Commit 650b2947 authored by Andreas Tille's avatar Andreas Tille

Imported Upstream version 1.2.1

parent bd6ead30

Too many changes to show.

To preserve performance only 136 of 136+ files are displayed.

* Clustal Omega:
Fabian Sievers UCD Dublin, Ireland
Andreas Wilm UCD Dublin, Ireland
David Dineen UCD Dublin, Ireland
Johannes Söding Gene Center Munich, Germany
Michael Remmert Gene Center Munich, Germany
* Clustal 2
Mark Larkin UCD Dublin, Ireland
* Clustal 1.X
Toby Gibson EMBL Heidelberg, Germany
Des Higgins UCC Cork, Ireland
Julie Thompson IGBMC Strasbourg, France
* Contributors:
Chenna Ramu EMBL Heidelberg, Germany
Nigel Brown EMBL Heidelberg, Germany
GNU GENERAL PUBLIC LICENSE
Version 2, June 1991
Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
Preamble
The licenses for most software are designed to take away your
freedom to share and change it. By contrast, the GNU General Public
License is intended to guarantee your freedom to share and change free
software--to make sure the software is free for all its users. This
General Public License applies to most of the Free Software
Foundation's software and to any other program whose authors commit to
using it. (Some other Free Software Foundation software is covered by
the GNU Lesser General Public License instead.) You can apply it to
your programs, too.
When we speak of free software, we are referring to freedom, not
price. Our General Public Licenses are designed to make sure that you
have the freedom to distribute copies of free software (and charge for
this service if you wish), that you receive source code or can get it
if you want it, that you can change the software or use pieces of it
in new free programs; and that you know you can do these things.
To protect your rights, we need to make restrictions that forbid
anyone to deny you these rights or to ask you to surrender the rights.
These restrictions translate to certain responsibilities for you if you
distribute copies of the software, or if you modify it.
For example, if you distribute copies of such a program, whether
gratis or for a fee, you must give the recipients all the rights that
you have. You must make sure that they, too, receive or can get the
source code. And you must show them these terms so they know their
rights.
We protect your rights with two steps: (1) copyright the software, and
(2) offer you this license which gives you legal permission to copy,
distribute and/or modify the software.
Also, for each author's protection and ours, we want to make certain
that everyone understands that there is no warranty for this free
software. If the software is modified by someone else and passed on, we
want its recipients to know that what they have is not the original, so
that any problems introduced by others will not reflect on the original
authors' reputations.
Finally, any free program is threatened constantly by software
patents. We wish to avoid the danger that redistributors of a free
program will individually obtain patent licenses, in effect making the
program proprietary. To prevent this, we have made it clear that any
patent must be licensed for everyone's free use or not licensed at all.
The precise terms and conditions for copying, distribution and
modification follow.
GNU GENERAL PUBLIC LICENSE
TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION
0. This License applies to any program or other work which contains
a notice placed by the copyright holder saying it may be distributed
under the terms of this General Public License. The "Program", below,
refers to any such program or work, and a "work based on the Program"
means either the Program or any derivative work under copyright law:
that is to say, a work containing the Program or a portion of it,
either verbatim or with modifications and/or translated into another
language. (Hereinafter, translation is included without limitation in
the term "modification".) Each licensee is addressed as "you".
Activities other than copying, distribution and modification are not
covered by this License; they are outside its scope. The act of
running the Program is not restricted, and the output from the Program
is covered only if its contents constitute a work based on the
Program (independent of having been made by running the Program).
Whether that is true depends on what the Program does.
1. You may copy and distribute verbatim copies of the Program's
source code as you receive it, in any medium, provided that you
conspicuously and appropriately publish on each copy an appropriate
copyright notice and disclaimer of warranty; keep intact all the
notices that refer to this License and to the absence of any warranty;
and give any other recipients of the Program a copy of this License
along with the Program.
You may charge a fee for the physical act of transferring a copy, and
you may at your option offer warranty protection in exchange for a fee.
2. You may modify your copy or copies of the Program or any portion
of it, thus forming a work based on the Program, and copy and
distribute such modifications or work under the terms of Section 1
above, provided that you also meet all of these conditions:
a) You must cause the modified files to carry prominent notices
stating that you changed the files and the date of any change.
b) You must cause any work that you distribute or publish, that in
whole or in part contains or is derived from the Program or any
part thereof, to be licensed as a whole at no charge to all third
parties under the terms of this License.
c) If the modified program normally reads commands interactively
when run, you must cause it, when started running for such
interactive use in the most ordinary way, to print or display an
announcement including an appropriate copyright notice and a
notice that there is no warranty (or else, saying that you provide
a warranty) and that users may redistribute the program under
these conditions, and telling the user how to view a copy of this
License. (Exception: if the Program itself is interactive but
does not normally print such an announcement, your work based on
the Program is not required to print an announcement.)
These requirements apply to the modified work as a whole. If
identifiable sections of that work are not derived from the Program,
and can be reasonably considered independent and separate works in
themselves, then this License, and its terms, do not apply to those
sections when you distribute them as separate works. But when you
distribute the same sections as part of a whole which is a work based
on the Program, the distribution of the whole must be on the terms of
this License, whose permissions for other licensees extend to the
entire whole, and thus to each and every part regardless of who wrote it.
Thus, it is not the intent of this section to claim rights or contest
your rights to work written entirely by you; rather, the intent is to
exercise the right to control the distribution of derivative or
collective works based on the Program.
In addition, mere aggregation of another work not based on the Program
with the Program (or with a work based on the Program) on a volume of
a storage or distribution medium does not bring the other work under
the scope of this License.
3. You may copy and distribute the Program (or a work based on it,
under Section 2) in object code or executable form under the terms of
Sections 1 and 2 above provided that you also do one of the following:
a) Accompany it with the complete corresponding machine-readable
source code, which must be distributed under the terms of Sections
1 and 2 above on a medium customarily used for software interchange; or,
b) Accompany it with a written offer, valid for at least three
years, to give any third party, for a charge no more than your
cost of physically performing source distribution, a complete
machine-readable copy of the corresponding source code, to be
distributed under the terms of Sections 1 and 2 above on a medium
customarily used for software interchange; or,
c) Accompany it with the information you received as to the offer
to distribute corresponding source code. (This alternative is
allowed only for noncommercial distribution and only if you
received the program in object code or executable form with such
an offer, in accord with Subsection b above.)
The source code for a work means the preferred form of the work for
making modifications to it. For an executable work, complete source
code means all the source code for all modules it contains, plus any
associated interface definition files, plus the scripts used to
control compilation and installation of the executable. However, as a
special exception, the source code distributed need not include
anything that is normally distributed (in either source or binary
form) with the major components (compiler, kernel, and so on) of the
operating system on which the executable runs, unless that component
itself accompanies the executable.
If distribution of executable or object code is made by offering
access to copy from a designated place, then offering equivalent
access to copy the source code from the same place counts as
distribution of the source code, even though third parties are not
compelled to copy the source along with the object code.
4. You may not copy, modify, sublicense, or distribute the Program
except as expressly provided under this License. Any attempt
otherwise to copy, modify, sublicense or distribute the Program is
void, and will automatically terminate your rights under this License.
However, parties who have received copies, or rights, from you under
this License will not have their licenses terminated so long as such
parties remain in full compliance.
5. You are not required to accept this License, since you have not
signed it. However, nothing else grants you permission to modify or
distribute the Program or its derivative works. These actions are
prohibited by law if you do not accept this License. Therefore, by
modifying or distributing the Program (or any work based on the
Program), you indicate your acceptance of this License to do so, and
all its terms and conditions for copying, distributing or modifying
the Program or works based on it.
6. Each time you redistribute the Program (or any work based on the
Program), the recipient automatically receives a license from the
original licensor to copy, distribute or modify the Program subject to
these terms and conditions. You may not impose any further
restrictions on the recipients' exercise of the rights granted herein.
You are not responsible for enforcing compliance by third parties to
this License.
7. If, as a consequence of a court judgment or allegation of patent
infringement or for any other reason (not limited to patent issues),
conditions are imposed on you (whether by court order, agreement or
otherwise) that contradict the conditions of this License, they do not
excuse you from the conditions of this License. If you cannot
distribute so as to satisfy simultaneously your obligations under this
License and any other pertinent obligations, then as a consequence you
may not distribute the Program at all. For example, if a patent
license would not permit royalty-free redistribution of the Program by
all those who receive copies directly or indirectly through you, then
the only way you could satisfy both it and this License would be to
refrain entirely from distribution of the Program.
If any portion of this section is held invalid or unenforceable under
any particular circumstance, the balance of the section is intended to
apply and the section as a whole is intended to apply in other
circumstances.
It is not the purpose of this section to induce you to infringe any
patents or other property right claims or to contest validity of any
such claims; this section has the sole purpose of protecting the
integrity of the free software distribution system, which is
implemented by public license practices. Many people have made
generous contributions to the wide range of software distributed
through that system in reliance on consistent application of that
system; it is up to the author/donor to decide if he or she is willing
to distribute software through any other system and a licensee cannot
impose that choice.
This section is intended to make thoroughly clear what is believed to
be a consequence of the rest of this License.
8. If the distribution and/or use of the Program is restricted in
certain countries either by patents or by copyrighted interfaces, the
original copyright holder who places the Program under this License
may add an explicit geographical distribution limitation excluding
those countries, so that distribution is permitted only in or among
countries not thus excluded. In such case, this License incorporates
the limitation as if written in the body of this License.
9. The Free Software Foundation may publish revised and/or new versions
of the General Public License from time to time. Such new versions will
be similar in spirit to the present version, but may differ in detail to
address new problems or concerns.
Each version is given a distinguishing version number. If the Program
specifies a version number of this License which applies to it and "any
later version", you have the option of following the terms and conditions
either of that version or of any later version published by the Free
Software Foundation. If the Program does not specify a version number of
this License, you may choose any version ever published by the Free Software
Foundation.
10. If you wish to incorporate parts of the Program into other free
programs whose distribution conditions are different, write to the author
to ask for permission. For software which is copyrighted by the Free
Software Foundation, write to the Free Software Foundation; we sometimes
make exceptions for this. Our decision will be guided by the two goals
of preserving the free status of all derivatives of our free software and
of promoting the sharing and reuse of software generally.
NO WARRANTY
11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY
FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN
OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED
OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF
MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS
TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE
PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,
REPAIR OR CORRECTION.
12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR
REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,
INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING
OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED
TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY
YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER
PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE
POSSIBILITY OF SUCH DAMAGES.
END OF TERMS AND CONDITIONS
How to Apply These Terms to Your New Programs
If you develop a new program, and you want it to be of the greatest
possible use to the public, the best way to achieve this is to make it
free software which everyone can redistribute and change under these terms.
To do so, attach the following notices to the program. It is safest
to attach them to the start of each source file to most effectively
convey the exclusion of warranty; and each file should have at least
the "copyright" line and a pointer to where the full notice is found.
<one line to give the program's name and a brief idea of what it does.>
Copyright (C) <year> <name of author>
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program; if not, write to the Free Software Foundation, Inc.,
51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
Also add information on how to contact you by electronic and paper mail.
If the program is interactive, make it output a short notice like this
when it starts in an interactive mode:
Gnomovision version 69, Copyright (C) year name of author
Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
This is free software, and you are welcome to redistribute it
under certain conditions; type `show c' for details.
The hypothetical commands `show w' and `show c' should show the appropriate
parts of the General Public License. Of course, the commands you use may
be called something other than `show w' and `show c'; they could even be
mouse-clicks or menu items--whatever suits your program.
You should also get your employer (if you work as a programmer) or your
school, if any, to sign a "copyright disclaimer" for the program, if
necessary. Here is a sample; alter the names:
Yoyodyne, Inc., hereby disclaims all copyright interest in the program
`Gnomovision' (which makes passes at compilers) written by James Hacker.
<signature of Ty Coon>, 1 April 1989
Ty Coon, President of Vice
This General Public License does not permit incorporating your program into
proprietary programs. If your program is a subroutine library, you may
consider it more useful to permit linking proprietary applications with the
library. If this is what you want to do, use the GNU Lesser General
Public License instead of this License.
2012-04-25 Release 1.1.0
DNA and RNA support now added. Sequence type can be specified manually
using --seqtype={Protein|DNA|RNA}
2012-03-27 Release 1.0.4
zipped input now supported
2011-09-07 Release 1.0.3
Bugs fixed:
input failed if first line in fasta file was empty
input failed if Clustal formatted file had trailing residue numbers
'*' character was causing problems, did not get filtered out by squid
--outfmt=fasta was not recognized
'~' gap characters were not recognized in MSF format
amended README re sequence/profile alignment
disallowed empty sequences
doxygen documentation fixes and fix of API example
2011-06-23 Release 1.0.2
2011-06-17 Release 1.0.0 (DeshilHollesEamus)
2010-06-17 Release 0.0.1 (Dubliniensis)
First "release" as program has been able for a while to perform
all basic tasks without problems.
Non-standard features already built-in include:
HMM-iteration (using HMMER for building an HMM) and guide-tree
iteration. On top of that HMM input works fine and
background-frequencies are added to the HHalign process.
Known issues: RNA/DNA alignment is considered buggy. Aligned
sequences have to be dealigned for HHalign to work properly.
The HMMER version message can be ignored if no HMM-iteration
was used.
# Doxyfile 1.5.8
# 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 = "Clustal Omega"
# 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 = 1.2.1
# 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 = ./doc/doxygen/
# 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 = NO
# 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 = YES
# 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 = 4
# 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 =
# 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
# Doxygen selects the parser to use depending on the extension of the files it parses.
# With this tag you can assign which parser to use for a given extension.
# Doxygen has a built-in mapping, but you can override or extend it using this tag.
# The format is ext=language, where ext is a file extension, and language is one of
# the parsers supported by doxygen: IDL, Java, Javascript, C#, C, C++, D, PHP,
# Objective-C, Python, Fortran, VHDL, C, C++. For instance to make doxygen treat
# .inc files as Fortran files (default is PHP), and .f files as C (default is Fortran),
# use: inc=Fortran f=C
EXTENSION_MAPPING =
# 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 = NO
# 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 = YES
# If the EXTRACT_PRIVATE tag is set to YES all private members of a class
# will be included in the documentation.
EXTRACT_PRIVATE = NO
# If the EXTRACT_STATIC tag is set to YES all static members of a file
# will be included in the documentation.
EXTRACT_STATIC = NO
# If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
# defined locally in source files will be included in the documentation.
# If set to NO only classes defined in header files are included.
EXTRACT_LOCAL_CLASSES = YES
# This flag is only useful for Objective-C code. When set to YES local
# methods, which are defined in the implementation section but not in
# the interface are included in the documentation.
# If set to NO (the default) only methods in the interface are included.
EXTRACT_LOCAL_METHODS = NO
# If this flag is set to YES, the members of anonymous namespaces will be
# extracted and appear in the documentation as a namespace called