian, Russian,
-# Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
-
OUTPUT_LANGUAGE = English
-
-# If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
-# include brief member descriptions after the members that are listed in
-# the file and class documentation (similar to JavaDoc).
-# Set to NO to disable this.
-
BRIEF_MEMBER_DESC = YES
-
-# If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
-# the brief description of a member or function before the detailed description.
-# Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
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REPEAT_BRIEF = YES
-
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-# "The $name file" "is" "provides" "specifies" "contains"
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ABBREVIATE_BRIEF =
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-
ALWAYS_DETAILED_SEC = NO
-
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-
INLINE_INHERITED_MEMB = NO
-
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-
STRIP_FROM_PATH =
-
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STRIP_FROM_INC_PATH =
-
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-# (but less readable) file names. This can be useful is your file systems
-# doesn't support long names like on DOS, Mac, or CD-ROM.
-
SHORT_NAMES = NO
-
-# If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
-# will interpret the first line (until the first dot) of a JavaDoc-style
-# comment as the brief description. If set to NO, the JavaDoc
-# comments will behave just like the Qt-style comments (thus requiring an
-# explicit @brief command for a brief description.
-
JAVADOC_AUTOBRIEF = NO
-
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-# treat a multi-line C++ special comment block (i.e. a block of //! or ///
-# comments) as a brief description. This used to be the default behaviour.
-# The new default is to treat a multi-line C++ comment block as a detailed
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-
+QT_AUTOBRIEF = NO
MULTILINE_CPP_IS_BRIEF = NO
-
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-
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-
-# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
-# tag is set to YES, then doxygen will reuse the documentation of the first
-# member in the group (if any) for the other members of the group. By default
-# all members of a group must be documented explicitly.
-
+SIP_SUPPORT = NO
DISTRIBUTE_GROUP_DOC = NO
-
-# Set the SUBGROUPING tag to YES (the default) to allow class member groups of
-# the same type (for instance a group of public functions) to be put as a
-# subgroup of that type (e.g. under the Public Functions section). Set it to
-# NO to prevent subgrouping. Alternatively, this can be done per class using
-# the \nosubgrouping command.
-
SUBGROUPING = YES
-
+TYPEDEF_HIDES_STRUCT = NO
#---------------------------------------------------------------------------
# Build related configuration options
#---------------------------------------------------------------------------
-
-# If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
-# documentation are documented, even if no documentation was available.
-# Private class members and static file members will be hidden unless
-# the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
-
EXTRACT_ALL = YES
-
-# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
-# will be included in the documentation.
-
EXTRACT_PRIVATE = NO
-
-# If the EXTRACT_STATIC tag is set to YES all static members of a file
-# will be included in the documentation.
-
EXTRACT_STATIC = NO
-
-# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
-# defined locally in source files will be included in the documentation.
-# If set to NO only classes defined in header files are included.
-
EXTRACT_LOCAL_CLASSES = YES
-
-# This flag is only useful for Objective-C code. When set to YES local
-# methods, which are defined in the implementation section but not in
-# the interface are included in the documentation.
-# If set to NO (the default) only methods in the interface are included.
-
EXTRACT_LOCAL_METHODS = NO
-
-# If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
-# undocumented members of documented classes, files or namespaces.
-# If set to NO (the default) these members will be included in the
-# various overviews, but no documentation section is generated.
-# This option has no effect if EXTRACT_ALL is enabled.
-
+EXTRACT_ANON_NSPACES = NO
HIDE_UNDOC_MEMBERS = NO
-
-# 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
-
-# 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
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# If set to NO (the default) these blocks will be appended to the
-# function's detailed documentation block.
-
HIDE_IN_BODY_DOCS = NO
-
-# The INTERNAL_DOCS tag determines if documentation
-# that is typed after a \internal command is included. If the tag is set
-# to NO (the default) then the documentation will be excluded.
-# Set it to YES to include the internal documentation.
-
INTERNAL_DOCS = NO
-
-# If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
-# file names in lower-case letters. If set to YES upper-case letters are also
-# allowed. This is useful if you have classes or files whose names only differ
-# in case and if your file system supports case sensitive file names. Windows
-# and Mac users are advised to set this option to NO.
-
CASE_SENSE_NAMES = YES
-
-# If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
-# will show members with their full class and namespace scopes in the
-# documentation. If set to YES the scope will be hidden.
-
HIDE_SCOPE_NAMES = NO
-
-# If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
-# will put a list of the files that are included by a file in the documentation
-# of that file.
-
SHOW_INCLUDE_FILES = YES
-
-# If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
-# is inserted in the documentation for inline members.
-
INLINE_INFO = YES
-
-# If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
-# will sort the (detailed) documentation of file and class members
-# alphabetically by member name. If set to NO the members will appear in
-# declaration order.
-
SORT_MEMBER_DOCS = YES
-
-# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
-# brief documentation of file, namespace and class members alphabetically
-# by member name. If set to NO (the default) the members will appear in
-# declaration order.
-
SORT_BRIEF_DOCS = NO
-
-# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
-# sorted by fully-qualified names, including namespaces. If set to
-# NO (the default), the class list will be sorted only by class name,
-# not including the namespace part.
-# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
-# Note: This option applies only to the class list, not to the
-# alphabetical list.
-
SORT_BY_SCOPE_NAME = NO
-
-# The GENERATE_TODOLIST tag can be used to enable (YES) or
-# disable (NO) the todo list. This list is created by putting \todo
-# commands in the documentation.
-
GENERATE_TODOLIST = YES
-
-# The GENERATE_TESTLIST tag can be used to enable (YES) or
-# disable (NO) the test list. This list is created by putting \test
-# commands in the documentation.
-
GENERATE_TESTLIST = YES
-
-# The GENERATE_BUGLIST tag can be used to enable (YES) or
-# disable (NO) the bug list. This list is created by putting \bug
-# commands in the documentation.
-
GENERATE_BUGLIST = YES
-
-# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
-# disable (NO) the deprecated list. This list is created by putting
-# \deprecated commands in the documentation.
-
GENERATE_DEPRECATEDLIST= YES
-
-# The ENABLED_SECTIONS tag can be used to enable conditional
-# documentation sections, marked by \if sectionname ... \endif.
-
ENABLED_SECTIONS =
-
-# The MAX_INITIALIZER_LINES tag determines the maximum number of lines
-# the initial value of a variable or define consists of for it to appear in
-# the documentation. If the initializer consists of more lines than specified
-# here it will be hidden. Use a value of 0 to hide initializers completely.
-# The appearance of the initializer of individual variables and defines in the
-# documentation can be controlled using \showinitializer or \hideinitializer
-# command in the documentation regardless of this setting.
-
MAX_INITIALIZER_LINES = 30
-
-# Set the SHOW_USED_FILES tag to NO to disable the list of files generated
-# at the bottom of the documentation of classes and structs. If set to YES the
-# list will mention the files that were used to generate the documentation.
-
SHOW_USED_FILES = YES
-
-# If the sources in your project are distributed over multiple directories
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy
-# in the documentation. The default is NO.
-
SHOW_DIRECTORIES = NO
-
-# The FILE_VERSION_FILTER tag can be used to specify a program or script that
-# doxygen should invoke to get the current version for each file (typically from the
-# version control system). Doxygen will invoke the program by executing (via
-# popen()) the command <command> <input-file>, where <command> is the value of
-# the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
-# provided by doxygen. Whatever the program writes to standard output
-# is used as the file version. See the manual for examples.
-
FILE_VERSION_FILTER =
-
#---------------------------------------------------------------------------
# configuration options related to warning and progress messages
#---------------------------------------------------------------------------
-
-# The QUIET tag can be used to turn on/off the messages that are generated
-# by doxygen. Possible values are YES and NO. If left blank NO is used.
-
QUIET = NO
-
-# The WARNINGS tag can be used to turn on/off the warning messages that are
-# generated by doxygen. Possible values are YES and NO. If left blank
-# NO is used.
-
WARNINGS = YES
-
-# If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
-# for undocumented members. If EXTRACT_ALL is set to YES then this flag will
-# automatically be disabled.
-
WARN_IF_UNDOCUMENTED = YES
-
-# If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
-# potential errors in the documentation, such as not documenting some
-# parameters in a documented function, or documenting parameters that
-# don't exist or using markup commands wrongly.
-
WARN_IF_DOC_ERROR = YES
-
-# This WARN_NO_PARAMDOC option can be abled to get warnings for
-# functions that are documented, but have no documentation for their parameters
-# or return value. If set to NO (the default) doxygen will only warn about
-# wrong or incomplete parameter documentation, but not about the absence of
-# documentation.
-
WARN_NO_PARAMDOC = NO
-
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text. Optionally the format may contain
-# $version, which will be replaced by the version of the file (if it could
-# be obtained via FILE_VERSION_FILTER)
-
-WARN_FORMAT = "$file:$line: $text"
-
-# The WARN_LOGFILE tag can be used to specify a file to which warning
-# and error messages should be written. If left blank the output is written
-# to stderr.
-
+WARN_FORMAT = "$file:$line: $text "
WARN_LOGFILE =
-
#---------------------------------------------------------------------------
# configuration options related to the input files
#---------------------------------------------------------------------------
-
-# The INPUT tag can be used to specify the files and/or directories that contain
-# documented source files. You may enter file names like "myfile.cpp" or
-# directories like "/usr/src/myproject". Separate the files or directories
-# with spaces.
-
-INPUT = ../../src ../../include
-
-# 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 also the default
-# input encoding. Doxygen uses libiconv (or the iconv built into libc) for the transcoding.
-# See http://www.gnu.org/software/libiconv for the list of possible encodings.
-
+INPUT = ../../include \
+ ../../src
INPUT_ENCODING = UTF-8
-
-# If the value of the INPUT tag contains directories, you can use the
-# FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank the following patterns are tested:
-# *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
-# *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py
-
-FILE_PATTERNS = *.c *.cc *.cpp *.h *.dox
-
-# The RECURSIVE tag can be used to turn specify whether or not subdirectories
-# should be searched for input files as well. Possible values are YES and NO.
-# If left blank NO is used.
-
+FILE_PATTERNS = *.c \
+ *.cc \
+ *.cpp \
+ *.h \
+ *.dox
RECURSIVE = YES
-
-# The EXCLUDE tag can be used to specify files and/or directories that should
-# 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 =
-
-# The EXCLUDE_SYMLINKS tag can be used select whether or not files or
-# directories that are symbolic links (a Unix filesystem feature) are excluded
-# from the input.
-
+EXCLUDE =
EXCLUDE_SYMLINKS = NO
-
-# If the value of the INPUT tag contains directories, you can use the
-# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
-# certain files from those directories. Note that the wildcards are matched
-# against the file with absolute path, so to exclude all test directories
-# for example use the pattern */test/*
-
-EXCLUDE_PATTERNS = */tests/* \
- */imp_wrap.* \
- */imp2.py
-
-# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
-# (namespaces, classes, functions, etc.) that should be excluded from the output.
-# The symbol name can be a fully qualified name, a word, or if the wildcard * is used,
-# a substring. Examples: ANamespace, AClass, AClass::ANamespace, ANamespace::*Test
-
+EXCLUDE_PATTERNS = */tests/* \
+ */imp_wrap.* \
+ */imp2.py \
+ ._*
EXCLUDE_SYMBOLS =
-
-# The EXAMPLE_PATH tag can be used to specify one or more files or
-# directories that contain example code fragments that are included (see
-# the \include command).
-
EXAMPLE_PATH =
-
-# If the value of the EXAMPLE_PATH tag contains directories, you can use the
-# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
-# and *.h) to filter out the source-files in the directories. If left
-# blank all files are included.
-
EXAMPLE_PATTERNS =
-
-# 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
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
-
EXAMPLE_RECURSIVE = NO
-
-# The IMAGE_PATH tag can be used to specify one or more files or
-# directories that contain image that are included in the documentation (see
-# the \image command).
-
IMAGE_PATH =
-
-# The INPUT_FILTER tag can be used to specify a program that doxygen should
-# invoke to filter for each input file. Doxygen will invoke the filter program
-# by executing (via popen()) the command <filter> <input-file>, where <filter>
-# is the value of the INPUT_FILTER tag, and <input-file> is the name of an
-# input file. Doxygen will then use the output that the filter program writes
-# to standard output. If FILTER_PATTERNS is specified, this tag will be
-# ignored.
-
INPUT_FILTER =
-
-# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
-# basis. Doxygen will compare the file name with each pattern and apply the
-# filter if there is a match. The filters are a list of the form:
-# pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
-# info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
-# is applied to all files.
-
FILTER_PATTERNS =
-
-# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
-# INPUT_FILTER) will be used to filter the input files when producing source
-# files to browse (i.e. when SOURCE_BROWSER is set to YES).
-
FILTER_SOURCE_FILES = NO
-
#---------------------------------------------------------------------------
# configuration options related to source browsing
#---------------------------------------------------------------------------
-
-# If the SOURCE_BROWSER tag is set to YES then a list of source files will
-# be generated. Documented entities will be cross-referenced with these sources.
-# Note: To get rid of all source code in the generated output, make sure also
-# VERBATIM_HEADERS is set to NO.
-
SOURCE_BROWSER = NO
-
-# Setting the INLINE_SOURCES tag to YES will include the body
-# of functions and classes directly in the documentation.
-
INLINE_SOURCES = NO
-
-# Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
-# doxygen to hide any special comment blocks from generated source code
-# fragments. Normal C and C++ comments will always remain visible.
-
STRIP_CODE_COMMENTS = YES
-
-# If the REFERENCED_BY_RELATION tag is set to YES (the default)
-# then for each documented function all documented
-# functions referencing it will be listed.
-
REFERENCED_BY_RELATION = YES
-
-# If the REFERENCES_RELATION tag is set to YES (the default)
-# then for each documented function all documented entities
-# called/used by that function will be listed.
-
REFERENCES_RELATION = YES
-
-# If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
-# and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
-# functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
-# link to the source code. Otherwise they will link to the documentstion.
-
REFERENCES_LINK_SOURCE = YES
-
-# If the USE_HTAGS tag is set to YES then the references to source code
-# will point to the HTML generated by the htags(1) tool instead of doxygen
-# built-in source browser. The htags tool is part of GNU's global source
-# tagging system (see http://www.gnu.org/software/global/global.html). You
-# will need version 4.8.6 or higher.
-
USE_HTAGS = NO
-
-# If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
-# will generate a verbatim copy of the header file for each class for
-# which an include is specified. Set to NO to disable this.
-
VERBATIM_HEADERS = YES
-
#---------------------------------------------------------------------------
# configuration options related to the alphabetical class index
#---------------------------------------------------------------------------
-
-# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
-# of all compounds will be generated. Enable this if the project
-# contains a lot of classes, structs, unions or interfaces.
-
ALPHABETICAL_INDEX = NO
-
-# If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
-# the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
-# in which this list will be split (can be a number in the range [1..20])
-
COLS_IN_ALPHA_INDEX = 5
-
-# In case all classes in a project start with a common prefix, all
-# classes will be put under the same header in the alphabetical index.
-# The IGNORE_PREFIX tag can be used to specify one or more prefixes that
-# should be ignored while generating the index headers.
-
IGNORE_PREFIX =
-
#---------------------------------------------------------------------------
# configuration options related to the HTML output
#---------------------------------------------------------------------------
-
-# If the GENERATE_HTML tag is set to YES (the default) Doxygen will
-# generate HTML output.
-
GENERATE_HTML = YES
-
-# The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `html' will be used as the default path.
-
HTML_OUTPUT = html
-
-# The HTML_FILE_EXTENSION tag can be used to specify the file extension for
-# each generated HTML page (for example: .htm,.php,.asp). If it is left blank
-# doxygen will generate files with .html extension.
-
HTML_FILE_EXTENSION = .html
-
-# The HTML_HEADER tag can be used to specify a personal HTML header for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard header.
-
HTML_HEADER =
-
-# 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 =
-
-# 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
-# fine-tune the look of the HTML output. If the tag is left blank doxygen
-# will generate a default style sheet. Note that doxygen will try to copy
-# the style sheet file to the HTML output directory, so don't put your own
-# stylesheet in the HTML output directory as well, or it will be erased!
-
HTML_STYLESHEET =
-
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
HTML_ALIGN_MEMBERS = YES
-
-# 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
-# Microsoft HTML help workshop to generate a compressed HTML help file (.chm)
-# of the generated HTML documentation.
-
GENERATE_HTMLHELP = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
-# be used to specify the file name of the resulting .chm file. You
-# can add a path in front of the file if the result should not be
-# written to the html output directory.
-
+HTML_DYNAMIC_SECTIONS = NO
CHM_FILE =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
-# be used to specify the location (absolute path including file name) of
-# the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
-# the HTML help compiler on the generated index.hhp.
-
HHC_LOCATION =
-
-# If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
-# controls if a separate .chi index file is generated (YES) or that
-# it should be included in the master .chm file (NO).
-
GENERATE_CHI = NO
-
-# If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
-# controls whether a binary table of contents is generated (YES) or a
-# normal table of contents (NO) in the .chm file.
-
BINARY_TOC = NO
-
-# The TOC_EXPAND flag can be set to YES to add extra items for group members
-# to the contents of the HTML help documentation and to the tree view.
-
TOC_EXPAND = NO
-
-# The DISABLE_INDEX tag can be used to turn on/off the condensed index at
-# top of each HTML page. The value NO (the default) enables the index and
-# the value YES disables it.
-
DISABLE_INDEX = NO
-
-# This tag can be used to set the number of enum values (range [1..20])
-# that doxygen will group on one line in the generated HTML documentation.
-
ENUM_VALUES_PER_LINE = 4
-
-# If the GENERATE_TREEVIEW tag is set to YES, a side panel will be
-# generated containing a tree-like index structure (just like the one that
-# is generated for HTML Help). For this to work a browser that supports
-# JavaScript, DHTML, CSS and frames is required (for instance Mozilla 1.0+,
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
-# probably better off using the HTML help feature.
-
GENERATE_TREEVIEW = NO
-
-# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
-# used to set the initial width (in pixels) of the frame in which the tree
-# is shown.
-
TREEVIEW_WIDTH = 250
-
#---------------------------------------------------------------------------
# configuration options related to the LaTeX output
#---------------------------------------------------------------------------
-
-# If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
-# generate Latex output.
-
GENERATE_LATEX = NO
-
-# The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `latex' will be used as the default path.
-
LATEX_OUTPUT = latex
-
-# The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
-# invoked. If left blank `latex' will be used as the default command name.
-
LATEX_CMD_NAME = latex
-
-# The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
-# generate index for LaTeX. If left blank `makeindex' will be used as the
-# default command name.
-
MAKEINDEX_CMD_NAME = makeindex
-
-# If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
-# LaTeX documents. This may be useful for small projects and may help to
-# save some trees in general.
-
COMPACT_LATEX = NO
-
-# The PAPER_TYPE tag can be used to set the paper type that is used
-# by the printer. Possible values are: a4, a4wide, letter, legal and
-# executive. If left blank a4wide will be used.
-
PAPER_TYPE = a4wide
-
-# The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
-# packages that should be included in the LaTeX output.
-
EXTRA_PACKAGES =
-
-# The LATEX_HEADER tag can be used to specify a personal LaTeX header for
-# the generated latex document. The header should contain everything until
-# the first chapter. If it is left blank doxygen will generate a
-# standard header. Notice: only use this tag if you know what you are doing!
-
LATEX_HEADER =
-
-# If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
-# is prepared for conversion to pdf (using ps2pdf). The pdf file will
-# contain links (just like the HTML output) instead of page references
-# This makes the output suitable for online browsing using a pdf viewer.
-
PDF_HYPERLINKS = NO
-
-# If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
-# plain latex in the generated Makefile. Set this option to YES to get a
-# higher quality PDF documentation.
-
USE_PDFLATEX = NO
-
-# If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
-# command to the generated LaTeX files. This will instruct LaTeX to keep
-# running if errors occur, instead of asking the user for help.
-# This option is also used when generating formulas in HTML.
-
LATEX_BATCHMODE = NO
-
-# If LATEX_HIDE_INDICES is set to YES then doxygen will not
-# include the index chapters (such as File Index, Compound Index, etc.)
-# in the output.
-
LATEX_HIDE_INDICES = NO
-
#---------------------------------------------------------------------------
# configuration options related to the RTF output
#---------------------------------------------------------------------------
-
-# If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
-# The RTF output is optimized for Word 97 and may not look very pretty with
-# other RTF readers or editors.
-
GENERATE_RTF = NO
-
-# The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `rtf' will be used as the default path.
-
RTF_OUTPUT = rtf
-
-# If the COMPACT_RTF tag is set to YES Doxygen generates more compact
-# RTF documents. This may be useful for small projects and may help to
-# save some trees in general.
-
COMPACT_RTF = NO
-
-# If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
-# will contain hyperlink fields. The RTF file will
-# contain links (just like the HTML output) instead of page references.
-# This makes the output suitable for online browsing using WORD or other
-# programs which support those fields.
-# Note: wordpad (write) and others do not support links.
-
RTF_HYPERLINKS = NO
-
-# Load stylesheet definitions from file. Syntax is similar to doxygen's
-# config file, i.e. a series of assignments. You only have to provide
-# replacements, missing definitions are set to their default value.
-
RTF_STYLESHEET_FILE =
-
-# Set optional variables used in the generation of an rtf document.
-# Syntax is similar to doxygen's config file.
-
RTF_EXTENSIONS_FILE =
-
#---------------------------------------------------------------------------
# configuration options related to the man page output
#---------------------------------------------------------------------------
-
-# If the GENERATE_MAN tag is set to YES (the default) Doxygen will
-# generate man pages
-
GENERATE_MAN = NO
-
-# The MAN_OUTPUT tag is used to specify where the man pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `man' will be used as the default path.
-
MAN_OUTPUT = man
-
-# The MAN_EXTENSION tag determines the extension that is added to
-# the generated man pages (default is the subroutine's section .3)
-
MAN_EXTENSION = .3
-
-# If the MAN_LINKS tag is set to YES and Doxygen generates man output,
-# then it will generate one additional man file for each entity
-# documented in the real man page(s). These additional files
-# only source the real man page, but without them the man command
-# would be unable to find the correct page. The default is NO.
-
MAN_LINKS = NO
-
#---------------------------------------------------------------------------
# configuration options related to the XML output
#---------------------------------------------------------------------------
-
-# If the GENERATE_XML tag is set to YES Doxygen will
-# generate an XML file that captures the structure of
-# the code including all documentation.
-
GENERATE_XML = NO
-
-# The XML_OUTPUT tag is used to specify where the XML pages will be put.
-# If a relative path is entered the value of OUTPUT_DIRECTORY will be
-# put in front of it. If left blank `xml' will be used as the default path.
-
XML_OUTPUT = xml
-
-# The XML_SCHEMA tag can be used to specify an XML schema,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
XML_SCHEMA =
-
-# The XML_DTD tag can be used to specify an XML DTD,
-# which can be used by a validating XML parser to check the
-# syntax of the XML files.
-
XML_DTD =
-
-# If the XML_PROGRAMLISTING tag is set to YES Doxygen will
-# dump the program listings (including syntax highlighting
-# and cross-referencing information) to the XML output. Note that
-# enabling this will significantly increase the size of the XML output.
-
XML_PROGRAMLISTING = YES
-
#---------------------------------------------------------------------------
# configuration options for the AutoGen Definitions output
#---------------------------------------------------------------------------
-
-# If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
-# generate an AutoGen Definitions (see autogen.sf.net) file
-# that captures the structure of the code including all
-# documentation. Note that this feature is still experimental
-# and incomplete at the moment.
-
GENERATE_AUTOGEN_DEF = NO
-
#---------------------------------------------------------------------------
# configuration options related to the Perl module output
#---------------------------------------------------------------------------
-
-# If the GENERATE_PERLMOD tag is set to YES Doxygen will
-# generate a Perl module file that captures the structure of
-# the code including all documentation. Note that this
-# feature is still experimental and incomplete at the
-# moment.
-
GENERATE_PERLMOD = NO
-
-# If the PERLMOD_LATEX tag is set to YES Doxygen will generate
-# the necessary Makefile rules, Perl scripts and LaTeX code to be able
-# to generate PDF and DVI output from the Perl module output.
-
PERLMOD_LATEX = NO
-
-# If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
-# nicely formatted so it can be parsed by a human reader. This is useful
-# if you want to understand what is going on. On the other hand, if this
-# tag is set to NO the size of the Perl module output will be much smaller
-# and Perl will parse it just the same.
-
PERLMOD_PRETTY = YES
-
-# The names of the make variables in the generated doxyrules.make file
-# are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
-# This is useful so different doxyrules.make files included by the same
-# Makefile don't overwrite each other's variables.
-
PERLMOD_MAKEVAR_PREFIX =
-
#---------------------------------------------------------------------------
# Configuration options related to the preprocessor
#---------------------------------------------------------------------------
-
-# If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
-# evaluate all C-preprocessor directives found in the sources and include
-# files.
-
ENABLE_PREPROCESSING = YES
-
-# If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
-# names in the source code. If set to NO (the default) only conditional
-# compilation will be performed. Macro expansion can be done in a controlled
-# way by setting EXPAND_ONLY_PREDEF to YES.
-
MACRO_EXPANSION = YES
-
-# If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
-# then the macro expansion is limited to the macros specified with the
-# PREDEFINED and EXPAND_AS_DEFINED tags.
-
EXPAND_ONLY_PREDEF = NO
-
-# If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
-# in the INCLUDE_PATH (see below) will be search if a #include is found.
-
SEARCH_INCLUDES = YES
-
-# The INCLUDE_PATH tag can be used to specify one or more directories that
-# contain include files that are not input files but should be processed by
-# the preprocessor.
-
INCLUDE_PATH =
-
-# You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
-# patterns (like *.h and *.hpp) to filter out the header-files in the
-# directories. If left blank, the patterns specified with FILE_PATTERNS will
-# be used.
-
INCLUDE_FILE_PATTERNS =
-
-# 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
-# gcc). The argument of the tag is a list of macros of the form: name
-# or name=definition (no spaces). If the definition and the = are
-# omitted =1 is assumed. To prevent a macro definition from being
-# undefined via #undef or recursively expanded use the := operator
-# instead of the = operator.
-
PREDEFINED =
-
-# If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
-# this tag can be used to specify a list of macro names that should be expanded.
-# The macro definition that is found in the sources will be used.
-# Use the PREDEFINED tag if you want to use a different macro definition.
-
EXPAND_AS_DEFINED =
-
-# If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
-# doxygen's preprocessor will remove all function-like macros that are alone
-# on a line, have an all uppercase name, and do not end with a semicolon. Such
-# function macros are typically used for boiler-plate code, and will confuse
-# the parser if not removed.
-
SKIP_FUNCTION_MACROS = YES
-
#---------------------------------------------------------------------------
# Configuration::additions related to external references
#---------------------------------------------------------------------------
-
-# The TAGFILES option can be used to specify one or more tagfiles.
-# Optionally an initial location of the external documentation
-# can be added for each tagfile. The format of a tag file without
-# this location is as follows:
-# TAGFILES = file1 file2 ...
-# Adding location for the tag files is done as follows:
-# TAGFILES = file1=loc1 "file2 = loc2" ...
-# where "loc1" and "loc2" can be relative or absolute paths or
-# URLs. If a location is present for each tag, the installdox tool
-# does not have to be run to correct the links.
-# Note that each tag file must have a unique name
-# (where the name does NOT include the path)
-# If a tag file is not located in the directory in which doxygen
-# is run, you must also specify the path to the tagfile here.
-
TAGFILES =
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
-
GENERATE_TAGFILE =
-
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
-
ALLEXTERNALS = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
-
EXTERNAL_GROUPS = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
-
PERL_PATH = /usr/bin/perl
-
#---------------------------------------------------------------------------
# Configuration options related to the dot tool
#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base
-# or super classes. Setting the tag to NO turns the diagrams off. Note that
-# this option is superseded by the HAVE_DOT option below. This is only a
-# fallback. It is recommended to install and use dot, since it yields more
-# powerful graphs.
-
CLASS_DIAGRAMS = YES
-
-# You can define message sequence charts within doxygen comments using the \msc
-# command. Doxygen will then run the mscgen tool (see http://www.mcternan.me.uk/mscgen/) to
-# produce the chart and insert it in the documentation. The MSCGEN_PATH tag allows you to
-# specify the directory where the mscgen tool resides. If left empty the tool is assumed to
-# be found in the default search path.
-
MSCGEN_PATH =
-
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
-
HIDE_UNDOC_RELATIONS = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
-
HAVE_DOT = NO
-
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# the CLASS_DIAGRAMS tag to NO.
-
CLASS_GRAPH = YES
-
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
-
COLLABORATION_GRAPH = YES
-
-# If the GROUP_GRAPHS and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for groups, showing the direct groups dependencies
-
GROUP_GRAPHS = YES
-
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
-# Language.
-
UML_LOOK = NO
-
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
-
TEMPLATE_RELATIONS = NO
-
-# 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
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
-
INCLUDE_GRAPH = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
-
INCLUDED_BY_GRAPH = YES
-
-# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will
-# generate a call dependency graph for every global function or class method.
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command.
-
CALL_GRAPH = NO
-
-# If the CALLER_GRAPH and HAVE_DOT tags are set to YES then doxygen will
-# generate a caller dependency graph for every global function or class method.
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable caller graphs for selected
-# functions only using the \callergraph command.
-
CALLER_GRAPH = NO
-
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will graphical hierarchy of all classes instead of a textual one.
-
GRAPHICAL_HIERARCHY = YES
-
-# If the DIRECTORY_GRAPH, SHOW_DIRECTORIES and HAVE_DOT tags are set to YES
-# then doxygen will show the dependencies a directory has on other directories
-# in a graphical way. The dependency relations are determined by the #include
-# relations between the files in the directories.
-
DIRECTORY_GRAPH = YES
-
-# 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
-# If left blank png will be used.
-
DOT_IMAGE_FORMAT = png
-
-# The tag DOT_PATH can be used to specify the path where the dot tool can be
-# found. If left blank, it is assumed the dot tool can be found in the path.
-
DOT_PATH =
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
-# \dotfile command).
-
DOTFILE_DIRS =
-
-# The MAX_DOT_GRAPH_MAX_NODES tag can be used to set the maximum number of
-# nodes that will be shown in the graph. If the number of nodes in a graph
-# becomes larger than this value, doxygen will truncate the graph, which is
-# visualized by representing a node as a red box. Note that doxygen will always
-# show the root nodes and its direct children regardless of this setting.
-
DOT_GRAPH_MAX_NODES = 50
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, which results in a white background.
-# Warning: Depending on the platform used, enabling this option may lead to
-# badly anti-aliased labels on the edges of a graph (i.e. they become hard to
-# read).
-
+MAX_DOT_GRAPH_DEPTH = 1000
DOT_TRANSPARENT = NO
-
-# 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
-
-# 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
-# arrows in the dot generated graphs.
-
GENERATE_LEGEND = YES
-
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
-# remove the intermediate dot files that are used to generate
-# the various graphs.
-
DOT_CLEANUP = YES
-
#---------------------------------------------------------------------------
# Configuration::additions related to the search engine
#---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be
-# used. If set to NO the values of all tags below this one will be ignored.
-
SEARCHENGINE = NO
Index: kernel/src/Model.cpp
===================================================================
--- kernel/src/Model.cpp (revision 363)
+++ kernel/src/Model.cpp (working copy)
@@ -101,7 +101,9 @@
DerivativeAccumulator *accpt = (calc_derivs ? &accum : NULL);
IMP_LOG(VERBOSE,
- "Evaluating restraints " << calc_derivs << std::endl);
+ "Evaluating restraints "
+ << (calc_derivs?"with derivatives":"without derivatives")
+ << std::endl);
for (RestraintIterator it = restraints_begin();
it != restraints_end(); ++it) {
IMP_CHECK_OBJECT(*it);
@@ -110,7 +112,7 @@
if ((*it)->get_is_active()) {
tscore = (*it)->evaluate(accpt);
}
- IMP_LOG(VERBOSE, tscore << std::endl);
+ IMP_LOG(VERBOSE, "Restraint score is " << tscore << std::endl);
score+= tscore;
}
IMP_LOG(VERBOSE, "done." << std::endl);
Index: kernel/src/Particle.cpp
===================================================================
--- kernel/src/Particle.cpp (revision 363)
+++ kernel/src/Particle.cpp (working copy)
@@ -96,7 +96,7 @@
//! Show the particle
/** \param[in] out Stream to write particle description to.
*/
-std::ostream& Particle::show(std::ostream& out) const
+void Particle::show(std::ostream& out) const
{
char* inset = " ";
out << std::endl;
@@ -118,7 +118,6 @@
out << inset << inset << "string attributes:" << std::endl;
string_indexes_.show(out, " ", get_model()->get_model_data());
}
- return out;
}
Index: kernel/src/pair_scores/DistancePairScore.cpp
===================================================================
--- kernel/src/pair_scores/DistancePairScore.cpp (revision 363)
+++ kernel/src/pair_scores/DistancePairScore.cpp (working copy)
@@ -58,8 +58,6 @@
score = (*f)(shifted_distance);
}
- IMP_LOG(VERBOSE, "For " << a->get_index() << " and " << b->get_index()
- << " distance: " << distance << " score: " << score << std::endl);
return score;
}
Index: kernel/include/IMP/unary_functions/Linear.h
===================================================================
--- kernel/include/IMP/unary_functions/Linear.h (revision 0)
+++ kernel/include/IMP/unary_functions/Linear.h (revision 0)
@@ -0,0 +1,43 @@
+/**
+ * \file Linear.h \brief A linear function.
+ *
+ * Copyright 2007-8 Sali Lab. All rights reserved.
+ */
+
+#ifndef __IMP_LINEAR_H
+#define __IMP_LINEAR_H
+
+#include "../UnaryFunction.h"
+
+namespace IMP
+{
+
+//! Linear function
+/** \ingroup unaryf
+ \note there is no offset since that is not meaningful for optimization
+ */
+class IMPDLLEXPORT Linear : public UnaryFunction
+{
+public:
+ Linear(Float slope) : slope_(slope) {}
+
+ virtual ~Linear() {}
+
+ virtual Float operator()(Float feature) { return feature*slope_;}
+
+ virtual Float operator()(Float feature, Float& deriv) {
+ deriv= slope_;
+ return operator()(feature);
+ }
+
+ void show(std::ostream &out=std::cout) const {
+ out << "Linear: " << slope_ << std::endl;
+ }
+
+protected:
+ Float slope_;
+};
+
+} // namespace IMP
+
+#endif /* __IMP_HARMONIC_H */