[med-svn] r114 - in trunk/packages/seaview/trunk: . debian examples
Charles Plessy
charles-guest at costa.debian.org
Tue Sep 19 14:21:39 UTC 2006
Author: charles-guest
Date: 2006-09-19 14:21:38 +0000 (Tue, 19 Sep 2006)
New Revision: 114
Added:
trunk/packages/seaview/trunk/config.h
trunk/packages/seaview/trunk/debian/
trunk/packages/seaview/trunk/debian/changelog
trunk/packages/seaview/trunk/debian/compat
trunk/packages/seaview/trunk/debian/control
trunk/packages/seaview/trunk/debian/copyright
trunk/packages/seaview/trunk/debian/install
trunk/packages/seaview/trunk/debian/menu
trunk/packages/seaview/trunk/debian/rules
trunk/packages/seaview/trunk/examples/
trunk/packages/seaview/trunk/examples/dna.phy
trunk/packages/seaview/trunk/examples/nuc.aln
trunk/packages/seaview/trunk/examples/seq.fas
trunk/packages/seaview/trunk/seaview.1
Modified:
trunk/packages/seaview/trunk/align.cxx
trunk/packages/seaview/trunk/makefile
trunk/packages/seaview/trunk/seaview.cxx
trunk/packages/seaview/trunk/seaview_align.sh
Log:
Load seaview-20021127 into trunk/packages/seaview/trunk.
Modified: trunk/packages/seaview/trunk/align.cxx
===================================================================
--- trunk/packages/seaview/trunk/align.cxx 2006-09-19 14:20:29 UTC (rev 113)
+++ trunk/packages/seaview/trunk/align.cxx 2006-09-19 14:21:38 UTC (rev 114)
@@ -3,6 +3,7 @@
#include <ctype.h>
#ifndef WIN32
#include <FL/x.H>
+#include <unistd.h>
#endif
@@ -94,6 +95,13 @@
return retval;
}
+static char tmpdir[] = "/tmp/seaviewXXXXXX";
+
+static void remove_tmpdir(void)
+{
+rmdir(tmpdir);
+}
+
void align_selected_parts(SEA_VIEW *view)
{
int debut, fin, status, withU, empty_seq, num_longest, l;
@@ -104,6 +112,11 @@
static char *prog_path;
if(first) { /* check for presence of xterm + clustalw + seaview_align.sh */
+ if(mkdtemp(tmpdir) == NULL || atexit(remove_tmpdir)) {
+ fl_alert("Cannot create temporary directory");
+ return;
+ }
+ sprintf(base_fname, "%s/align", tmpdir);
first = FALSE;
#ifdef WIN32
status = check_path("clustalw.exe");
@@ -121,7 +134,7 @@
#else
status = check_path("clustalw");
if(status == 0) {
- status = check_path("xterm");
+ status = check_path("x-terminal-emulator");
}
if(status == 0) {
status = check_path("seaview_align.sh");
@@ -134,7 +147,7 @@
#elif defined(__APPLE__)
"program clustalw\n"
#else
- "one of the programs xterm, clustalw, seaview_align.sh\n"
+ "one of the programs x-terminal-emulator, clustalw, seaview_align.sh\n"
#endif
"is missing");
((Fl_Menu_ *)view->menu_edit)->mode(ALIGN_SEQS,
@@ -155,11 +168,6 @@
#endif
debut = view->active_region->list->debut;
fin = view->active_region->list->fin;
-tmpnam(base_fname);
-/*
-convertir en minuscules car clustalw n'accepte pas les majuscules ds filenames
-*/
-p = base_fname - 1; while( *(++p) != 0) *p = tolower( *p);
#ifdef WIN32 /* pas de . et pas plus de 8 car */
p = base_fname; while( ( q = strchr(p, '\\')) != NULL ) p = q + 1;
p[8] = 0;
@@ -204,7 +212,7 @@
base_fname, base_fname);
#else
-strcpy(commande, "xterm -T \"clustalw alignment\" -n clustalw -sb -sl 2000 "
+strcpy(commande, "x-terminal-emulator -T \"clustalw alignment\" -n clustalw -sb -sl 2000 "
"-e seaview_align.sh " );
l = strlen(commande);
sprintf(commande + l,
Added: trunk/packages/seaview/trunk/config.h
===================================================================
--- trunk/packages/seaview/trunk/config.h (rev 0)
+++ trunk/packages/seaview/trunk/config.h 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1 @@
+#define HAVE_DIRENT_H 1
Added: trunk/packages/seaview/trunk/debian/changelog
===================================================================
--- trunk/packages/seaview/trunk/debian/changelog (rev 0)
+++ trunk/packages/seaview/trunk/debian/changelog 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,130 @@
+seaview (20021127-4.1) unstable; urgency=medium
+
+ * Non-maintainer upload.
+ * Medium-urgency upload for RC bugfix.
+ * Rebuild for the C++ ABI transition. Closes: #328175.
+
+ -- Steve Langasek <vorlon at debian.org> Thu, 22 Sep 2005 02:07:07 -0700
+
+seaview (20021127-4) unstable; urgency=low
+
+ * Cleaned up debian/rules file.
+ * Conforms to Standards version 3.6.1.
+
+ -- Brian R Furry <bfurry at nac.net> Sun, 30 Nov 2003 00:04:02 +0000
+
+seaview (20021127-3) unstable; urgency=low
+
+ * Adopted by new maintainer; closes: 100261
+ * Conforms to Standards version 3.6.0.
+
+ -- Brian R Furry <bfurry at nac.net> Thu, 11 Sep 2003 21:12:40 -0400
+
+seaview (20021127-2.2) unstable; urgency=low
+
+ * NMU.
+ * Downgrade dependency on clustalw to a recommendation, since we don't
+ absolutely need it and it doesn't exist on mips(el).
+
+ -- Aaron M. Ucko <ucko at debian.org> Tue, 17 Jun 2003 13:22:55 -0400
+
+seaview (20021127-2.1) unstable; urgency=low
+
+ * NMU.
+ * Rebuild with Xft2-based FLTK (>= 1.1.3-2.1).
+
+ -- Aaron M. Ucko <ucko at debian.org> Wed, 7 May 2003 20:36:02 -0400
+
+seaview (20021127-2) unstable; urgency=low
+
+ * QA upload.
+ * Built with g++ 3.2 and libfltk1.1c102 (closes: #176147).
+
+ -- Colin Watson <cjwatson at debian.org> Sat, 11 Jan 2003 02:50:11 +0000
+
+seaview (20021127-1) unstable; urgency=low
+
+ * QA upload.
+ * New upstream release.
+ * Conforms to Standards version 3.5.8.
+
+ -- Matej Vela <vela at debian.org> Sun, 1 Dec 2002 22:14:33 +0100
+
+seaview (20021010-1) unstable; urgency=low
+
+ * QA upload.
+ * New upstream release.
+ * Provide a config.h for old_file_chooser.cxx.
+ * debian/menu: Use `section=Apps/Science hints=Biology' (see #162812).
+
+ -- Matej Vela <vela at debian.org> Sat, 19 Oct 2002 21:26:13 +0200
+
+seaview (20020409-1) unstable; urgency=low
+
+ * QA upload.
+ * New upstream version (there's no version number in the sources).
+ Closes: #128357.
+ * align.cxx:
+ - Handle temporary files securely (seaview 0.0 is not vulnerable).
+ - Use x-terminal-emulator rather than xterm or rxvt.
+ * seaview.1:
+ - List NEXUS among the supported formats.
+ - `-reducefonts' is no longer accepted.
+ * Switched to debhelper 4.
+ * Moved /usr/lib/seaview/seaview.help to /usr/share/seaview as
+ architecture-independent.
+ * Changed section from contrib/misc to contrib/science.
+ * Added menu support.
+ * debian/changelog: Remove obsolete Emacs local variables.
+ * Conforms to Standards version 3.5.7.
+
+ -- Matej Vela <vela at debian.org> Fri, 20 Sep 2002 18:25:47 +0200
+
+seaview (0.0-6.1) unstable; urgency=low
+
+ * NMU
+ * Update to build against XForms 0.89. (closes: Bug#118138)
+
+ -- Doug Porter <dsp at debian.org> Mon, 12 Nov 2001 11:43:51 -0500
+
+seaview (0.0-6) unstable; urgency=low
+
+ * Maintainer set to Debian QA Group <packages at qa.debian.org>.
+
+ -- Adrian Bunk <bunk at fs.tum.de> Fri, 24 Aug 2001 23:58:22 +0200
+
+seaview (0.0-5) unstable; urgency=low
+
+ * Adopted by new maintainer; closes: #92802
+ * Moved all doc files to /usr/share/doc; closes: #91647
+ * Moved manpage to /usr/share/man; closes: #91064
+ * Updated to latest policy, and added Build-Depends.
+ * Removed some unnecessary files in debian dir.
+
+ -- Dr. Guenter Bechly <gbechly at debian.org> Sat, 7 Apr 2001 18:00:30 +0200
+
+seaview (0.0-4) unstable; urgency=low
+
+ * A few examples added
+ * New bug in seaview_align.sh, this time fixed seriously.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Thu, 3 Jun 1999 10:07:55 +0200
+
+seaview (0.0-3) unstable; urgency=low
+
+ * Big bug in seaview_align.sh (not all parameters were passed).
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Wed, 26 May 1999 14:39:26 +0200
+
+seaview (0.0-2) unstable; urgency=low
+
+ * No longer depends on c-shell or xterm. Closes #34700
+ * Manual page. Closes #34615
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Tue, 25 May 1999 14:42:15 +0200
+
+seaview (0.0-1) unstable; urgency=low
+
+ * Initial Release.
+
+ -- Stephane Bortzmeyer <bortzmeyer at debian.org> Mon, 1 Mar 1999 16:41:51 +0100
Added: trunk/packages/seaview/trunk/debian/compat
===================================================================
--- trunk/packages/seaview/trunk/debian/compat (rev 0)
+++ trunk/packages/seaview/trunk/debian/compat 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1 @@
+4
Added: trunk/packages/seaview/trunk/debian/control
===================================================================
--- trunk/packages/seaview/trunk/debian/control (rev 0)
+++ trunk/packages/seaview/trunk/debian/control 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,16 @@
+Source: seaview
+Section: contrib/science
+Priority: optional
+Maintainer: Brian R. Furry <bfurry at nac.net>
+Build-Depends: debhelper ( >= 4 ), libfltk1.1-dev (>= 1.1.3-2.1)
+Standards-Version: 3.6.1
+
+Package: seaview
+Architecture: any
+Depends: ${shlibs:Depends}
+Recommends: clustalw, xterm | x-terminal-emulator
+Description: [Biology] A multiple sequence alignment editor
+ This is a graphical editor to deal with biosequences. SeaView is able
+ to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE,
+ NEXUS). It allows one to manually edit the alignment, and also to run
+ ClustalW to locally improve the alignment.
Added: trunk/packages/seaview/trunk/debian/copyright
===================================================================
--- trunk/packages/seaview/trunk/debian/copyright (rev 0)
+++ trunk/packages/seaview/trunk/debian/copyright 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,20 @@
+This package was debianized by Dr. Guenter Bechly <gbechly at debian.org> on
+Sat, 7 Apr 2001 18:00:30 +0200.
+
+It was downloaded from:
+ftp://pbil.univ-lyon1.fr/pub/mol_phylogeny/seaview/
+
+The reference Web page is:
+http://pbil.univ-lyon1.fr/software/seaview.html
+
+Upstream Author: Manolo Gouy <mgouy at biomserv.univ-lyon1.fr>
+
+Copyright: Artistic
+
+This software is copyright (c) by Manolo Gouy
+
+You are free to distribute this software under the terms of
+the Artistic Licence.
+
+On Debian systems, the complete text of the Artistic License can be
+found in /usr/share/common-licenses/Artistic.
Added: trunk/packages/seaview/trunk/debian/install
===================================================================
--- trunk/packages/seaview/trunk/debian/install (rev 0)
+++ trunk/packages/seaview/trunk/debian/install 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,2 @@
+seaview seaview_align.sh usr/bin
+seaview.help usr/share/seaview
Added: trunk/packages/seaview/trunk/debian/menu
===================================================================
--- trunk/packages/seaview/trunk/debian/menu (rev 0)
+++ trunk/packages/seaview/trunk/debian/menu 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,7 @@
+?package(seaview):\
+ needs=x11\
+ section=Apps/Science\
+ hints=Biology\
+ longtitle="SeaView: multiple sequence alignment editor"\
+ title=SeaView\
+ command=seaview
Added: trunk/packages/seaview/trunk/debian/rules
===================================================================
--- trunk/packages/seaview/trunk/debian/rules (rev 0)
+++ trunk/packages/seaview/trunk/debian/rules 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,67 @@
+#!/usr/bin/make -f
+
+# These are used for cross-compiling and for saving the configure script
+# from having to guess our platform (since we know it already)
+DEB_HOST_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_HOST_GNU_TYPE)
+DEB_BUILD_GNU_TYPE ?= $(shell dpkg-architecture -qDEB_BUILD_GNU_TYPE)
+
+CFLAGS+=-Wall
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+ifneq (,$(findstring debug,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -g
+endif
+
+build: build-stamp
+build-stamp:
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE) OPT="$(CFLAGS)"
+
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+
+ # Add here commands to clean up after the build process.
+ $(MAKE) clean
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs -v
+
+ # Add here commands to install the package into debian/<packagename>
+ dh_install
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+ dh_installexamples examples/*
+ dh_installmenu
+ dh_installman seaview.1
+ dh_link usr/share/man/man1/seaview.1 \
+ usr/share/man/man1/seaview_align.sh.1
+ dh_strip
+ dh_compress
+ dh_fixperms
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/seaview/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/seaview/trunk/examples/dna.phy
===================================================================
--- trunk/packages/seaview/trunk/examples/dna.phy (rev 0)
+++ trunk/packages/seaview/trunk/examples/dna.phy 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,32 @@
+ 7 232
+Bovine CCAAACCTGT CCCCACCATC TAACACCAAC CCACATATAC AAGCTAAACC AAAAATACCA
+Mouse CCAAAAAAAC ATCCAAACAC CAACCCCAGC CCTTACGCAA TAGCCATACA AAGAATATTA
+Gibbon CTATACCCAC CCAACTCGAC CTACACCAAT CCCCACATAG CACACAGACC AACAACCTCC
+Orang CCCCACCCGT CTACACCAGC CAACACCAAC CCCCACCTAC TATACCAACC AATAACCTCT
+Gorilla CCCCATTTAT CCATAAAAAC CAACACCAAC CCCCATCTAA CACACAAACT AATGACCCCC
+Chimp CCCCATCCAC CCATACAAAC CAACATTACC CTCCATCCAA TATACAAACT AACAACCTCC
+Human CCCCACTCAC CCATACAAAC CAACACCACT CTCCACCTAA TATACAAATT AATAACCTCC
+
+ TACTACTAAA AACTCAAATT AACTCTTTAA TCTTTATACA ACATTCCACC AACCTATCCA
+ TACAACCATA AATAAGACTA ATCTATTAAA ATAACCCATT ACGATACAAA ATCCCTTTCG
+ CACCTTCCAT ACCAAGCCCC GACTTTACCG CCAACGCACC TCATCAAAAC ATACCTACAA
+ CAACCCCTAA ACCAAACACT ATCCCCAAAA CCAACACACT CTACCAAAAT ACACCCCCAA
+ CACCCTCAAA GCCAAACACC AACCCTATAA TCAATACGCC TTATCAAAAC ACACCCCCAA
+ CACTCTTCAG ACCGAACACC AATCTCACAA CCAACACGCC CCGTCAAAAC ACCCCTTCAG
+ CACCTTCAGA ACTGAACGCC AATCTCATAA CCAACACACC CCATCAAAGC ACCCCTCCAA
+
+ CACAAAAAAA CTCATATTTA TCTAAATACG AACTTCACAC AACCTTAACA CATAAACATA
+ TCTAGATACA AACCACAACA CACAATTAAT ACACACCACA ATTACAATAC TAAACTCCCA
+ CACAAACAAA TGCCCCCCCA CCCTCCTTCT TCAAGCCCAC TAGACCATCC TACCTTCCTA
+ TTCACATCCG CACACCCCCA CCCCCCCTGC CCACGTCCAT CCCATCACCC TCTCCTCCCA
+ CATAAACCCA CGCACCCCCA CCCCTTCCGC CCATGCTCAC CACATCATCT CTCCCCTTCA
+ CACAAATTCA TACACCCCTA CCTTTCCTAC CCACGTTCAC CACATCATCC CCCCCTCTCA
+ CACAAACCCG CACACCTCCA CCCCCCTCGT CTACGCTTAC CACGTCATCC CTCCCTCTCA
+
+ CCCCAGCCCA ACACCCTTCC ACAAATCCTT AATATACGCA CCATAAATAA CA
+ TCCCACCAAA TCACCCTCCA TCAAATCCAC AAATTACACA ACCATTAACC CA
+ GCACGCCAAG CTCTCTACCA TCAAACGCAC AACTTACACA TACAGAACCA CA
+ ACACCCTAAG CCACCTTCCT CAAAATCCAA AACCCACACA ACCGAAACAA CA
+ ACACCTCAAT CCACCTCCCC CCAAATACAC AATTCACACA AACAATACCA CA
+ ACATCTTGAC TCGCCTCTCT CCAAACACAC AATTCACGCA AACAACGCCA CA
+ ACACCTTAAC TCACCTTCTC CCAAACGCAC AATTCGCACA CACAACGCCA CA
Added: trunk/packages/seaview/trunk/examples/nuc.aln
===================================================================
--- trunk/packages/seaview/trunk/examples/nuc.aln (rev 0)
+++ trunk/packages/seaview/trunk/examples/nuc.aln 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,34 @@
+CLUSTAL W (1.7) multiple sequence alignment
+
+
+seq4 ----------------------------NNNNATACTCTG-GTTTCTCTTCAGATCGTAT
+seq6 ----------------------------NNNNATACTCTG-GTTTCTCTTCAGATCGCAT
+seq5 ------------------------------------------------------------
+seq2 TATGCAGACAATTATGATTACATGGGGTAAAAATACTCCAAGATAGTATTCAGTTCTCAA
+seq1 ------AAGCTTTATTTTTCCATCTCTTTTACAT--TCAATGATTCTATTCATTTGT-AA
+seq3 ------------------------------------------------------------
+
+
+seq4 AAATCTTTCCCCTTTCANCAAAGATTTCCGTGGAGAGGAATAACTCTGAGTC--TTAAGC
+seq6 AAATCTTTCCCCTTTCANCAAAGATTTCCGTGGAGAGGAACAACTCTGAGTC--TTAACC
+seq5 ------------------------------------------------------------
+seq2 GATGGTTCATCACATTTGCCAAGTTTTTCTACCATAAAATTCCCCACCAATCCATTTATG
+seq1 GAGAAGTAAGCANNNNNNACTCCAACAGTGGAGAAAGTCAGACTGATTAAACAGGTNNAC
+seq3 -----------------------GTCTACGGCCATACCACCCTGAACGCGCCCGATCTCG
+
+
+seq4 TAATTTTTTGAGCCTT------GCTCCGACAAGGCTA-----------------------
+seq6 CAATTTTTTGAGCCTT------GCCTTGGCAAGGCTA-----------------------
+seq5 ----------AGCCTT------GTTCCGACAAGGCTA-----------------------
+seq2 TATAGAGTTGATAGTTAACAGAGATCGGAAATGGCCATTGCATCTTTAGTCTGGATTTCC
+seq1 CAAACACGTAAATGTTTTT--GNAGAAGGAAGGGNAACTCTGGTGAGCCCGCAGAGGTGC
+seq3 TCTGATCTCGGAAGCTAAGCAGGGTCGGGCCTGGTTAGTACTTGGATGG--GAGACCGCC
+ * * ** *
+
+seq4 -------------------------------
+seq6 -------------------------------
+seq5 -------------------------------
+seq2 TGAGACCTTTGGTTTATTTCTAGGGCTGC--
+seq1 ACAGGCTNNNTAGAGACAGCAGTGTCAGTCC
+seq3 TGGGAATACCGGGTGCTGTAGGCTTT-----
+
Added: trunk/packages/seaview/trunk/examples/seq.fas
===================================================================
--- trunk/packages/seaview/trunk/examples/seq.fas (rev 0)
+++ trunk/packages/seaview/trunk/examples/seq.fas 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,115 @@
+>gi|2981175 deltex
+MSRPGHGGLMPVNGLGFPPQNVARVVVWECLNEHSRWRPYTATVCHHIENVLKEDARGSVVLGQVDAQLV
+PYIIDLQSMHQFRQDTGTMRPVRRNFYDPSSAPGKGIVWEWENDGGAWTAYDMDICITIQNAYEKQHPWL
+DLSSLGFCYLIYFNSMSQMNRQTRRRRRLRRRLDLAYPLTVGSIPKSQSWPVGASSGQPCSCQQCLLVNS
+TRAVSNVILASQRRKVPPAPPLPPPPPPGGPPGALAVRPSATFTGAALWAAPAAGPAEPAPPPGAPPRSP
+GAPGGARTPGQNNLNRPGPQRTTSVSARASIPPGVPALPVKNLNGTGPVHPALAGMTGILLCAAGLPVCL
+TRAPKPILHPPPVSKSDVKPVPGVPGVCRKTKKKHLKKSKNPEDVVRRYMQKVKNPPDEDCTICMERLVT
+ASGYEGVLRHKGVRPELVGRLGRCGHMYHLLCLVAMYSNGNKDGSLQCPTCKAIYGEKTGTQPPGKMEFH
+LIPHSLPGFPDTQTIRIVYDIPTGIQGPEHPNPGKKFTARGFPRHCYLPNNEKGRKVLRLLITAWERRLI
+FTIGTSNTTGESDTVVWNEIHHKTEFGSNLTGHGYPDASYLDNVLAELTAQGVSEAAGKAU
+>gi|927067 longation factor 1-alpha 1
+MQSERGITIDISLWKFETSKYYVTIIDAPGHRDFIQNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTR
+EHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEP
+SANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLGLPLQDVYKIGGIGTVPVGRVETGVLKP
+GMVVTFGPVNVTTEVKSVEMHHEALGEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFPAQV
+IILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVES
+FSDYPPLGCFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
+>gi|927065 elongation factor 1-alpha 1
+MQSERGITIDISLWKFETSKYYVTIIDAPGHRDFIQNMITGTSQADCAVLIVAAGVGEFEAGISKNGQTR
+EHALLAYTLGVKQLIVGVNKMDSTEPPYSQKRYEEIVKEVSTYIKKIGYNPDTVAFVPISGWNGDNMLEP
+SANMPWFKGWKVTRKDGNASGTTLLEALDCILPPTRPTDKPLGLPLQDVYKIGGIGTVPVGRVETGVLKP
+GMVVTFGPVNVTTEVKSVEMHHEALGEALPGDNVGFNVKNVSVKDVRRGNVAGDSKNDPPMEAAGFPAQV
+IILNHPGQISAGYAPVLDCHTAHIACKFAELKEKIDRRSGKKLEDGPKFLKSGDAAIVDMVPGKPMCVES
+FSDYPPLGCFAVRDMRQTVAVGVIKAVDKKAAGAGKVTKSAQKAQKAK
+>gi|2981019 transcription factor POU4F3
+MMAMNSKQPFGMHPVLQEPKFSSLHSGSEAMRRVCLPAPQLQGNIFGSFDESLLARAEALAAVDIVFHGK
+NHPFKPDATYHTMSSVPCTSTSSTVPISHPAALTSHPHHAVHQGLEGDLLEHISPTLSVSGLGAPEHSVM
+PAQIHPHHLGAMGHLHQAMGMSHPHTVAPHSAMPACLSDVESDPRELEAFAERFKQRRIKLGVTQADVGA
+ALANLKIPGVGSLSQSTICRFESLTLSHNNMIALKPVLQAWLEEAEAAYREKNSKPELFNGSERKRKRTS
+IAAPEKRSLEAYFAIQPRPSSEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKYSAVH
+>gi|2980872|gnl|PID|e1283615 homeobox protein SHOTb
+MEDEGQTKIKQRRSRTNFTLEQLNELERLFDETHYPDAFMREELSQRLGLSEARVQVWFQNRRAKCRKQE
+NQLHKGVLIGAASQFEACRVAPYVNVGALRMPFQQVQAQLQLDSAVAHAHHHLHPHLAAHAPYMMFPAPP
+FGLPLATLAADSASAASVVAAAAAAKTTSKDSSIADLRLKAKKHAAALGL
+>gi|2980870|gnl|PID|e1283613 homeobox protein SHOTa
+GGAGGGAGGGRSPVRELDMGAAERSREPGSPRLTEVSPELKDRKEDAKGMEDEGQTKIKQRRSRTNFTLE
+QLNELERLFDETHYPDAFMREELSQRLGLSEARVQVWFQNRRAKCRKQENQLHKGVLIGAASQFEACRVA
+PYVNVGALRMPFQQDSHCNVTPLPFQVQAQLQLDSAVAHAHHHLHPHLAAHAPYMMFPAPPFGLPLATLA
+ADSASAASVVAAAAAAKTTSKDSSIADLRLKAKKHAAALGL
+>gi|2980865|gnl|PID|e1283649 NKG2D
+MGWIRGRRSRHSWEMSEFHNYNLDLKKSDFSTRWQKQRCPVVKSKCRENASPFFFCCFIAVAMGIRFIIM
+VAIWSAVFLNSLFNQEVQIPLTESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYSK
+EDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGYIENCSTPNTYI
+CMQRTV
+>gi|2980863|gnl|PID|e1283645 NKG2F
+MNKQRGTYSEVSLAQDPKRQQRKLKGNKSSISGTKQEIFQVELNLQNASSDHQGNDKTYHCKGLLPPPEK
+LTAEVLGIICIVLMATVLKTIVLIPCIGVLEQNSFSLNRRMQKARHCGHCPEEWITYSNSCYYIGKERRT
+WEERVCWPVLRRTLICFL
+>gi|2980861|gnl|PID|e1283610 NKG2E
+MNKQRGTFSEVSLAQDPKPQQRKPKGNKSSISGTEQEIFQVELNLQNASLNHQGIDKIYDCQGLLPPPEK
+LTAEVLGIICIVLMATVLKTIVLIPFLEQNNSSPNTRTQKARPCGHCPEEWITYSNSCYYIGKERRTWEE
+SLQACASKNSSSLLSIDNEEEMKFLASILPSSWIGVFRNSSHHPWVTINGLAFKHEIKDSDHAERNCAML
+HVRGLISDQCGSSRIIRRGFIMLTRLVLNS
+>gi|2980859|gnl|PID|e1283608 NKG2C
+MSKQRGTFSEVSLAQDPKRQQRKPKGNKSSISGTEQEIFQVELNLQNPSLNHQGIDKIYDCQGLLPPPEK
+LTAEVLGIICIVLMATVLKTIVLIPFLEQNNSSPNTRTQKARHCGHCPEEWITYSNSCYYIGKERRTWEE
+SLLACTSKNSSLLSIDNEEEMKFLASILPSSWIGVFRNSSHHPWVTINGLAFKHKIKDSDNAELNCAVLQ
+VNRLKSAQCGSSMIYHCKHKL
+>gi|2980857|gnl|PID|e1283606 NKG2F
+MNKQRGTYSEVSLAQDPKRQQRKLKGNKISISGTKQEIFQVELNLQNASSDHQGNDKTYHCKGLLPPPEK
+LTAEVLGIICIVLMATVLKTIVLIPCIGVLEQNNFSLNRRMQKARHCGHCPEEWITYSNSCYYIGKERRT
+WEERVCWPVLRRTLICFL
+>gi|2979422|gnl|PID|d1026124 PCDH7 (BH-Pcdh)c
+MLRMRTAGWARGWCLGCCLLLPLSFSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLES
+GSEYLKIDNLTGELSTSERRIDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNT
+PTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERYELLQEPGGGGSGGESRRAGAADSAPYPGGG
+GNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGVYEADLAENSAPGTPI
+LQLRAADLDVGVNGQIEYVFGAATESVRRLLRLDETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTD
+KATVVLNIKDENDNVPSIEIRKIGRIPLKDGVANVAEDVLVDTPIALVQVSDRDQGENGVVTCTVVGDVP
+FQLKPASDTEGDQNKKKYFLHTSTPLDYEATREFNVVIVAVDSGSPSLSSKNSLIVKVGDTNDNPPMFGQ
+SVVEVYFPENNIPGERVATVLATDADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEF
+KVNAKDKGIPVLQGSTTVIVQVADKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLY
+IEENNNIFSIENDTGTIYSTMSFDREHQTTYTFRVKAVDGGDPPRSATATVSLFVMDENDNAPTVTLPKN
+ISYTLLPPSSNVRTVVATVLATDSDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQKHYGLHRL
+VVQVNDSGQPSQSTTTVVHVFVNESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAG
+IMTVILIILIVVMARYCRSKNKNGYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEAS
+KPNGQRYDSVNEKLSDSPSMGRYRSVNGGPGSPDLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPA
+NTFVGAGDNISIGSDHCSEYSCQTNNKYSKQPFRRVTFSVVSQPQDPHQGSLQSCYDSGLEESETPSSKS
+SSGPRLGALPLPEDNYERTTPDGSVDSRPLPDVALTGKCTRECDEYGHSDSCWMPVRTSPERKKSQPKLS
+TFMPVDERGSQEKLANGEAAIMGDRNRNLLNKKLTSSYETFSAASFSKNEEANPEDIPLTKTGEYKPSPV
+NTLTRREVYL
+>gi|2979420|gnl|PID|d1026123 PCDH7 (BH-Pcdh)b
+MLRMRTAGWARGWCLGCCLLLPLSFSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLES
+GSEYLKIDNLTGELSTSERRIDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNT
+PTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERYELLQEPGGGGSGGESRRAGAADSAPYPGGG
+GNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGALDREQRDSYELTLRV
+RDGGDPPRSSQAILRVLITDVNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAA
+TESVRRLLRLDETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVPSIEIRKI
+GRIPLKDGVANVAEDVLVDTPIALVQVSDRDQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTS
+TPLDYEATREFNVVIVAVDSGSPSLSSKNSLIVKVGDTNDNPPMFGQSVVEVYFPENNIPGERVATVLAT
+DADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEFKVNAKDKGIPVLQGSTTVIVQVA
+DKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLYIEENNNIFSIENDTGTIYSTMSF
+DREHQTTYTFRVKAVDGGDPPRSATATVSLFVMDENDNAPTVTLPKNISYTLLPPSSNVRTVVATVLATD
+SDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQKHYGLHRLVVQVNDSGQPSQSTTTVVHVFVN
+ESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAGIMTVILIILIVVMARYCRSKNKN
+GYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEASKPNGQRYDSVNEKLSDSPSMGRY
+RSVNGGPGSPDLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPANTFVGAGDNISIGSDHCSEYSCQ
+TNNKYSKQVRCIPNIFKYPREG
+>gi|2979418|gnl|PID|d1026122 PCDH7 (BH-Pcdh)a
+MLRMRTAGWARGWCLGCCLLLPLSFSLAAAKQLLRYRLAEEGPADVRIGNVASDLGIVTGSGEVTFSLES
+GSEYLKIDNLTGELSTSERRIDREKLPQCQMIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNT
+PTFPSPVLTLTVEENRPVGTLYLLPTATDRDFGRNGIERYELLQEPGGGGSGGESRRAGAADSAPYPGGG
+GNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVADTPDGEKQPQLIVKGALDREQRDSYELTLRV
+RDGGDPPRSSQAILRVLITDVNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAA
+TESVRRLLRLDETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKATVVLNIKDENDNVPSIEIRKI
+GRIPLKDGVANVAEDVLVDTPIALVQVSDRDQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTS
+TPLDYEATREFNVVIVAVDSGSPSLSSKNSLIVKVGDTNDNPPMFGQSVVEVYFPENNIPGERVATVLAT
+DADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDREQTDRYEFKVNAKDKGIPVLQGSTTVIVQVA
+DKNDNDPKFMQDVFTFYVKENLQPNSPVGMVTVMDADKGRNAEMSLYIEENNNIFSIENDTGTIYSTMSF
+DREHQTTYTFRVKAVDGGDPPRSATATVSLFVMDENDNAPTVTLPKNISYTLLPPSSNVRTVVATVLATD
+SDDGINADLNYSIVGGNPFKLFEIDPTSGVVSLVGKLTQKHYGLHRLVVQVNDSGQPSQSTTTVVHVFVN
+ESVSNATAIDSQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAGIMTVILIILIVVMARYCRSKNKN
+GYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSSIVTVEASKPNGQRYDSVNEKLSDSPSMGRY
+RSVNGGPGSPDLARHYKSSSPLPTVQLHPQSPTAGKKHQAVQDLPPANTFVGAGDNISIGSDHCSEYSCQ
+TNNKYSKQMRLHPYITVFG
Modified: trunk/packages/seaview/trunk/makefile
===================================================================
--- trunk/packages/seaview/trunk/makefile 2006-09-19 14:20:29 UTC (rev 113)
+++ trunk/packages/seaview/trunk/makefile 2006-09-19 14:21:38 UTC (rev 114)
@@ -2,15 +2,18 @@
OBJECTS = seaview.o use_mase_files.o regions.o load_seq.o align.o xfmatpt.o comlines.o chooser_plus.o resource.o nexus.o old_file_chooser.o
-CFLAGS = -c $(OPT) -I$(FLTK) $(DEBUG)
+CFLAGS = -c $(OPT) -I. $(DEBUG)
-CXX = CC
+CXX = g++
seaview : $(OBJECTS)
- $(CXX) $(DEBUG) -o $@ $(OBJECTS) -L$(FLTK)/lib -lfltk -lX11 -lm
+ $(CXX) $(DEBUG) -o $@ $(OBJECTS) `fltk-config --ldflags`
.SUFFIXES: .cxx .h .o
.cxx.o :
$(CXX) $(CFLAGS) $<
+
+clean :
+ rm -f seaview $(OBJECTS)
Added: trunk/packages/seaview/trunk/seaview.1
===================================================================
--- trunk/packages/seaview/trunk/seaview.1 (rev 0)
+++ trunk/packages/seaview/trunk/seaview.1 2006-09-19 14:21:38 UTC (rev 114)
@@ -0,0 +1,43 @@
+.TH SEAVIEW 1
+.\" NAME should be all caps, SECTION should be 1-8, maybe w/ subsection
+.\" other parms are allowed: see man(7), man(1)
+.SH NAME
+seaview \- a multiple sequence alignment editor
+.SH SYNOPSIS
+.B seaview
+.I "[options] [filename]"
+.SH "DESCRIPTION"
+This manual page documents briefly the
+.BR seaview ,
+command.
+This manual page was written for the Debian GNU/Linux distribution
+because the original program does not have a manual page.
+Instead, it has online documentation, see below.
+.PP
+.B seaview
+is a graphical multiple sequence alignment editor. SeaView is able
+to read various alignment formats (MSF, CLUSTAL, FASTA, PHYLIP, MASE, NEXUS).
+It allows one to manually
+edit the alignment, and also to run DOT-PLOT or CLUSTAL programs to locally
+improve the alignment.
+.SH OPTIONS
+.TP
+.B \-save <format_name>
+format_name, either mase, clustal, phylip, msf, fasta, or nexus, sets the
+default file format for saving operations
+.TP
+.B \-fast
+sequences will be displayed faster but less smoothly
+.TP
+.B \-inverted
+residues will appear as black letters on a colored background
+.SH ARGUMENT
+"filename"
+is an optional alignment file to be loaded. The expected format for this file
+is that of the default format for saving operations.
+.SH "SEE ALSO"
+The program is fully documented online. Press the "help" button in the
+main window.
+.SH AUTHOR
+This manual page was written by Stephane Bortzmeyer <bortzmeyer at debian.org>,
+for the Debian GNU/Linux system (but may be used by others).
Modified: trunk/packages/seaview/trunk/seaview.cxx
===================================================================
--- trunk/packages/seaview/trunk/seaview.cxx 2006-09-19 14:20:29 UTC (rev 113)
+++ trunk/packages/seaview/trunk/seaview.cxx 2006-09-19 14:21:38 UTC (rev 114)
@@ -165,7 +165,7 @@
#elif defined(__APPLE__)
NULL,
#else
- "seaview.help",
+ "/usr/share/seaview/seaview.help",
#endif
resources );
strcpy(customdnacolors, get_res_value("dnacolors", "", resources) );
@@ -2851,14 +2851,14 @@
#ifdef __APPLE__
get_next_help_line(data, NULL, 0);
#else
- data = (void *)open_path( (char *)data );
+ data = (void *)fopen( (char *)data, "r" );
#endif
if(data == NULL) {
fl_alert(
#ifdef __APPLE__
"No help information in program resources"
#else
- "Help file %s\nnot found in PATH directories nor in current directory", (char *)data
+ "Help file %s\nnot found", (char *)data
#endif
);
return;
Modified: trunk/packages/seaview/trunk/seaview_align.sh
===================================================================
--- trunk/packages/seaview/trunk/seaview_align.sh 2006-09-19 14:20:29 UTC (rev 113)
+++ trunk/packages/seaview/trunk/seaview_align.sh 2006-09-19 14:21:38 UTC (rev 114)
@@ -11,7 +11,7 @@
echo ' '
echo ' '
echo 'Program clustalw terminated.'
-echo 'Load new alignment? [(y)/n] \c'
+echo -n 'Load new alignment? [(y)/n] '
read rep
if [ "$rep" = "n" ]; then
echo aborted > $arg1.status
Property changes on: trunk/packages/seaview/trunk/seaview_align.sh
___________________________________________________________________
Name: svn:executable
-
+ *
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