Update to 2.1, from Wen Heping(myself) in PR 43395

Add LICENSE
Remove unneeded MESSAGE file

Upstream changes:
Version 2.1
----------------------------------------------------------------------
* Fixed bug 196 "clustalx: user feedback about use of secondary structure
  printed to console" - secondary structure is now used if specified
  in Alignment -> Alignment Parameters -> Secondary Structure Parameters
  UserParameters->getGui() should be used when ClustalW code needs to
  know if a function has been called from ClustalX

* Fixed bug 204 "Nexus alignment format contain invalid line" - the amino
  acid alphabet line has been removed

* Missing/corrupted file names in ClustalX status messages have been
  fixed

* Fixed bug 175 "msf/pileup files cannot be read if sequences names are
  all numbers" - this happened if a line such as
528244          .......... .......... .......... .......... ..........
  was present in the first block of the file

* Fixed bug 192 "Alignment in Phylip Format broken for big Alignments"

* Fixed bug 198 "Warning about divergent sequences gets printed to
  console in ClustalX"

* Fixed bug 151 "clustalx doesn't switch to profile alignment mode when
  profile12 is given on cmdline"

----------------------------------------------------------------------
Version 2.0.12
----------------------------------------------------------------------

* Fixed bug 189 "Fixed filename used for iteration":
Now Creating temporary file and added error check

* Fixed bug 180 "Pairwise NJ tree: final bracket missing"

* Fixed bug 178 "Seg-fault on 64bit when -quicktree -upgma for sequences with high identity":
  Using relative error now to avoid unsafe comparison which led to
  incorrect branching

* Fixed Bug 176 "iteration doesn't iterate if -usetree is used as well"

* Fixed bug 162 "percent identity file option in clustalW not working":
Added -pim as command line option. See help

* Fixed bug 155 "upgma trees cannot be read"

* Fixed bug 147 "report duplicate sequences":
 "ClustalW/X now report offending sequences which are empty, duplicates etc

* Fixed bug 134 "Exit when encountering unrecognized cmdline params":
ClustalW now exits when encountering invalid values for command line
arguments instead of just reverting to default values

* Fixed bug 185 "clustal alignments differ between interactive and commandline mode"
window-gap and ktuple initialisation now fixed and made the same
between commandline and interactive mode

* Fixed bug 184 "error messages are send to stdout"

* Fixed bug when weights are 0, and nseq > INT_SCALE_FACTOR in UPGMA
  code (see RootedGuideTree.cpp)

* General code cleanup
- Introduced return values where control reached end of non-void function
- Removed unused variables
- Removed comparison between signed and unsigned integer expressions
- Removed deprecated conversion from string constant to char*



----------------------------------------------------------------------
Version 2.0.11
----------------------------------------------------------------------

* fixed file extension bug 166 in interactive mode

* Fixed bug 169, memory violation for DNA/RNA k-tuple

* Cut down distance calculation, symmetric matrix


----------------------------------------------------------------------
Version 2.0.10
----------------------------------------------------------------------

* Fixed g++-4.3 compilation errors

* Added new -quiet command line flag

* Added new -stats=<file> command line flag

* Fixed bug 142: command separator can now be mixed "/" and "-" on all platforms

* Fixed bug 141: profile merging and saving failed

* Fixed bug 139: saving of column quality scores

* Updated help files (new flags, new colour parameter format)


----------------------------------------------------------------------
Version 2.0.9
----------------------------------------------------------------------

* GUI now responding and giving feedback during alignment

* automatic automake os detection

* new OS_ define (set by clustalw/configure clustalx/clustalx.pro)

* got rid of qt3 dependencies

* removed QScrollArea bug workaround (fixed in Qt 4.3)

* Fixed bug 135: Last sequence and last residue not displayed on MacOSX

* Fixed bug 123: secondary structure profile alignment in clustalX on Mac

* Fixed g++-4.3 build error (include climits.h)


----------------------------------------------------------------------
Version 2.0.8
----------------------------------------------------------------------

* Implemented maxseqlen cmdline switch

* Updated help-file

* Fixed Bug 123: loading profile using gap penalties (ClustalX, Mac)

* Fixed bug 133: providing profiles on command line fails (ClustalX)

* Fixed bug 125: Angle bracket inside sequence

* Fixed bug 129: Early exit on empty sequence

* Fixed a couple of possible memory leaks


----------------------------------------------------------------------
Version 2.0.7
----------------------------------------------------------------------

* Fixed bug 121: CRLF  in sequence names (Pearson) are not trimmed

* Fixed bug 122: convert option broken

* Fixed reopened bug 114: profile alignment input didn't work with new
  getSeqRange routines

* Fixed bug 119: build with g++ 4.3

----------------------------------------------------------------------
Version 2.0.6
----------------------------------------------------------------------

* Fixed bug 77: fasta input performance issue

* Fixed bug 114: segfault while doing profile alignment with secondary
  structure mask

* Removed unncessary id console output in EMBLFileParser.cpp

* Fixed Bugs 108 and 109 and allowed mixed-case command line options


----------------------------------------------------------------------
Version 2.0.5
----------------------------------------------------------------------

* Fixed bug 105: Disallowed combination of "Reset Gaps"
  and Iteration in GUI

* Fixed bug 104 "reset all gaps doesn't work"

* Changed command line separator for Mac to hyphen instead slash

* Fixed full command line parsing for ClustalX after help flag


----------------------------------------------------------------------
Version 2.0.4
----------------------------------------------------------------------

* Updated URLs in help files

* Fixed bug 96: error message when loading alignment with identical
  sequence names

* Made console output look more like 1.83

* Fixed bug 100: "Scores in clustalw2.0 don't match clustalw1.83"
  getMatrix was called with wrong scaling factor

* Fixed bug 99: "stars in input not ignored"
  Asterisks were changed to gaps in alignment

* New command line option: -fullhelp which dumps the built-in help
  file content.

* Quickfix for bug 94 "quicktree seqfault"


----------------------------------------------------------------------
<= Version 2.0.3
----------------------------------------------------------------------

* Added LICENSE file to distribution
This file contains the information about commercial licensing of
clustal as well as FAQ for licensing issues

* Added README file to distribution
This is the file that lists the files and directories on the Clustal
FTP site.  It also includes acknowledgements of people who have
contributed binaries

* Removed .pro Qt file from the distribution
pro-file should be generated anew using qmake and modified according
to build requirements, i.e. no need for version control.

* Fixed bug where ClustalX2 was not processing command line args

* Fixed Segfault on opening helpfile.  Happened on Linux only with -O2
and when calling binary directly, not using the wrapper

* Added debian packaging files

* Added support for help command line flag GUI/xmenus version
When requesting help file, graphical version of command line help is
displayed (1.83 tried to open clustalw help)

* Added complete automake (configure etc) system according to the
following websites:
- http://www.openismus.com/documents/linux/automake/automake.shtml
- http://www.bioinf.uni-freiburg.de/~mmann/HowTo/automake.html

* clustalw files source files have been moved to subdir

* Fixed bug #53 change MAXNAMESTODISPLAY back to 10 from 30.
This fixes problem of large amount of space between sequence name and
actual alignment in clustal output files

* This solves bug #72 with long lines (5000+) in fasta files
changed code to use strings rather than arrays.  Needed to add delim
parameter to getline in order to read files formatted for different
OSs on different platforms.

* Fixed Bug 79:
"The count of amino acids in the ClustalX Postscript output not correct"
Off-by-one issue

* ClustalX and ClustalW version numbers are now the same and defined in
ClustalW code (automake)

* Fixed problem with compilation of ClustalX2 with gcc3
avoiding gcc3 error message: cannot declare member function
QDir::currentPath'

* Target now clustalw2 instead of clustalw

* Fixed Bug 46
added in aminoacid code O for pyrrolysine

* Fixed bug 89
changed clustalw2.0 to conform to 1.83 behaviour for width of sequence
ID and alignment

* Fixed bug 90
changed clustalw2.0 to conform to 1.83 behaviour leading spaces are
stripped from FASTA identifiers.

* Fixed bug 91
Clustalw2.0 now handles pseudo-FASTA/MoST format files. Strips out
numbers and spaces.

7 files changed, 13 insertions, 94 deletions

diff --git a/biology/clustalw/MESSAGE b/biology/clustalw/MESSAGE
deleted file mode 100644
index 77eb1381117..00000000000
--- a/biology/clustalw/MESSAGE
+++ /dev/null
@@ -1,18 +0,0 @@
-===========================================================================
-$NetBSD: MESSAGE,v 1.3 2004/08/16 23:34:58 ben Exp $
-
-POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W
-
-Clustal W is freely available to the user community. However, Clustal
-W is increasingly being distributed as part of commercial sequence
-analysis packages. To help us safeguard future maintenance and
-development, commercial distributors of Clustal W must take out a
-NON-EXCLUSIVE LICENCE. Anyone wishing to commercially distribute
-version 1.83 of Clustal W should contact the authors unless they have
-previously taken out a licence.
-
-        gibson@embl-heidelberg.de
-        thompson@embl-heidelberg.de
-        d.higgins@ucc.ie
-
-===========================================================================
diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile
index 4899a7c60ab..df0c9789f33 100644
--- a/biology/clustalw/Makefile
+++ b/biology/clustalw/Makefile
@@ -1,36 +1,20 @@
-# $NetBSD: Makefile,v 1.12 2012/09/11 20:32:11 asau Exp $
+# $NetBSD: Makefile,v 1.13 2012/12/13 13:27:13 wen Exp $
 
-DISTNAME=	clustalw1.83.UNIX
-PKGNAME=	clustalw-1.83
+DISTNAME=	clustalw-2.1
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ \
-		ftp://ftp.ebi.ac.uk/pub/software/unix/clustalw/
+MASTER_SITES=	ftp://ftp.ebi.ac.uk/pub/software/clustalw2/2.1/ \
+		http://www.clustal.org/download/current/
 
 MAINTAINER=	babafou@babafou.eu.org
 HOMEPAGE=	http://bips.u-strasbg.fr/fr/Documentation/ClustalW/
 COMMENT=	General purpose multiple alignment program for DNA or proteins
+LICENSE=	gnu-gpl-v3 AND gnu-lgpl-v3
 
 PKG_INSTALLATION_TYPES=	overwrite pkgviews
 
-MAKE_FILE=	makefile
-BUILD_TARGET=	clustalw
-WRKSRC=		${WRKDIR}/clustalw1.83
-
-MAKE_FLAGS+=	CC=${CC:Q}
+GNU_CONFIGURE=	yes
+USE_LANGUAGES=	c c++
 
 INSTALLATION_DIRS=	bin
 
-post-patch:
-	@${SED} -e 's:@PREFIX@:${PREFIX}:' < ${WRKSRC}/clustalw.c \
-		> ${WRKSRC}/clustalw.c.tmp \
-		&& ${MV} ${WRKSRC}/clustalw.c.tmp ${WRKSRC}/clustalw.c
-
-do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/clustalw ${DESTDIR}${PREFIX}/bin
-	${INSTALL_DATA_DIR} ${DESTDIR}${PREFIX}/share/doc/clustalw
-	for f in clustalv.doc clustalw.doc clustalw.ms clustalw_help; do \
-		${INSTALL_DATA} ${WRKSRC}/$$f \
-			${DESTDIR}${PREFIX}/share/doc/clustalw; \
-	done
-
 .include "../../mk/bsd.pkg.mk"
diff --git a/biology/clustalw/PLIST b/biology/clustalw/PLIST
index 637727a70be..674a7a77ec4 100644
--- a/biology/clustalw/PLIST
+++ b/biology/clustalw/PLIST
@@ -1,6 +1,2 @@
-@comment $NetBSD: PLIST,v 1.2 2009/06/14 17:34:33 joerg Exp $
-bin/clustalw
-share/doc/clustalw/clustalv.doc
-share/doc/clustalw/clustalw.doc
-share/doc/clustalw/clustalw.ms
-share/doc/clustalw/clustalw_help
+@comment $NetBSD: PLIST,v 1.3 2012/12/13 13:27:13 wen Exp $
+bin/clustalw2
diff --git a/biology/clustalw/distinfo b/biology/clustalw/distinfo
index d1f33f6da92..23a17aaae23 100644
--- a/biology/clustalw/distinfo
+++ b/biology/clustalw/distinfo
@@ -1,8 +1,5 @@
-$NetBSD: distinfo,v 1.5 2012/10/20 22:02:07 joerg Exp $
+$NetBSD: distinfo,v 1.6 2012/12/13 13:27:13 wen Exp $
 
-SHA1 (clustalw1.83.UNIX.tar.gz) = 801ce911749171471b7964a1cff93c53c876c282
-RMD160 (clustalw1.83.UNIX.tar.gz) = 20c0ec7739be6747ae08220e5abf2bae412f039e
-Size (clustalw1.83.UNIX.tar.gz) = 166863 bytes
-SHA1 (patch-aa) = 96f95acb4a312c96440275ca65f7f908c9b9032f
-SHA1 (patch-ab) = 75fb21b88132bdf18e7f6bc13d1d35051a1babea
-SHA1 (patch-interface.c) = 4c5f76efee503d55aafec87edcb5cbb40f71579d
+SHA1 (clustalw-2.1.tar.gz) = f29784f68585544baa77cbeca6392e533d4cf433
+RMD160 (clustalw-2.1.tar.gz) = e193769955a6270797fcb039ca398a4b59d9248d
+Size (clustalw-2.1.tar.gz) = 350761 bytes
diff --git a/biology/clustalw/patches/patch-aa b/biology/clustalw/patches/patch-aa
deleted file mode 100644
index db1644e8641..00000000000
--- a/biology/clustalw/patches/patch-aa
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-aa,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $
-
---- clustalw.c.orig	Fri Jan 16 04:44:05 1998
-+++ clustalw.c	Tue Feb 16 11:58:13 1999
-@@ -33,7 +33,7 @@
- #ifdef MSDOS
-         char *help_file_name = "clustalw.hlp";
- #else
--        char *help_file_name = "clustalw_help";
-+        char *help_file_name = "@PREFIX@/share/doc/clustalw/clustalw_help";
- #endif
- 
- sint max_names; /* maximum length of names in current alignment file */
diff --git a/biology/clustalw/patches/patch-ab b/biology/clustalw/patches/patch-ab
deleted file mode 100644
index 30350a74a67..00000000000
--- a/biology/clustalw/patches/patch-ab
+++ /dev/null
@@ -1,14 +0,0 @@
-$NetBSD: patch-ab,v 1.1.1.1 1999/07/28 20:07:01 rh Exp $
-
---- amenu.c.orig	Mon Dec  8 08:49:12 1997
-+++ amenu.c	Sat Apr 10 22:07:58 1999
-@@ -13,7 +13,9 @@
- static jmp_buf jmpbuf;
- #ifndef VMS
- #ifndef AIX
-+#ifndef BADSIG
- #define BADSIG (void (*)())-1
-+#endif
- #endif
- #endif
- 
diff --git a/biology/clustalw/patches/patch-interface.c b/biology/clustalw/patches/patch-interface.c
deleted file mode 100644
index f1666bda383..00000000000
--- a/biology/clustalw/patches/patch-interface.c
+++ /dev/null
@@ -1,13 +0,0 @@
-$NetBSD: patch-interface.c,v 1.1 2012/10/20 22:02:07 joerg Exp $
-
---- interface.c.orig	2012-10-20 14:27:11.000000000 +0000
-+++ interface.c
-@@ -210,7 +210,7 @@ static sint check_param(char **args,char
- 		Boolean 	name1 = FALSE;
- 		sint ajb;
- 
--	if(args[0]==NULL) return;
-+	if(args[0]==NULL) return -1;
- 
- 
-