Commit 9d2a8534 authored by Charles Plessy's avatar Charles Plessy

Imported Upstream version 2.1

parent ae982fd3
This diff is collapsed.
GNU LESSER GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
Everyone is permitted to copy and distribute verbatim copies
of this license document, but changing it is not allowed.
This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.
0. Additional Definitions.
As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.
"The Library" refers to a covered work governed by this License,
other than an Application or a Combined Work as defined below.
An "Application" is any work that makes use of an interface provided
by the Library, but which is not otherwise based on the Library.
Defining a subclass of a class defined by the Library is deemed a mode
of using an interface provided by the Library.
A "Combined Work" is a work produced by combining or linking an
Application with the Library. The particular version of the Library
with which the Combined Work was made is also called the "Linked
Version".
The "Minimal Corresponding Source" for a Combined Work means the
Corresponding Source for the Combined Work, excluding any source code
for portions of the Combined Work that, considered in isolation, are
based on the Application, and not on the Linked Version.
The "Corresponding Application Code" for a Combined Work means the
object code and/or source code for the Application, including any data
and utility programs needed for reproducing the Combined Work from the
Application, but excluding the System Libraries of the Combined Work.
1. Exception to Section 3 of the GNU GPL.
You may convey a covered work under sections 3 and 4 of this License
without being bound by section 3 of the GNU GPL.
2. Conveying Modified Versions.
If you modify a copy of the Library, and, in your modifications, a
facility refers to a function or data to be supplied by an Application
that uses the facility (other than as an argument passed when the
facility is invoked), then you may convey a copy of the modified
version:
a) under this License, provided that you make a good faith effort to
ensure that, in the event an Application does not supply the
function or data, the facility still operates, and performs
whatever part of its purpose remains meaningful, or
b) under the GNU GPL, with none of the additional permissions of
this License applicable to that copy.
3. Object Code Incorporating Material from Library Header Files.
The object code form of an Application may incorporate material from
a header file that is part of the Library. You may convey such object
code under terms of your choice, provided that, if the incorporated
material is not limited to numerical parameters, data structure
layouts and accessors, or small macros, inline functions and templates
(ten or fewer lines in length), you do both of the following:
a) Give prominent notice with each copy of the object code that the
Library is used in it and that the Library and its use are
covered by this License.
b) Accompany the object code with a copy of the GNU GPL and this license
document.
4. Combined Works.
You may convey a Combined Work under terms of your choice that,
taken together, effectively do not restrict modification of the
portions of the Library contained in the Combined Work and reverse
engineering for debugging such modifications, if you also do each of
the following:
a) Give prominent notice with each copy of the Combined Work that
the Library is used in it and that the Library and its use are
covered by this License.
b) Accompany the Combined Work with a copy of the GNU GPL and this license
document.
c) For a Combined Work that displays copyright notices during
execution, include the copyright notice for the Library among
these notices, as well as a reference directing the user to the
copies of the GNU GPL and this license document.
d) Do one of the following:
0) Convey the Minimal Corresponding Source under the terms of this
License, and the Corresponding Application Code in a form
suitable for, and under terms that permit, the user to
recombine or relink the Application with a modified version of
the Linked Version to produce a modified Combined Work, in the
manner specified by section 6 of the GNU GPL for conveying
Corresponding Source.
1) Use a suitable shared library mechanism for linking with the
Library. A suitable mechanism is one that (a) uses at run time
a copy of the Library already present on the user's computer
system, and (b) will operate properly with a modified version
of the Library that is interface-compatible with the Linked
Version.
e) Provide Installation Information, but only if you would otherwise
be required to provide such information under section 6 of the
GNU GPL, and only to the extent that such information is
necessary to install and execute a modified version of the
Combined Work produced by recombining or relinking the
Application with a modified version of the Linked Version. (If
you use option 4d0, the Installation Information must accompany
the Minimal Corresponding Source and Corresponding Application
Code. If you use option 4d1, you must provide the Installation
Information in the manner specified by section 6 of the GNU GPL
for conveying Corresponding Source.)
5. Combined Libraries.
You may place library facilities that are a work based on the
Library side by side in a single library together with other library
facilities that are not Applications and are not covered by this
License, and convey such a combined library under terms of your
choice, if you do both of the following:
a) Accompany the combined library with a copy of the same work based
on the Library, uncombined with any other library facilities,
conveyed under the terms of this License.
b) Give prominent notice with the combined library that part of it
is a work based on the Library, and explaining where to find the
accompanying uncombined form of the same work.
6. Revised Versions of the GNU Lesser General Public License.
The Free Software Foundation may publish revised and/or new versions
of the GNU Lesser 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
Library as you received it specifies that a certain numbered version
of the GNU Lesser General Public License "or any later version"
applies to it, you have the option of following the terms and
conditions either of that published version or of any later version
published by the Free Software Foundation. If the Library as you
received it does not specify a version number of the GNU Lesser
General Public License, you may choose any version of the GNU Lesser
General Public License ever published by the Free Software Foundation.
If the Library as you received it specifies that a proxy can decide
whether future versions of the GNU Lesser General Public License shall
apply, that proxy's public statement of acceptance of any version is
permanent authorization for you to choose that version for the
Library.
# Andreas Wilm (UCD): 2007-12-10
# Generated using the following sites
# http://www.openismus.com/documents/linux/automake/automake.shtml
# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
# we do not use GNU-style files: NEWS README AUTHORS ChangeLog
AUTOMAKE_OPTIONS = foreign
SUBDIRS = m4 src
EXTRA_DIST = README LICENSE clustalw_help
This diff is collapsed.
Please see also ftp://ftp.ebi.ac.uk/pub/software/clustalw2/README
and http://www.clustal.org/
HOWTO COMPILE THE SOURCE AND INSTALL
----------------------------------------------------------------------
You will need a Unix environment with a working C++ compiler to
compile the ClustalW source. We recommened GCC>=4.2. ICC users
need to configure the package as follows:
./configure CXX=icpc
For compilation under Windows you will probably need to install
mingw and cygwin.
Type
$ ./configure
$ make
This will create a clustalw binary in the src directory.
To install the software type
$ make install
(might have to be executed as superuser)
or simply copy the clustalw binary to a directory of your choice.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
# Andreas Wilm (UCD): 2007-12-10
# Generated using the following sites
# http://www.openismus.com/documents/linux/automake/automake.shtml
# http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html
#
# autoconf looks for a file called configure.ac (or, previously,
# configure.in). It then creates the configure script, based on the
# macros which it finds. Whenever you add a macro to configure.ac,
# you should run aclocal as well as autoconf, because aclocal scans
# configure.ac to find which macros it should provide.
# This is all black magic and we (as well as all reasonable
# developers) should change to a sane system like e.g. SCons
# http://freshmeat.net/articles/stop-the-autoconf-insanity-why-we-need-a-new-build-system
# Andreas Wilm (UCD):
# you will only have to change the version number here!
# after apllying any changes you will have to run
# $ autoreconf
#
AC_INIT([clustalw], [2.1], [clustalw@ucd.ie])
#
# The AC_INIT macro can take any source file as an argument. It just
# checks that the file is there, which should, in turn, mean that the
# source directory is there.
# AC_INIT generates the following m4 macros, output variables and preprocessor symbols:
# * [AC_]PACKAGE_NAME
# * [AC_]PACKAGE_TARNAME
# * [AC_]PACKAGE_VERSION
# * [AC_]PACKAGE_STRING
# * [AC_]PACKAGE_BUGREPORT
# Detect the canonical host and target build environment
# see e.g. http://cvs.haskell.org/darcs/ghc/configure.ac for howto use
# AC_CANONICAL_HOST or AC_CANONICAL_TARGET?
# AC_CANONICAL_SYSTEM will also run AC_CANONICAL_HOST and allows to use --target
AC_CANONICAL_SYSTEM
# DEFINES here are going to config.h and have to be the same as in clustalx.pro
#echo "host_os $host_os"
case $target_os in
*linux*|*solaris*|*bsd*)
AC_DEFINE([OS_UNIX], [1], [Host OS])
;;
*darwin*)
AC_DEFINE([OS_MAC], [1], [Host OS])
AC_DEFINE([OS_UNIX], [1], [Host OS])
;;
*cygwin*|*mingw*)
AC_DEFINE([OS_WINDOWS], [1], [Host OS])
;;
*)
AC_MSG_WARN(["Couldn't determine target operating system. Using Unix"]);
AC_DEFINE([OS_UNIX], [1], [Host OS])
;;
esac
echo "building for $target_os"
# set in clustalw_version.h[.in] rather than config.h to avoid name clashes
#AC_DEFINE_UNQUOTED(CLUSTALW_VERSION, "${PACKAGE_VERSION}", [ClustalW version])
#AC_DEFINE_UNQUOTED(CLUSTALW_NAME, "ClustalW", [ClustalW name])
CLUSTALW_VERSION="${PACKAGE_VERSION}"
AC_SUBST(CLUSTALW_VERSION)
CLUSTALW_NAME="ClustalW"
AC_SUBST(CLUSTALW_NAME)
# The AM_INIT_AUTOMAKE line adds several standard checks.
# This macro is always needed for automake
# Obsolete: It takes the program name and version number as arguments.
AM_INIT_AUTOMAKE([])
AC_PROG_MAKE_SET
# AC_PROG_CC indicates that the source code may be in C. If the source
# code is C++ then we also need AC_PROG_CXX.
AC_PROG_CC
AC_PROG_CXX
# AC_PROG_RANLIB will allow you to build code in sub-directories into
# temporary libraries, which make will then link in with the rest of
# the code.
AC_PROG_RANLIB
# AC_PROG_INSTALL will generate an install target so that users may
# just type 'make install' to install the software.
AC_PROG_INSTALL
# use C++ compiler and linker
AC_LANG_CPLUSPLUS
# Checks for header files.
AC_HEADER_STDC
# AC_CHECK_HEADERS([a.h b.h])
# Checks for typedefs, structures, and compiler characteristics.
AC_HEADER_STDBOOL
AC_C_CONST
AC_TYPE_SIZE_T
# This may beincluded by your source code and provides a way for
# people to customise the configuration for their platform, via
# #defines. config.h.in can be generated automatically with the
# autoheader tool. However, you need a stamp-h file in your project
# to ensure that automake regenerates config.h from config.h.in. Type
# 'touch stamp-h' to add this file to your project.
# Andreas Wilm: standard would be config.h but let's avoid conflicts with
AM_CONFIG_HEADER(src/config.h)
AC_FUNC_MALLOC
# enable hashing if requested (--with-mhash)
# will set HAVE_MHASH_H only
AC_ARG_WITH([mhash],
[AS_HELP_STRING([--with-mhash],
[Enable mhash support in stats])],
[with_mhash=$withval],
[with_mhash=no])
if test "$with_mhash" = "yes"; then
AC_CHECK_LIB([mhash], [mhash_init], ,
[AC_MSG_ERROR([mhash lib not found])])
AC_CHECK_HEADERS([mhash.h], ,
[AC_MSG_ERROR([mhash header not found])])
fi
# AC_OUTPUT indicates the name of the Makefile which will be generated.
### AC_CONFIG_FILES([ Makefile ])
AC_OUTPUT(Makefile m4/Makefile src/Makefile src/clustalw_version.h)
This diff is collapsed.
This diff is collapsed.
# Install m4 macros in this directory
m4datadir = $(datadir)/aclocal
# List your m4 macros here
#m4macros = AC_CHECK_VERSION
m4macros =
# The following is boilerplate
m4data_DATA =
EXTRA_DIST = $(m4data_DATA)
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
/**
* Author: Andreas Wilm
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
/**
* This is the clustalw help class which replaces the old help file
*
*/
#ifndef HELP_H
#define HELP_H
#include <string>
#include <iostream>
using namespace std;
typedef struct {
string marker;
string title;
string content;
} section;
class Help {
public:
/* Functions */
Help();
~Help();
string GetSection(string marker);
string GetSection(char marker);
string GetSectionTitle(string marker);
string GetSectionTitle(char marker);
vector<string> ListSectionMarkers();
/* Attributes */
private:
/* Functions */
/* Attributes */
vector<section> sections;
};
#endif
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
#ifndef CLUSTALW_VERSION_H
#define CLUSTALW_VERSION_H
#define CLUSTALW_NAME "ClustalW"
#define CLUSTALW_VERSION "2.1"
#endif
#ifndef CLUSTALW_VERSION_H
#define CLUSTALW_VERSION_H
#define CLUSTALW_NAME "@CLUSTALW_NAME@"
#define CLUSTALW_VERSION "@CLUSTALW_VERSION@"
#endif
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
/**
* Author: Mark Larkin
*
* Copyright (c) 2007 Des Higgins, Julie Thompson and Toby Gibson.
*/
#ifdef HAVE_CONFIG_H
#include "config.h"
#endif
#include "SymMatrix.h"
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment