[IMP-dev] doc changes

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 -# brief descriptions will be completely suppressed. - REPEAT_BRIEF = YES - -# This tag implements a quasi-intelligent brief description abbreviator -# that is used to form the text in various listings. 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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 */