Index: doc/usage.xml
===================================================================
--- doc/usage.xml (revision 1005)
+++ doc/usage.xml (working copy)
@@ -1,546 +0,0 @@
-<chapter id="usage">
-<title>Usage</title>
-
-<sect1 id="compilation">
-<title>Compilation from source code</title>
-
-<sect2 id="prereq">
-<title>Prerequisites</title>
-
-<para>In order to obtain and compile &IMP;, you will need:</para>
-
-<itemizedlist>
-<listitem><para>
-<ulink url="http://www.swig.org">SWIG</ulink> (1.3.33 or later).
-</para></listitem>
-
-<listitem><para>
-<ulink url="http://www.scons.org">scons</ulink> (0.98 or later).
-</para></listitem>
-
-<listitem><para><ulink url="http://www.boost.org">Boost</ulink> (1.30 or later).
-At the moment &IMP; only uses the Boost headers (not the libraries), so
-installing these headers in <filename>/usr/local/include/boost</filename>
-should suffice.</para></listitem>
-
-<listitem><para><ulink url="http://www.python.org">Python</ulink> 2.3 or
-later.</para></listitem>
-
-<listitem><para>A <ulink url="http://subversion.tigris.org/">Subversion</ulink>
-(svn) client to access the repository.</para></listitem>
-
-</itemizedlist>
-
-<sect3 id="mac">
-<title>Mac</title>
-<para> Mac users should use one of the available collections of Unix tools,
-either <ulink url="http://www.macports.org/">MacPorts</ulink> or
-<ulink url="http://www.finkproject.org/">Fink</ulink>. These both include SWIG,
-scons, Subversion and Boost (for example, to install Boost with MacPorts, use
-the command <command>sudo port install boost</command>). At the moment Fink
-does not have a binary installer for Mac OS 10.5, so MacPorts is
-preferred.</para>
-
-<para>Do not install any C++ headers in <filename>/usr/include</filename> on
-your Mac as the compiler assumes any such headers are C headers. Extra headers
-not owned by MacPorts or Fink should be placed in
-<filename>/usr/local/include</filename>.</para>
-</sect3>
-
-<sect3 id="windows">
-<title>Windows</title>
-<para> Windows users should probably install
-<ulink url="http://www.cygwin.org/">Cygwin</ulink>, but we don't have any of
-those yet, so we don't really know.</para>
-
-</sect3>
-
-</sect2>
-
-<sect2 id="optionallibs">
-<title>Optional dependencies</title>
-
-<itemizedlist>
-<listitem><para>If you want to use &IMP; with &MODELLER; (optional), you should
-use version 9v5 or later.</para></listitem>
-</itemizedlist>
-
-</sect2>
-
-<sect2 id="gettingbuilding">
-<title>Getting and building IMP</title>
-<para>
-If you have Subversion installed you can get the current &IMP; code by running
-the following:
-<screen>
-<command>svn co https://svn.salilab.org/imp/trunk imp</command>
-</screen>
-</para>
-<para>
-To build &IMP;, in the <filename>imp</filename> directory type:
-<screen>
-<command>scons</command>
-</screen>
-</para>
-<para>
-Finally, to use &IMP; within Python, type the following in the
-<filename>imp</filename> directory:
-<screen>
-<command>bin/imppy.sh python</command>
-</screen>
-</para>
-
-<para>
-Some other useful commands:
-<itemizedlist>
-
-<listitem>If you have checked out a copy of &IMP;, you can update it to the
-current code by typing
-<screen>
-<command>svn update</command>
-</screen></listitem>
-
-<listitem> To install &IMP; into <filename>install_dir</filename>, type
-<screen>
-<command>scons install prefix=install_dir</command>
-</screen>
-Note that installation does not currently work on Mac OS.
-</listitem>
-<listitem>
-If you want to use &IMP; with &MODELLER;, set the <command>scons</command>
-<varname>modeller</varname> variable to the directory where you have
-&MODELLER; installed, e.g. <screen><command>scons modeller=~/modinstall</command> </screen>
-Type <command>scons -h</command> to get help on this and other command-line
-options.
-</listitem>
-
-</itemizedlist>
-</para>
-
-</sect2>
-
-</sect1>
-
-<sect1 id="reference">
-<title>Reference manual</title>
-<para>
-For information on the low-level &IMP; code, see the
-<ulink url="doxygen/index.html">C++ API reference</ulink>.
-</para>
-</sect1>
-
-<sect1 id="modules">
-<title>IMP modules</title>
-<para>
-IMP is divided into modules, with different uses and dependencies. The IMP
-kernel only defines the simplest classes used in IMP, such as the particles,
-and provides defined interfaces (abstract base classes) for functionality such
-as restraints. The real work (or implementation) is done by modules.
-</para>
-
-<para>
-Typically, a module groups functionality (such as restraints or specialized
-optimizers) for specific applications or problem domains, such as the
-<filename>em</filename> module for cryo EM fitting. Modules may also pull in
-interfaces to external libraries (for example, the <filename>em</filename>
-and <filename>modeller</filename> modules interface with EMBED and MODELLER
-respectively) or may depend on other IMP modules (for example, many modules
-depend on the <filename>core</filename> module).
-</para>
-
-<para>
-There are also two "general purpose" modules: the <filename>misc</filename>
-module, which contains miscellaneous features which are
-generally <emphasis>not</emphasis> used by other modules, and
-the <filename>core</filename> module, which contains features expected to be
-used by almost everybody, and upon which many other modules depend.
-The <filename>misc</filename> module can be used for features that do not
-neatly fit into a specialized module, such as code that implements proposed
-new methodologies.
-</para>
-
-<para>
-It is also possible to create your IMP modules outside of IMP itself. This
-is ideal if you have different licensing requirements, your code is very
-experimental, or you do not want to share your source code, for example.
-Of course, if you go down this route, you must do your own book keeping to
-make sure that the IMP kernel and any modules you depend on are correctly built
-before your own.
-</para>
-</sect1>
-
-<sect1 id="style">
-<title>Style guide</title>
-
-<para>
-To ensure code consistency and readability, certain conventions should be
-adhered to when writing code for &IMP;. Some of these conventions are
-automatically checked for by source control before allowing a new commit, and
-should also be checked yourself in new code by running
-<command>scons standards</command>.
-</para>
-
-<sect2>
-<title>C++ formatting</title>
-
-<sect3>
-<title>Indentation</title>
-<para>All C++ headers and code should be indented in 'Linux' style, with
-2-space indents. Do not use tabs. This is roughly the output of
-<ulink url="http://astyle.sourceforge.net/">Artistic Style</ulink> with
-the <parameter>--convert-tabs --style=linux --indent=spaces=2 --unpad=paren --pad=oper</parameter>
-parameters. Split lines if necessary to ensure that no line is longer than
-80 characters.
-</para>
-
-<para><emphasis>Rationale:</emphasis>
-Different users have different-sized windows or terminals, and different tab
-settings. This is also similar to other lab C and Fortran projects.
-</para>
-</sect3>
-
-<sect3>
-<title>Comments</title>
-
-<para>Format to allow
-<ulink url="http://www.stack.nl/~dimitri/doxygen/">Doxygen</ulink>
-automated documentation creation. If possible, specify both a 'brief'
-description and a more detailed one (in which parameters, return values,
-and exceptions are documented). Use //! for the one-line brief description
-and /** ... */ for the multi-line detailed description (put the closing */ on
-a new line, so that these comments are always multi-line (Doxygen will not
-accept both a 'brief' comment and a one-line detailed comment). All header
-and source files should have a starting comment header, using the
-<command>\file</command> command to document the purpose of the file.
-For example:</para>
-<informalexample><programlisting>
-//! Calculates the square root.
-/** \param[in] the_value Calculate the square root of this value.
- \exception std::domain_error value is out of range (negative).
- \return the square root of the given value.
- */
-</programlisting></informalexample>
-</sect3>
-
-<sect3>
-<title>Class names</title>
-
-<para>Use CamelCase (i.e. capitalized concatenated words). For example:</para>
-<informalexample><programlisting>
-class SpecialVector
-{
-};
-</programlisting></informalexample>
-
-<para><emphasis>Rationale:</emphasis>
-This makes it easier to tell between class names and function names where
-this is ambiguous (particularly an issue with the Python interface). The
-Python guys also mandate CamelCase for their class names, so this avoids
-any need to rename classes between C++ and Python to ensure clean Python code.
-</para>
-</sect3>
-
-<sect3>
-<title>Exceptions</title>
-<para>Exceptions are classes, so name as for classes, above. Do not use
-exception specifications, but do document the possible exceptions thrown by
-a function with the Doxygen <command>\exception</command> command.
-</para>
-
-<para><emphasis>Rationale:</emphasis>
-Exception specifications do not guarantee that only the listed exceptions will
-be thrown, and actually hurt compiler optimizations in many cases. Many
-libraries (such as Boost) <ulink url="http://www.gotw.ca/publications/mill22.htm">advise against using them</ulink>.
-</para>
-
-</sect3>
-
-<sect3>
-<title>Member functions (class methods)</title>
-
-<para>Use lower case, with words separated by underscores. For example:</para>
-<informalexample><programlisting>
-void SpecialVector::add_constant(int the_constant)
-</programlisting></informalexample>
-
-<para>Use set_ at the beginning of setting accessor functions, and get_ at the
-beginning of accessor functions used to get a member variable value.
-For example:</para>
-
-<informalexample><programlisting>
-float Sphere::get_radius(void) const;
-void Sphere::set_radius(float);
-</programlisting></informalexample>
-</sect3>
-
-<sect3>
-<title>Member variables (class variables)</title>
-
-<para>Use lower case, with words separated by underscores. End name in an
-underscore. For example:</para>
-<informalexample><programlisting>
-std::vector<int> spec_vector_;
-</programlisting></informalexample>
-</sect3>
-
-<sect3>
-<title>Local variables</title>
-
-<para>Use lower case, with words separated by underscores. For example:</para>
-<informalexample><programlisting>
-int i, num_particles;
-</programlisting></informalexample>
-
-<para><emphasis>Rationale:</emphasis>
-A trailing underscore makes it simple to tell between class members and
-local variables.</para>
-</sect3>
-
-</sect2>
-
-<sect2>
-<title>C++ libraries and namespaces</title>
-<para>Explicitly use namespace prefixes rather than the "using namespace"
-syntax.</para>
-
-<para><emphasis>Rationale:</emphasis>
-Avoids namespace pollution, and removes any ambiguity.
-</para>
-
-<para>Use the provided macros such as <code>IMP_BEGIN_NAMESPACE</code> and
-<code>IMP_END_NAMESPACE</code> to begin and end the namespace for the kernel
-or a module.
-</para>
-
-</sect2>
-
-<sect2>
-<title>Includes</title>
-<para>Always import headers for the current module first, followed by headers
-for any dependent modules (e.g. the kernel), and finally any system headers.
-Use angle brackets and the full name of the header (with IMP/ prefix).
-For example,
-</para>
-<informalexample><programlisting>
-#include <IMP/mymodule/MyClass.h>
-#include <IMP/mymodule/MyOtherClass.h>
-
-#include <IMP/KernelBaseClass.h>
-
-#include <math>
-</programlisting></informalexample>
-
-<para><emphasis>Rationale:</emphasis>
-This makes any dependencies in your code obvious, and by including standard
-headers <emphasis>after</emphasis> IMP headers, any missing includes in the
-headers themselves show up early (rather than being masked by other headers
-you include). Adding the IMP prefix and using angle brackets reduces the
-likelihood that uninstalled rogue headers in the source code directory are
-used, which could break the build.
-</para>
-
-<para>For simplicity, to include a header from the same module within another
-header, you can use a relative path (i.e. without the IMP/ prefix) and use
-double quotes rather than angle brackets. This makes it obvious to the reader
-that the include is from the same module. Since headers are staged to a build
-directory, there is no danger of including an uninstalled header this way.
-</para>
-</sect2>
-
-<sect2>
-<title>Python formatting</title>
-<para>All Python code should conform to the
-<ulink url="http://www.python.org/dev/peps/pep-0008/">Python style
-guide</ulink>. In essence this translates to 4-space indents, no tabs, and
-similar class, method and variable naming to the C++ code. You can ensure that
-your Python code is correctly indented by using the
-<ulink url="http://docutils.sourceforge.net/sandbox/py-rest-doc/utils/reindent.py">reindent.py</ulink>
-script, available as part of the Python distribution.
-</para>
-
-</sect2>
-
-</sect1>
-
-<sect1 id="adding-code">
-<title>Adding code to IMP</title>
-
-<sect2 id="choose-module">
-<title>Choosing a module for your code</title>
-
-<para>
-By far the easiest way to contribute to IMP is to create a module for your
-specific problem domain. For example, restraints and optimizers specific to
-ligands could go in a <filename>ligand</filename> module. Please contact Ben
-to have a new module created. If you feel your code doesn't belong in its
-own module, you can add it to the <filename>misc</filename> module instead.
-If you feel your new functionality is of use to everybody and should live in the
-<filename>core</filename> module, you should request this on the IMP mailing
-list and have it approved by Ben, who has the final say on where code should
-end up. This is partly to prevent the <filename>core</filename> module from
-becoming too bloated with specialized code.
-</para>
-
-<para>
-Code should generally <emphasis>not</emphasis> be moved from one
-module to another, unless there is an exceptionally good reason to do so. If
-for some reason you do want to move things between modules, ask Ben to do it.
-</para>
-</sect2>
-
-<sect2 id="define-interfaces">
-<title>Defining your interfaces</title>
-
-<para>
-Before you sit down and write your new code or change existing code, you
-should think about the interfaces. These are the classes and their methods,
-without any implementation. It is recommended that you discuss these
-interfaces on the <email>imp-dev@salilab.org</email> mailing list before you
-proceed with implementation, so that you do not duplicate work, others can
-make valuable suggestions or point out problems, and people are made aware of
-your contribution. If you want to add to or change the interfaces in the
-kernel or the <filename>core</filename> module, this discussion is
-mandatory, since potentially everybody could be affected by your changes. Any
-issues raised by users with changes to the kernel or <filename>core</filename>
-must be resolved to their satisfaction before the changes are made. For clarity,
-the following should be considered changes that warrant discussion:
-</para>
-
-<itemizedlist>
-<listitem><para>Change the API (e.g. remove or rename existing methods or
-classes, change the arguments taken by existing methods, change the behavior
-of existing methods, change the return values or thrown exceptions of existing
-methods).</para></listitem>
-
-<listitem><para>Remove or modify existing test cases.</para></listitem>
-</itemizedlist>
-
-<para>
-Conversely, changes in internal implementation or documentation to any module,
-or changes in the interfaces of your own modules or the
-<filename>misc</filename> module, do not need to be announced, and neither does
-the addition of new methods to existing classes, although it may be helpful
-to tell people about such changes.
-</para>
-
-</sect2>
-
-<sect2 id="patches">
-<title>Creating a patch</title>
-
-<para>
-Generally speaking, to add code to IMP, your changes should be made to your
-checkout of the IMP repository, and then a patch generated by using the
-<command>svn di</command> command.
-</para>
-
-<para>Patches should contain a related set of changes. For example, a patch
-which adds a new method <methodname>foo</methodname>, a new testcase for
-<methodname>foo</methodname>, and some documentation for the
-<classname>SpecialVector</classname> class, should be split into two patches:
-one for the <methodname>foo</methodname> method and test, and the other for
-the <classname>SpecialVector</classname> documentation.</para>
-
-<para>New code in patches should also adhere to the
-<link linkend="style">coding style guidelines</link>.</para>
-
-<para>If new methods and/or classes are added, it is
-<emphasis>strongly</emphasis> recommended that unit tests are added for these.
-(Even a simple call of each method with no checking of the return values or
-other effects is better than nothing.)</para>
-
-<para><emphasis>Rationale:</emphasis>
-It is much easier for others to understand your patch's changes if it is small
-and contains only relevant changes. Test cases also help to document the
-intent of code changes, as well as making sure that the new additions are not
-accidentally broken in future.
-</para>
-
-</sect2>
-
-<sect2 id="commit-patch">
-<title>Committing a patch</title>
-
-<para>
-Once your patch is complete and you have run the testcases to make sure you
-didn't break anything, and reviewed the patch to check your work, it can be
-committed to the source control system, provided that any interface changes
-have <link linkend="define-interfaces">been discussed</link> if required.
-How this is done depends on whether you have commit rights for the affected
-module(s). If you do, you can simply use <command>svn ci</command>. If you do
-not, send the patch to the owner of the module for integration, with a brief
-description of your changes for the source control logs:
-</para>
-
-<sect3 id="kernel-ci">
-<title>IMP kernel</title>
-<para>
-All changes to the IMP kernel, since they affect everybody, must be approved
-by Ben. Send your patch to <email>imp-dev@salilab.org</email> for integration.
-</para>
-</sect3>
-
-<sect3 id="core-misc-ci">
-<title>core and misc modules</title>
-<para>
-Anybody can commit to these modules after approval; ask Ben to get your
-account activated.
-</para>
-</sect3>
-
-<sect3 id="other-ci">
-<title>Other modules</title>
-<para>
-Domain-specific modules all have a responsible owner, and it is up to them
-whether they want to allow others commit rights. Email them and ask for
-commit rights (a sysadmin can add these), or send them your patch for
-integration. If in doubt, post it on the <email>imp-dev@salilab.org</email>
-mailing list.
-</para>
-</sect3>
-
-</sect2>
-
-<sect2 id="code-maturity">
-<title>Code maturity</title>
-<para>
-IMP is a work shared by many developers, and they would prefer not to have
-spend time working around problems introduced by others elsewhere in the code.
-Therefore, it is expected that any code committed to IMP should at least
-compile. Any test cases you write for your code should also be expected to
-pass, or at least if they do not, you should quickly fix things so that they
-do. (As a rule of thumb, your changes should not break the nightly builds
-for more than 3 consecutive days; if they do, your changes risk being reverted.)
-</para>
-
-<para>
-It is fine to add code to IMP that is not yet fully complete or ready for
-others to use (provided that it compiles and tests, as above). However, any
-such classes or methods should be marked in their Doxygen comments as
-immature.
-</para>
-
-</sect2>
-
-<sect2 id="bugs">
-<title>Finding and fixing bugs in IMP</title>
-<para>
-If you find a bug in IMP, please report it on the
-<ulink url="https://salilab.org/imp/bugs/">IMP bug tracker</ulink>. This will
-ensure it does not get lost. The best way to report a bug is to provide a
-short script file that demonstrates the problem.
-</para>
-
-<para>
-If you create a patch which fixes a bug, please cite the bug ID in the commit
-log for that patch. The patch should also include a testcase which triggers
-the bug, so that we can ensure your fix for the bug does not break in future.
-In many cases, the demonstration script in the bug report can be trivially
-adapted into a test case.
-</para>
-
-</sect2>
-
-</sect1>
-
-</chapter>
Index: doc/html/SConscript
===================================================================
--- doc/html/SConscript (revision 1005)
+++ doc/html/SConscript (working copy)
@@ -1,9 +0,0 @@
-import os.path
-
-Import('env')
-
-docbook = env.DocBook("index.html", "../manual.xml")
-
-docdir = env['docdir']
-env.DocBookInstall(os.path.join(docdir, 'index.html'), docbook)
-env.Alias('docinstall', docdir)
Index: doc/html/doxygen
===================================================================
--- doc/html/doxygen (revision 1005)
+++ doc/html/doxygen (working copy)
@@ -1 +0,0 @@
-link ../internal/html/
\ No newline at end of file
Index: doc/SConscript
===================================================================
--- doc/SConscript (revision 1005)
+++ doc/SConscript (working copy)
@@ -1,3 +1,2 @@
-SConscript('html/SConscript')
-SConscript('internal/SConscript')
+SConscript('doxygen/SConscript')
SConscript('examples/SConscript')
Index: doc/internal/doxygen.conf
===================================================================
--- doc/internal/doxygen.conf (revision 1005)
+++ doc/internal/doxygen.conf (working copy)
@@ -1,1486 +0,0 @@
-# Doxyfile 1.5.7
-
-# 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, Farsi, Finnish, French, German, Greek,
-# Hungarian, Italian, Japanese, Japanese-en (Japanese with English messages),
-# Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian, Polish,
-# Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, 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. Each string
-# in this list, if found as the leading text of the brief description, will be
-# stripped from the text and the result after processing the whole list, is
-# used as the annotated text. Otherwise, the brief description is used as-is.
-# If left blank, the following values are used ("$name" is automatically
-# replaced with the name of the entity): "The $name class" "The $name widget"
-# "The $name file" "is" "provides" "specifies" "contains"
-# "represents" "a" "an" "the"
-
-ABBREVIATE_BRIEF =
-
-# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
-# Doxygen will generate a detailed section even if there is only a brief
-# description.
-
-ALWAYS_DETAILED_SEC = NO
-
-# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
-# inherited members of a class in the documentation of that class as if those
-# members were ordinary class members. Constructors, destructors and assignment
-# operators of the base classes will not be shown.
-
-INLINE_INHERITED_MEMB = YES
-
-# If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
-# path before files name in the file list and in the header files. If set
-# to NO the shortest path that makes the file name unique will be used.
-
-FULL_PATH_NAMES = NO
-
-# If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
-# can be used to strip a user-defined part of the path. Stripping is
-# only done if one of the specified strings matches the left-hand part of
-# the path. The tag can be used to show relative paths in the file list.
-# If left blank the directory from which doxygen is run is used as the
-# path to strip.
-
-STRIP_FROM_PATH =
-
-# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
-# the path mentioned in the documentation of a class, which tells
-# the reader which header file to include in order to use a class.
-# If left blank only the name of the header file containing the class
-# definition is used. Otherwise one should specify the include paths that
-# are normally passed to the compiler using the -I flag.
-
-STRIP_FROM_INC_PATH =
-
-# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
-# (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 regular Qt-style comments
-# (thus requiring an explicit @brief command for a brief description.)
-
-JAVADOC_AUTOBRIEF = NO
-
-# If the QT_AUTOBRIEF tag is set to YES then Doxygen will
-# interpret the first line (until the first dot) of a Qt-style
-# comment as the brief description. If set to NO, the comments
-# will behave just like regular Qt-style comments (thus requiring
-# an explicit \brief command for a brief description.)
-
-QT_AUTOBRIEF = NO
-
-# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
-# 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
-# description. Set this tag to YES if you prefer the old behaviour instead.
-
-MULTILINE_CPP_IS_BRIEF = NO
-
-# If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
-# member inherits the documentation from any documented member that it
-# re-implements.
-
-INHERIT_DOCS = YES
-
-# If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
-# a new page for each member. If set to NO, the documentation of a member will
-# be part of the file/class/namespace that contains it.
-
-SEPARATE_MEMBER_PAGES = NO
-
-# The TAB_SIZE tag can be used to set the number of spaces in a tab.
-# Doxygen uses this value to replace tabs by spaces in code fragments.
-
-TAB_SIZE = 2
-
-# This tag can be used to specify a number of aliases that acts
-# as commands in the documentation. An alias has the form "name=value".
-# For example adding "sideeffect=\par Side Effects:\n" will allow you to
-# put the command \sideeffect (or @sideeffect) in the documentation, which
-# will result in a user-defined paragraph with heading "Side Effects:".
-# You can put \n's in the value part of an alias to insert newlines.
-
-ALIASES = "command{1}=\code \1 \endcode" \
- "imp=\p IMP"
-
-# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
-# sources only. Doxygen will then generate output that is more tailored for C.
-# For instance, some of the names that are used will be different. The list
-# of all members will be omitted, etc.
-
-OPTIMIZE_OUTPUT_FOR_C = YES
-
-# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
-# sources only. Doxygen will then generate output that is more tailored for
-# Java. For instance, namespaces will be presented as packages, qualified
-# scopes will look different, etc.
-
-OPTIMIZE_OUTPUT_JAVA = NO
-
-# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
-# sources only. Doxygen will then generate output that is more tailored for
-# Fortran.
-
-OPTIMIZE_FOR_FORTRAN = NO
-
-# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
-# sources. Doxygen will then generate output that is tailored for
-# VHDL.
-
-OPTIMIZE_OUTPUT_VHDL = NO
-
-# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
-# to include (a tag file for) the STL sources as input, then you should
-# set this tag to YES in order to let doxygen match functions declarations and
-# definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
-# func(std::string) {}). This also make the inheritance and collaboration
-# diagrams that involve STL classes more complete and accurate.
-
-BUILTIN_STL_SUPPORT = YES
-
-# If you use Microsoft's C++/CLI language, you should set this option to YES to
-# enable parsing support.
-
-CPP_CLI_SUPPORT = NO
-
-# Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
-# Doxygen will parse them like normal C++ but will assume all classes use public
-# instead of private inheritance when no explicit protection keyword is present.
-
-SIP_SUPPORT = NO
-
-# For Microsoft's IDL there are propget and propput attributes to indicate getter
-# and setter methods for a property. Setting this option to YES (the default)
-# will make doxygen to replace the get and set methods by a property in the
-# documentation. This will only work if the methods are indeed getting or
-# setting a simple type. If this is not the case, or you want to show the
-# methods anyway, you should set this option to NO.
-
-IDL_PROPERTY_SUPPORT = YES
-
-# 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.
-
-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
-
-# When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
-# is documented as struct, union, or enum with the name of the typedef. So
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
-# with name TypeT. When disabled the typedef will appear as a member of a file,
-# namespace, or class. And the struct will be named TypeS. This can typically
-# be useful for C code in case the coding convention dictates that all compound
-# types are typedef'ed and only the typedef is referenced, never the tag name.
-
-TYPEDEF_HIDES_STRUCT = NO
-
-# The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
-# determine which symbols to keep in memory and which to flush to disk.
-# When the cache is full, less often used symbols will be written to disk.
-# For small to medium size projects (<1000 input files) the default value is
-# probably good enough. For larger projects a too small cache size can cause
-# doxygen to be busy swapping symbols to and from disk most of the time
-# causing a significant performance penality.
-# If the system has enough physical memory increasing the cache will improve the
-# performance by keeping more symbols in memory. Note that the value works on
-# a logarithmic scale so increasing the size by one will rougly double the
-# memory usage. The cache size is given by this formula:
-# 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
-# corresponding to a cache size of 2^16 = 65536 symbols
-
-SYMBOL_CACHE_SIZE = 0
-
-#---------------------------------------------------------------------------
-# 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 = NO
-
-# 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 = NO
-
-# 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 this flag is set to YES, the members of anonymous namespaces will be
-# extracted and appear in the documentation as a namespace called
-# 'anonymous_namespace{file}', where file will be replaced with the base
-# name of the file that contains the anonymous namespace. By default
-# anonymous namespace are hidden.
-
-EXTRACT_ANON_NSPACES = 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.
-
-HIDE_UNDOC_MEMBERS = YES
-
-# If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
-# undocumented classes that are normally visible in the class hierarchy.
-# If set to NO (the default) these classes will be included in the various
-# overviews. This option has no effect if EXTRACT_ALL is enabled.
-
-HIDE_UNDOC_CLASSES = YES
-
-# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
-# friend (class|struct|union) declarations.
-# If set to NO (the default) these declarations will be included in the
-# documentation.
-
-HIDE_FRIEND_COMPOUNDS = YES
-
-# If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
-# documentation blocks found inside the body of a function.
-# 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 = NO
-
-# 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_GROUP_NAMES tag is set to YES then doxygen will sort the
-# hierarchy of group names into alphabetical order. If set to NO (the default)
-# the group names will appear in their defined order.
-
-SORT_GROUP_NAMES = 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 = NO
-
-# 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 = NO
-
-# 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
-
-# Set the SHOW_FILES tag to NO to disable the generation of the Files page.
-# This will remove the Files entry from the Quick Index and from the
-# Folder Tree View (if specified). The default is YES.
-
-SHOW_FILES = NO
-
-# Set the SHOW_NAMESPACES tag to NO to disable the generation of the
-# Namespaces page. This will remove the Namespaces entry from the Quick Index
-# and from the Folder Tree View (if specified). The default is YES.
-
-SHOW_NAMESPACES = YES
-
-# 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 =
-
-# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed by
-# doxygen. The layout file controls the global structure of the generated output files
-# in an output format independent way. The create the layout file that represents
-# doxygen's defaults, run doxygen with the -l option. You can optionally specify a
-# file name after the option, if omitted DoxygenLayout.xml will be used as the name
-# of the layout file.
-
-LAYOUT_FILE =
-
-#---------------------------------------------------------------------------
-# 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_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 = ../../build/include \
- ../../kernel/doc \
- ../../modules/core/doc \
- ../../modules/misc/doc \
- ../../modules/em/doc \
- ../../modules/domino/doc \
- ../../modules/modeller/doc \
- ../../modules/saxs/doc
-
-
-# This tag can be used to specify the character encoding of the source files
-# that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
-# 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_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 *.f90
-
-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.
-
-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_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.* \
- */internal/* \
- */imp2.py \
- */.svn \
- ._*
-
-# 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_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 = ../examples
-
-# 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 = *.py
-
-# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
-# searched for input files to be used with the \include or \dontinclude
-# commands irrespective of the value of the RECURSIVE tag.
-# Possible values are YES and NO. If left blank NO is used.
-
-EXAMPLE_RECURSIVE = YES
-
-# 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
-# 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
-# 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 = ../../kernel/doc/header.html
-
-# The HTML_FOOTER tag can be used to specify a personal HTML footer for
-# each generated HTML page. If it is left blank doxygen will generate a
-# standard footer.
-
-HTML_FOOTER = ../../kernel/doc/footer.html
-
-# The HTML_STYLESHEET tag can be used to specify a user-defined cascading
-# style sheet that is used by each HTML page. It can be used to
-# 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 HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
-# documentation will contain sections that can be hidden and shown after the
-# page has loaded. For this to work a browser that supports
-# JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
-# Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
-
-HTML_DYNAMIC_SECTIONS = YES
-
-# If the GENERATE_DOCSET tag is set to YES, additional index files
-# will be generated that can be used as input for Apple's Xcode 3
-# integrated development environment, introduced with OSX 10.5 (Leopard).
-# To create a documentation set, doxygen will generate a Makefile in the
-# HTML output directory. Running make will produce the docset in that
-# directory and running "make install" will install the docset in
-# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
-# it at startup.
-# See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html for more information.
-
-GENERATE_DOCSET = YES
-
-# When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
-# feed. A documentation feed provides an umbrella under which multiple
-# documentation sets from a single provider (such as a company or product suite)
-# can be grouped.
-
-DOCSET_FEEDNAME = IMP
-
-# When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
-# should uniquely identify the documentation set bundle. This should be a
-# reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
-# will append .docset to the name.
-
-DOCSET_BUNDLE_ID = org.salilab.imp
-
-# If the GENERATE_HTMLHELP tag is set to YES, additional index files
-# will be generated that can be used as input for tools like the
-# Microsoft HTML help workshop to generate a compiled 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.
-
-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 CHM_INDEX_ENCODING
-# is used to encode HtmlHelp index (hhk), content (hhc) and project file
-# content.
-
-CHM_INDEX_ENCODING =
-
-# 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
-
-# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and QHP_VIRTUAL_FOLDER
-# are set, an additional index file will be generated that can be used as input for
-# Qt's qhelpgenerator to generate a Qt Compressed Help (.qch) of the generated
-# HTML documentation.
-
-GENERATE_QHP = NO
-
-# If the QHG_LOCATION tag is specified, the QCH_FILE tag can
-# be used to specify the file name of the resulting .qch file.
-# The path specified is relative to the HTML output folder.
-
-QCH_FILE =
-
-# The QHP_NAMESPACE tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# <a href="http://doc.trolltech.com/qthelpproject.html#namespace">Qt Help Project / Namespace</a>.
-
-QHP_NAMESPACE = org.doxygen.Project
-
-# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
-# Qt Help Project output. For more information please see
-# <a href="http://doc.trolltech.com/qthelpproject.html#virtual-folders">Qt Help Project / Virtual Folders</a>.
-
-QHP_VIRTUAL_FOLDER = doc
-
-# If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
-# be used to specify the location of Qt's qhelpgenerator.
-# If non-empty doxygen will try to run qhelpgenerator on the generated
-# .qhp file .
-
-QHG_LOCATION =
-
-# 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
-
-# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
-# structure should be generated to display hierarchical information.
-# If the tag value is set to FRAME, 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. Other possible values
-# for this tag are: HIERARCHIES, which will generate the Groups, Directories,
-# and Class Hierarchy pages using a tree view instead of an ordered list;
-# ALL, which combines the behavior of FRAME and HIERARCHIES; and NONE, which
-# disables this behavior completely. For backwards compatibility with previous
-# releases of Doxygen, the values YES and NO are equivalent to FRAME and NONE
-# respectively.
-
-GENERATE_TREEVIEW = HIERARCHIES
-
-# 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
-
-# Use this tag to change the font size of Latex formulas included
-# as images in the HTML documentation. The default is 10. Note that
-# when you change the font size after a successful doxygen run you need
-# to manually remove any form_*.png images from the HTML output directory
-# to force them to be regenerated.
-
-FORMULA_FONTSIZE = 10
-
-#---------------------------------------------------------------------------
-# 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 = ../../build/include
-
-# 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 = *.h
-
-# The PREDEFINED tag can be used to specify one or more macro names that
-# are defined before the preprocessor is started (similar to the -D option of
-# 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
-
-# By default doxygen will write a font called FreeSans.ttf to the output
-# directory and reference it in all dot files that doxygen generates. This
-# font does not include all possible unicode characters however, so when you need
-# these (or just want a differently looking font) you can specify the font name
-# using DOT_FONTNAME. You need need to make sure dot is able to find the font,
-# which can be done by putting it in a standard location or by setting the
-# DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory
-# containing the font.
-
-DOT_FONTNAME = FreeSans
-
-# By default doxygen will tell dot to use the output directory to look for the
-# FreeSans.ttf font (which doxygen will put there itself). If you specify a
-# different font using DOT_FONTNAME you can set the path where dot
-# can find it using this tag.
-
-DOT_FONTPATH =
-
-# 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 = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# 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 options 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 = NO
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are png, jpg, or gif
-# 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 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 if the
-# number of direct children of the root node in a graph is already larger than
-# DOT_GRAPH_MAX_NODES then the graph will not be shown at all. Also note
-# that the size of a graph can be further restricted by MAX_DOT_GRAPH_DEPTH.
-
-DOT_GRAPH_MAX_NODES = 50
-
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
-# graphs generated by dot. A depth value of 3 means that only nodes reachable
-# from the root by following a path via at most 3 edges will be shown. Nodes
-# that lay further from the root node will be omitted. Note that setting this
-# option to 1 or 2 may greatly reduce the computation time needed for large
-# code bases. Also note that the size of a graph can be further restricted by
-# DOT_GRAPH_MAX_NODES. Using a depth of 0 means no depth restriction.
-
-MAX_DOT_GRAPH_DEPTH = 1000
-
-# Set the DOT_TRANSPARENT tag to YES to generate images with a transparent
-# background. This is disabled by default, because dot on Windows does not
-# seem to support this out of the box. 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).
-
-DOT_TRANSPARENT = YES
-
-# Set the DOT_MULTI_TARGETS tag to YES allow dot to generate multiple output
-# files in one run (i.e. multiple -o and -T options on the command line). This
-# makes dot run faster, but since only newer versions of dot (>1.8.10)
-# support this, this feature is disabled by default.
-
-DOT_MULTI_TARGETS = YES
-
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
-# generate a legend page explaining the meaning of the various boxes and
-# 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 = YES
Index: doc/internal/SConscript
===================================================================
--- doc/internal/SConscript (revision 1005)
+++ doc/internal/SConscript (working copy)
@@ -1,14 +0,0 @@
-Import('env')
-
-import os.path
-
-dox = env.Doxygen("doxygen.conf")
-# Force the population of the build/include/ directory with generated headers
-env.Depends(dox, '#/build/include')
-
-docdir = os.path.join(env['docdir'], 'doxygen')
-
-# Install all files from 'dox' directory into the 'docdir' directory (cannot
-# use env.InstallAs() right now, due to scons bug #1751)
-env.Command(Dir(env.subst(docdir)), dox,
- "install -d $TARGET && install ${SOURCE.dir}/* $TARGET")
Index: doc/manual.xml
===================================================================
--- doc/manual.xml (revision 1005)
+++ doc/manual.xml (working copy)
@@ -1,38 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<!DOCTYPE book PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
- "http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd" [
- <!ENTITY IMP "<application>IMP</application>">
- <!ENTITY MODELLER "<application>MODELLER</application>">
- <!ENTITY doxygen "doxygen/">
- <!ENTITY usage SYSTEM "usage.xml">
-]>
-<book lang="en">
-
-<bookinfo>
-<title>IMP, an Integrative Modeling Platform</title>
-<authorgroup>
- <author><firstname>Andrej</firstname> <surname>Šali</surname></author>
- <author><firstname>Bret</firstname> <surname>Peterson</surname></author>
- <author><firstname>Ben</firstname> <surname>Webb</surname></author>
- <author><firstname>Daniel</firstname> <surname>Russel</surname></author>
-</authorgroup>
-<address>
-University of California at San Francisco
-California Institute for Quantitiative Biomedical Research
-<street>1700 4th Street</street>, Rm 503B
-<city>San Francisco</city>, <state>CA</state> <postcode>94158</postcode>
-<phone>+1-415-514 4227</phone>
-<fax>+1-415-514 4231</fax>
-<email>sali@salilab.org</email>
-</address>
-
-<copyright>
-<year>2007-2008</year>
-<holder>Andrej Šali</holder>
-</copyright>
-
-</bookinfo>
-
-&usage;
-
-</book>
Property changes on: doc/doxygen
___________________________________________________________________
Added: svn:mergeinfo
Index: doc/doxygen/doxygen.conf
===================================================================
--- doc/doxygen/doxygen.conf (revision 1005)
+++ doc/doxygen/doxygen.conf (working copy)
@@ -765,7 +765,7 @@
# 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
+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
@@ -1227,7 +1227,7 @@
# undefined via #undef or recursively expanded use the := operator
# instead of the = operator.
-PREDEFINED =
+PREDEFINED = IMP_DOXYGEN
# 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.