adding doxygraph support to build UML diagrams from doxygen...

adding Implicit MR support

doc/Doxyfile

@@ -1390,7 +1390,7 @@ MAN_LINKS              = NO
 # generate an XML file that captures the structure of
 # the code including all documentation.
 
-GENERATE_XML           = NO
+GENERATE_XML           = YES
 
 # 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

doc/doxygraph/COPYING

+Mozilla Public License Version 2.0
+==================================
+
+1. Definitions
+--------------
+
+1.1. "Contributor"
+    means each individual or legal entity that creates, contributes to
+    the creation of, or owns Covered Software.
+
+1.2. "Contributor Version"
+    means the combination of the Contributions of others (if any) used
+    by a Contributor and that particular Contributor's Contribution.
+
+1.3. "Contribution"
+    means Covered Software of a particular Contributor.
+
+1.4. "Covered Software"
+    means Source Code Form to which the initial Contributor has attached
+    the notice in Exhibit A, the Executable Form of such Source Code
+    Form, and Modifications of such Source Code Form, in each case
+    including portions thereof.
+
+1.5. "Incompatible With Secondary Licenses"
+    means
+
+    (a) that the initial Contributor has attached the notice described
+        in Exhibit B to the Covered Software; or
+
+    (b) that the Covered Software was made available under the terms of
+        version 1.1 or earlier of the License, but not also under the
+        terms of a Secondary License.
+
+1.6. "Executable Form"
+    means any form of the work other than Source Code Form.
+
+1.7. "Larger Work"
+    means a work that combines Covered Software with other material, in 
+    a separate file or files, that is not Covered Software.
+
+1.8. "License"
+    means this document.
+
+1.9. "Licensable"
+    means having the right to grant, to the maximum extent possible,
+    whether at the time of the initial grant or subsequently, any and
+    all of the rights conveyed by this License.
+
+1.10. "Modifications"
+    means any of the following:
+
+    (a) any file in Source Code Form that results from an addition to,
+        deletion from, or modification of the contents of Covered
+        Software; or
+
+    (b) any new file in Source Code Form that contains any Covered
+        Software.
+
+1.11. "Patent Claims" of a Contributor
+    means any patent claim(s), including without limitation, method,
+    process, and apparatus claims, in any patent Licensable by such
+    Contributor that would be infringed, but for the grant of the
+    License, by the making, using, selling, offering for sale, having
+    made, import, or transfer of either its Contributions or its
+    Contributor Version.
+
+1.12. "Secondary License"
+    means either the GNU General Public License, Version 2.0, the GNU
+    Lesser General Public License, Version 2.1, the GNU Affero General
+    Public License, Version 3.0, or any later versions of those
+    licenses.
+
+1.13. "Source Code Form"
+    means the form of the work preferred for making modifications.
+
+1.14. "You" (or "Your")
+    means an individual or a legal entity exercising rights under this
+    License. For legal entities, "You" includes any entity that
+    controls, is controlled by, or is under common control with You. For
+    purposes of this definition, "control" means (a) the power, direct
+    or indirect, to cause the direction or management of such entity,
+    whether by contract or otherwise, or (b) ownership of more than
+    fifty percent (50%) of the outstanding shares or beneficial
+    ownership of such entity.
+
+2. License Grants and Conditions
+--------------------------------
+
+2.1. Grants
+
+Each Contributor hereby grants You a world-wide, royalty-free,
+non-exclusive license:
+
+(a) under intellectual property rights (other than patent or trademark)
+    Licensable by such Contributor to use, reproduce, make available,
+    modify, display, perform, distribute, and otherwise exploit its
+    Contributions, either on an unmodified basis, with Modifications, or
+    as part of a Larger Work; and
+
+(b) under Patent Claims of such Contributor to make, use, sell, offer
+    for sale, have made, import, and otherwise transfer either its
+    Contributions or its Contributor Version.
+
+2.2. Effective Date
+
+The licenses granted in Section 2.1 with respect to any Contribution
+become effective for each Contribution on the date the Contributor first
+distributes such Contribution.
+
+2.3. Limitations on Grant Scope
+
+The licenses granted in this Section 2 are the only rights granted under
+this License. No additional rights or licenses will be implied from the
+distribution or licensing of Covered Software under this License.
+Notwithstanding Section 2.1(b) above, no patent license is granted by a
+Contributor:
+
+(a) for any code that a Contributor has removed from Covered Software;
+    or
+
+(b) for infringements caused by: (i) Your and any other third party's
+    modifications of Covered Software, or (ii) the combination of its
+    Contributions with other software (except as part of its Contributor
+    Version); or
+
+(c) under Patent Claims infringed by Covered Software in the absence of
+    its Contributions.
+
+This License does not grant any rights in the trademarks, service marks,
+or logos of any Contributor (except as may be necessary to comply with
+the notice requirements in Section 3.4).
+
+2.4. Subsequent Licenses
+
+No Contributor makes additional grants as a result of Your choice to
+distribute the Covered Software under a subsequent version of this
+License (see Section 10.2) or under the terms of a Secondary License (if
+permitted under the terms of Section 3.3).
+
+2.5. Representation
+
+Each Contributor represents that the Contributor believes its
+Contributions are its original creation(s) or it has sufficient rights
+to grant the rights to its Contributions conveyed by this License.
+
+2.6. Fair Use
+
+This License is not intended to limit any rights You have under
+applicable copyright doctrines of fair use, fair dealing, or other
+equivalents.
+
+2.7. Conditions
+
+Sections 3.1, 3.2, 3.3, and 3.4 are conditions of the licenses granted
+in Section 2.1.
+
+3. Responsibilities
+-------------------
+
+3.1. Distribution of Source Form
+
+All distribution of Covered Software in Source Code Form, including any
+Modifications that You create or to which You contribute, must be under
+the terms of this License. You must inform recipients that the Source
+Code Form of the Covered Software is governed by the terms of this
+License, and how they can obtain a copy of this License. You may not
+attempt to alter or restrict the recipients' rights in the Source Code
+Form.
+
+3.2. Distribution of Executable Form
+
+If You distribute Covered Software in Executable Form then:
+
+(a) such Covered Software must also be made available in Source Code
+    Form, as described in Section 3.1, and You must inform recipients of
+    the Executable Form how they can obtain a copy of such Source Code
+    Form by reasonable means in a timely manner, at a charge no more
+    than the cost of distribution to the recipient; and
+
+(b) You may distribute such Executable Form under the terms of this
+    License, or sublicense it under different terms, provided that the
+    license for the Executable Form does not attempt to limit or alter
+    the recipients' rights in the Source Code Form under this License.
+
+3.3. Distribution of a Larger Work
+
+You may create and distribute a Larger Work under terms of Your choice,
+provided that You also comply with the requirements of this License for
+the Covered Software. If the Larger Work is a combination of Covered
+Software with a work governed by one or more Secondary Licenses, and the
+Covered Software is not Incompatible With Secondary Licenses, this
+License permits You to additionally distribute such Covered Software
+under the terms of such Secondary License(s), so that the recipient of
+the Larger Work may, at their option, further distribute the Covered
+Software under the terms of either this License or such Secondary
+License(s).
+
+3.4. Notices
+
+You may not remove or alter the substance of any license notices
+(including copyright notices, patent notices, disclaimers of warranty,
+or limitations of liability) contained within the Source Code Form of
+the Covered Software, except that You may alter any license notices to
+the extent required to remedy known factual inaccuracies.
+
+3.5. Application of Additional Terms
+
+You may choose to offer, and to charge a fee for, warranty, support,
+indemnity or liability obligations to one or more recipients of Covered
+Software. However, You may do so only on Your own behalf, and not on
+behalf of any Contributor. You must make it absolutely clear that any
+such warranty, support, indemnity, or liability obligation is offered by
+You alone, and You hereby agree to indemnify every Contributor for any
+liability incurred by such Contributor as a result of warranty, support,
+indemnity or liability terms You offer. You may include additional
+disclaimers of warranty and limitations of liability specific to any
+jurisdiction.
+
+4. Inability to Comply Due to Statute or Regulation
+---------------------------------------------------
+
+If it is impossible for You to comply with any of the terms of this
+License with respect to some or all of the Covered Software due to
+statute, judicial order, or regulation then You must: (a) comply with
+the terms of this License to the maximum extent possible; and (b)
+describe the limitations and the code they affect. Such description must
+be placed in a text file included with all distributions of the Covered
+Software under this License. Except to the extent prohibited by statute
+or regulation, such description must be sufficiently detailed for a
+recipient of ordinary skill to be able to understand it.
+
+5. Termination
+--------------
+
+5.1. The rights granted under this License will terminate automatically
+if You fail to comply with any of its terms. However, if You become
+compliant, then the rights granted under this License from a particular
+Contributor are reinstated (a) provisionally, unless and until such
+Contributor explicitly and finally terminates Your grants, and (b) on an
+ongoing basis, if such Contributor fails to notify You of the
+non-compliance by some reasonable means prior to 60 days after You have
+come back into compliance. Moreover, Your grants from a particular
+Contributor are reinstated on an ongoing basis if such Contributor
+notifies You of the non-compliance by some reasonable means, this is the
+first time You have received notice of non-compliance with this License
+from such Contributor, and You become compliant prior to 30 days after
+Your receipt of the notice.
+
+5.2. If You initiate litigation against any entity by asserting a patent
+infringement claim (excluding declaratory judgment actions,
+counter-claims, and cross-claims) alleging that a Contributor Version
+directly or indirectly infringes any patent, then the rights granted to
+You by any and all Contributors for the Covered Software under Section
+2.1 of this License shall terminate.
+
+5.3. In the event of termination under Sections 5.1 or 5.2 above, all
+end user license agreements (excluding distributors and resellers) which
+have been validly granted by You or Your distributors under this License
+prior to termination shall survive termination.
+
+************************************************************************
+*                                                                      *
+*  6. Disclaimer of Warranty                                           *
+*  -------------------------                                           *
+*                                                                      *
+*  Covered Software is provided under this License on an "as is"       *
+*  basis, without warranty of any kind, either expressed, implied, or  *
+*  statutory, including, without limitation, warranties that the       *
+*  Covered Software is free of defects, merchantable, fit for a        *
+*  particular purpose or non-infringing. The entire risk as to the     *
+*  quality and performance of the Covered Software is with You.        *
+*  Should any Covered Software prove defective in any respect, You     *
+*  (not any Contributor) assume the cost of any necessary servicing,   *
+*  repair, or correction. This disclaimer of warranty constitutes an   *
+*  essential part of this License. No use of any Covered Software is   *
+*  authorized under this License except under this disclaimer.         *
+*                                                                      *
+************************************************************************
+
+************************************************************************
+*                                                                      *
+*  7. Limitation of Liability                                          *
+*  --------------------------                                          *
+*                                                                      *
+*  Under no circumstances and under no legal theory, whether tort      *
+*  (including negligence), contract, or otherwise, shall any           *
+*  Contributor, or anyone who distributes Covered Software as          *
+*  permitted above, be liable to You for any direct, indirect,         *
+*  special, incidental, or consequential damages of any character      *
+*  including, without limitation, damages for lost profits, loss of    *
+*  goodwill, work stoppage, computer failure or malfunction, or any    *
+*  and all other commercial damages or losses, even if such party      *
+*  shall have been informed of the possibility of such damages. This   *
+*  limitation of liability shall not apply to liability for death or   *
+*  personal injury resulting from such party's negligence to the       *
+*  extent applicable law prohibits such limitation. Some               *
+*  jurisdictions do not allow the exclusion or limitation of           *
+*  incidental or consequential damages, so this exclusion and          *
+*  limitation may not apply to You.                                    *
+*                                                                      *
+************************************************************************
+
+8. Litigation
+-------------
+
+Any litigation relating to this License may be brought only in the
+courts of a jurisdiction where the defendant maintains its principal
+place of business and such litigation shall be governed by laws of that
+jurisdiction, without reference to its conflict-of-law provisions.
+Nothing in this Section shall prevent a party's ability to bring
+cross-claims or counter-claims.
+
+9. Miscellaneous
+----------------
+
+This License represents the complete agreement concerning the subject
+matter hereof. If any provision of this License is held to be
+unenforceable, such provision shall be reformed only to the extent
+necessary to make it enforceable. Any law or regulation which provides
+that the language of a contract shall be construed against the drafter
+shall not be used to construe this License against a Contributor.
+
+10. Versions of the License
+---------------------------
+
+10.1. New Versions
+
+Mozilla Foundation is the license steward. Except as provided in Section
+10.3, no one other than the license steward has the right to modify or
+publish new versions of this License. Each version will be given a
+distinguishing version number.
+
+10.2. Effect of New Versions
+
+You may distribute the Covered Software under the terms of the version
+of the License under which You originally received the Covered Software,
+or under the terms of any subsequent version published by the license
+steward.
+
+10.3. Modified Versions
+
+If you create software not governed by this License, and you want to
+create a new license for such software, you may create and use a
+modified version of this License if you rename the license and remove
+any references to the name of the license steward (except to note that
+such modified license differs from this License).
+
+10.4. Distributing Source Code Form that is Incompatible With Secondary
+Licenses
+
+If You choose to distribute Source Code Form that is Incompatible With
+Secondary Licenses under the terms of this version of the License, the
+notice described in Exhibit B of this License must be attached.
+
+Exhibit A - Source Code Form License Notice
+-------------------------------------------
+
+  This Source Code Form is subject to the terms of the Mozilla Public
+  License, v. 2.0. If a copy of the MPL was not distributed with this
+  file, You can obtain one at http://mozilla.org/MPL/2.0/.
+
+If it is not possible or desirable to put the notice in a particular
+file, then You may include the notice in a location (such as a LICENSE
+file in a relevant directory) where a recipient would be likely to look
+for such a notice.
+
+You may add additional accurate notices of copyright ownership.
+
+Exhibit B - "Incompatible With Secondary Licenses" Notice
+---------------------------------------------------------
+
+  This Source Code Form is "Incompatible With Secondary Licenses", as
+  defined by the Mozilla Public License, v. 2.0.

doc/doxygraph/README

+About
+=====
+
+http://code.google.com/p/doxygraph
+
+This is doxygraph, a free system for reverse engineering UML class diagrams
+from source code, and presenting those diagrams as interactive web apps. It
+relies on Doxygen for parsing source code, so it supports all the languages
+that Doxygen supports: C, C++, C#, Objective C, Java, Python, PHP, Tcl, D, IDL,
+VHDL, and Fortran.
+
+Doxygraph is composed of two parts:
+
+doxygraph
+	A Perl script that will generate a diagram in Graphviz dot format, using
+	as input the XML based format generated by Doxygen.
+
+doxyviz
+	A JavaScript app that will interactively present a diagram generated
+	by the doxygraph Perl script. The manipulation and rendering of graphs
+	relies on bindviz, which is an automated JavaScript port of Graphviz
+	ported using emscripten.
+
+Quick Start
+===========
+
+If you have a project for which you want to generate a class diagram, and you
+are already using Doxygen to generate API documentation for this project, then
+as a preliminary step, you simply need to edit your Doxyfile and ensure that it
+sets the option GENERATE_XML = YES.
+
+If you are not already using Doxygen to generate API documentation for your
+project, then the preliminary step is to install Doxygen and configure it to
+process your project's header files. This is a simple process, documented at
+http://www.doxygen.org/. During this process, make sure to set the option
+GENERATE_XML = YES. In addition, if you set the option EXTRACT_ALL = YES then
+you won't need to worry about adding special Doxygen comments to all of your
+classes; this option will cause Doxygen to parse the classes even if the
+comments are not present.
+
+When you have a project with a Doxyfile properly set up for generating Doxygen
+XML files from your project's header files, then the first step in the doxygraph
+pipeline is to run Doxygen, which will generate a set of XML files.
+
+If you don't have a specific project for which you want to generate a diagram,
+but just want to try out doxygraph and see how it works, there are some example
+Doxygen XML files provided in the examples directory.
+
+When you have your Doxygen XML files, the next step is to run the following
+command from within the doxygraph root directory, which will convert the XML
+files into a Graphviz dot file:
+perl doxygraph/doxygraph /path/to/your/index.xml doxyviz/htdocs/graph.dot
+
+If Perl emits any errors of the form "Can't locate ____ in @INC", that is
+usually an indication that you are missing one or more of the dependencies of
+the script, which can easily be installed using Perl's cpan utility.
+
+When you have generated your graph.dot file, then you are ready to go. You
+can open doxyviz/htdocs/index.html in your web browser to view your interactive
+UML class diagram locally, or copy the contents of the htdocs directory into a
+subdirectory of your web server's htdocs directory in order to deploy your
+interactive diagram to the web.
+
+More Details
+============
+
+More detailed documentation for the component parts of doxygraph is provided in
+the relevant subdirectories.
+
+License
+=======
+
+Copyright 2013 Doxygraph project
+
+These Source Code Forms are subject to the terms of the Mozilla Public License
+version 2.0. If a copy of the MPL was not distributed with this file, You can
+obtain one at http://mozilla.org/MPL/2.0/.
\ No newline at end of file

doc/doxygraph/doxygraph/MANIFEST

+doxygraph
+Makefile.PL
+MANIFEST
+lib/Doxygen/XML.pm
+lib/GraphViz/UML.pm
+README
\ No newline at end of file

doc/doxygraph/doxygraph/Makefile.PL

+use ExtUtils::MakeMaker;
+
+WriteMakefile(
+	NAME => 'doxygraph',
+	AUTHOR => 'Doxygraph project http://code.google.com/p/doxygraph',
+	ABSTRACT_FROM => 'doxygraph',
+	VERSION_FROM => 'doxygraph',
+	LICENSE => 'mozilla',
+	EXE_FILES => ['doxygraph'],
+	PREREQ_PM => {qw(
+		File::Spec		0
+		GraphViz2		0
+		Hash::FieldHash		0
+		lib::abs		0
+		Moose			0
+		namespace::autoclean	0
+		XML::Rabbit		0
+	)}
+);
\ No newline at end of file

doc/doxygraph/doxygraph/README

+About
+=====
+
+http://code.google.com/p/doxygraph
+
+This is doxygraph, a Perl script that will generate a diagram in Graphviz dot
+format, using as input the XML based format generated by Doxygen. Doxygraph is
+part of doxygraph, a free system for reverse engineering UML class diagrams from
+source code, and presenting those diagrams as interactive web apps.
+
+Dependencies
+============
+
+The following CPAN modules are required:
+
+    File::Spec
+    GraphViz2
+    Hash::FieldHash
+    lib::abs
+    Moose
+    namespace::autoclean
+    XML::Rabbit
+
+Usage
+=====
+
+The doxygraph Perl script can be used without needing to install it, although a
+Makefile is provided for optional installation.
+
+The script expects two commandline arguments: the first is the name of the input
+file (usually index.xml generated by Doxygen) and the second is the name of the
+output file.
+
+To instruct Doxygen to generate XML output, set the option GENERATE_XML = YES
+in your Doxyfile.
+
+Installation
+============
+
+If you want to install doxygraph, follow the usual procedure for installing Perl
+modules:
+
+    perl Makefile.PL
+    make
+    make install
+
+License
+=======
+
+Copyright 2013 Doxygraph project
+
+These Source Code Forms are subject to the terms of the Mozilla Public License,
+version 2.0. If a copy of the MPL was not distributed with this file, You can
+obtain one at http://mozilla.org/MPL/2.0/.
\ No newline at end of file

doc/doxygraph/doxygraph/doxygraph

+#!/usr/bin/perl
+
+package doxygraph 0.1;
+use strict;
+use warnings;
+use lib::abs 'lib';
+use Doxygen::XML;
+use GraphViz::UML;
+
+@ARGV == 2 or usage();
+grep { /^-/ } @ARGV and usage();
+my ($index, $output) = @ARGV;
+
+my $uml = GraphViz::UML->new;
+my $xml = Doxygen::XML->new({ handler => $uml });
+my @compounds = $xml->parse_index($index);
+$xml->parse_compound($_) for @compounds;
+my $dot = $uml->export->command;
+
+open my $fh, '>', $output or die "$output: $!";
+$dot->foreach(sub { print $fh $_ });
+print $fh "}\n";
+close $fh;
+
+sub usage
+{
+  print STDERR << "EOF";
+Expected commandline usage:
+  doxygraph path/to/index.xml path/to/output.dot
+EOF
+  exit 0;
+}
+
+=head1 NAME
+
+doxygraph - Create Graphviz UML class diagram from Doxygen XML output
+
+=head1 SYNOPSIS
+
+ doxygraph index.xml graph.dot
+
+=head1 DESCRIPTION
+
+Doxygen can output an XML representation of all the documented entities it
+encounters in the source code it examines, by setting C<GENERATE_XML = YES> in
+your C<Doxyfile>. Doxygraph will convert this XML representation into a UML
+class diagram in the format recognized by Graphviz and its C<dot> command.
+
+All the heavy lifting is done in the L<Doxygen::XML> and L<GraphViz::UML>
+modules.
+
+=head1 OPTIONS
+
+None.
+
+=head1 EXAMPLES
+
+ doxygen
+ doxygraph xml/index.xml graph.dot
+ dot -T svg -o graph.svg graph.dot
+
+=head1 AUTHORS
+
+Available through the git repository at L<http://code.google.com/p/doxygraph>.
+
+=head1 COPYRIGHT AND LICENSE
+
+Copyright 2013 Doxygraph project
+
+This Source Code Form is subject to the terms of the Mozilla Public License,
+version 2.0. If a copy of the MPL was not distributed with this file, You can
+obtain one at L<http://mozilla.org/MPL/2.0/>.
+
+=head1 SEE ALSO
+
+L<http://www.doxygen.org/>, L<http://www.graphviz.org/>.

doc/doxygraph/doxygraph/lib/Doxygen/XML.pm

+package Doxygen::XML;
+
+use strict;
+use warnings;
+use namespace::autoclean;
+use Moose;
+use Moose::Util::TypeConstraints;
+use File::Spec;
+
+duck_type 'Doxygen::XML::Handler' => [qw(
+	add_class