Date: Mon, 12 Jul 2004 14:34:58 GMT From: Choe@FreeBSD.org, Cheng-Dae <whitekid@netian.com> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/68950: [UPDATE] textproc/py-docutil from 2.4.1 to 2.8.0 Message-ID: <200407121434.i6CEYwlv010083@www.freebsd.org> Resent-Message-ID: <200407121440.i6CEeNqN026075@freefall.freebsd.org>
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>Number: 68950
>Category: ports
>Synopsis: [UPDATE] textproc/py-docutil from 2.4.1 to 2.8.0
>Confidential: no
>Severity: non-critical
>Priority: medium
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: change-request
>Submitter-Id: current-users
>Arrival-Date: Mon Jul 12 14:40:22 GMT 2004
>Closed-Date:
>Last-Modified:
>Originator: Choe, Cheng-Dae
>Release: FreeBSD 5.2.1-RELEASE-p9 i386
>Organization:
>Environment:
FreeBSD w.comdongin.com 5.2.1-RELEASE-p9 FreeBSD 5.2.1-RELEASE-p9 #3: Fri Jul 9 20:07:30 KST 2004 root@w.comdongin.com:/usr/obj/usr/src/sys/CDI i386
>Description:
[UPDATE] textproc/py-docutil from 2.4.1 to 2.8.0
>How-To-Repeat:
N/A
>Fix:
diff -ruN emboss.orig/Makefile emboss/Makefile
--- emboss.orig/Makefile Fri Jul 2 13:13:59 2004
+++ emboss/Makefile Mon Jul 12 18:45:11 2004
@@ -6,11 +6,10 @@
#
PORTNAME= emboss
-PORTVERSION= 2.4.1
-PORTREVISION= 3
+PORTVERSION= 2.8.0
CATEGORIES= biology
-MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/old/ \
- ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/old/
+MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
+ ftp://ftp.es.embnet.org/software/emboss/EMBOSS/
# ftp://ftp.ebi.ac.uk/pub/software/unix/EMBOSS/
DISTFILES= ${PORTNAME:U}-${PORTVERSION}${EXTRACT_SUFX}
DIST_SUBDIR= ${PORTNAME}
@@ -19,7 +18,8 @@
MAINTAINER= wjv@FreeBSD.org
COMMENT= A collection of open source tools for genetic sequence analysis
-LIB_DEPENDS= gd.4:${PORTSDIR}/graphics/gd
+LIB_DEPENDS= png.5:${PORTSDIR}/graphics/png \
+ gd.4:${PORTSDIR}/graphics/gd
USE_SUBMAKE= yes
USE_GMAKE= yes
@@ -101,7 +101,7 @@
@ cd ${${app}_WRKSRC} && \
${SETENV} CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" \
CXXFLAGS="${CXXFLAGS}" \
- INSTALL="/usr/bin/install -c -o ${BINOWN} -g ${BINGRP}" \
+ INSTALL="${INSTALL_PROGRAM} -c -o ${BINOWN} -g ${BINGRP}" \
INSTALL_DATA="${INSTALL_DATA}" \
INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
diff -ruN emboss.orig/Makefile.inc emboss/Makefile.inc
--- emboss.orig/Makefile.inc Mon Jul 12 18:48:56 2004
+++ emboss/Makefile.inc Thu Jan 1 09:00:00 1970
@@ -1,6 +0,0 @@
-WITH_EMNU= yes
-WITH_HMMER= yes
-WITH_MEME= yes
-WITH_MSE= yes
-WITH_PHYLIP= yes
-WITH_TOPO= yes
diff -ruN emboss.orig/distinfo emboss/distinfo
--- emboss.orig/distinfo Fri Jul 2 13:13:59 2004
+++ emboss/distinfo Mon Jul 12 23:22:35 2004
@@ -1,7 +1,14 @@
-MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad
+MD5 (emboss/EMBOSS-2.8.0.tar.gz) = 5692e52632546dfe4103b51dd1eaa3c3
+SIZE (emboss/EMBOSS-2.8.0.tar.gz) = 14024961
MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66
-MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21
-MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c
-MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9
-MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084
-MD5 (emboss/TOPO-0.1.tar.gz) = a5131f2e0d58e06ce071250b62cbe65a
+SIZE (emboss/EMNU-1.0.5.tar.gz) = 155143
+MD5 (emboss/HMMER-2.1.1.tar.gz) = 01686894a1d5ca4b93555648e4e192bd
+SIZE (emboss/HMMER-2.1.1.tar.gz) = 279298
+MD5 (emboss/MEME-2.3.1.tar.gz) = 941921287a49a691d2a78b8726b5ac88
+SIZE (emboss/MEME-2.3.1.tar.gz) = 145248
+MD5 (emboss/MSE-0.0.4.tar.gz) = 20661dce0e542b25d17bff86858f6cb2
+SIZE (emboss/MSE-0.0.4.tar.gz) = 133619
+MD5 (emboss/PHYLIP-3.573c.tar.gz) = 55c91edc768003f83342f4c8e5b345e4
+SIZE (emboss/PHYLIP-3.573c.tar.gz) = 571349
+MD5 (emboss/TOPO-0.1.tar.gz) = 416f5211bd9a7caee009c743e5a1a268
+SIZE (emboss/TOPO-0.1.tar.gz) = 81613
diff -ruN emboss.orig/files/patch-aa emboss/files/patch-aa
--- emboss.orig/files/patch-aa Fri Jul 2 13:13:59 2004
+++ emboss/files/patch-aa Thu Jan 1 09:00:00 1970
@@ -1,26 +0,0 @@
-Add ${PREFIX}/etc as an acceptable location for emboss.default. (I'm still
-waiting for this to be incorporated into an official release of EMBOSS.)
-
-The port installs ${PREFIX}/etc/emboss.default.sample
-
--- Johann <wjv@FreeBSD.org>
-
-
---- ajax/ajnam.c.orig Thu Aug 17 20:31:30 2000
-+++ ajax/ajnam.c Mon Aug 28 15:12:09 2000
-@@ -984,6 +984,15 @@
- prefixRootFile = fopen (ajStrStr(namRootStr), "r");
- }
-
-+ /* look for $(PREFIX)_ROOT/../emboss.default */
-+
-+ if (!prefixRootFile)
-+ {
-+ ajFmtPrintS (&namRootStr, "%s/etc/%s.default",
-+ namInstallRoot, prefix);
-+ prefixRootFile = fopen (ajStrStr(namRootStr), "r");
-+ }
-+
- if (namFileOrig)
- (void) ajStrAppC (&namFileOrig, ", ");
- (void) ajStrApp (&namFileOrig, namRootStr);
diff -ruN emboss.orig/files/patch-ajax::ajjava.c emboss/files/patch-ajax::ajjava.c
--- emboss.orig/files/patch-ajax::ajjava.c Fri Jul 2 13:13:59 2004
+++ emboss/files/patch-ajax::ajjava.c Thu Jan 1 09:00:00 1970
@@ -1,11 +0,0 @@
---- ajax/ajjava.c.orig Thu May 2 22:06:08 2002
-+++ ajax/ajjava.c Sun May 26 09:14:20 2002
-@@ -75,7 +75,7 @@
- #endif
-
- #ifndef __ppc__
--#include <crypt.h>
-+#include <unistd.h>
- #endif
-
-
diff -ruN emboss.orig/files/patch-configure emboss/files/patch-configure
--- emboss.orig/files/patch-configure Fri Jul 2 13:13:59 2004
+++ emboss/files/patch-configure Thu Jan 1 09:00:00 1970
@@ -1,11 +0,0 @@
---- configure.orig Mon Jan 22 23:28:17 2001
-+++ configure Thu Jan 25 19:07:33 2001
-@@ -1473,7 +1473,7 @@
-
-
-
--AJAX_FIXED_ROOT="\\\"`pwd`/emboss\\\""
-+AJAX_FIXED_ROOT="\\\"${datadir}/${PACKAGE}\\\""
-
- #AC_PROG_CXX
- for ac_prog in mawk gawk nawk awk
diff -ruN emboss.orig/files/patch-emboss-emboss.default.template emboss/files/patch-emboss-emboss.default.template
--- emboss.orig/files/patch-emboss-emboss.default.template Fri Jul 2 13:13:59 2004
+++ emboss/files/patch-emboss-emboss.default.template Thu Jan 1 09:00:00 1970
@@ -1,38 +0,0 @@
---- emboss/emboss.default.template.orig Thu May 24 19:36:39 2001
-+++ emboss/emboss.default.template Wed May 30 10:23:48 2001
-@@ -1,9 +1,31 @@
--#SET emboss_tempdata name_of_emboss_test_database_directory
-+#####################################################
-+### Configuration options for FreeBSD EMBOSS port ###
-+#####################################################
-
--# Logfile - set this to a file that any user can append to
--# and EMBOSS applications will automatically write log information
-+# The directory where EMBOSS expects to find run-time
-+# databases. This is the compiled-in default - change
-+# only if you know what you're doing!
-+#
-+#SET emboss_data %%PREFIX%%/share/EMBOSS/data
-
--#SET emboss_logfile /packages/emboss/emboss/log
-+# This is an alias which is internal to this
-+# configuration file and is set here merely as a
-+# convenience. It points to the location where you
-+# have placed your local databases (this will differ
-+# from site to site).
-+#
-+SET emboss_tempdata %%PREFIX%%/share/EMBOSS/databases
-+
-+# Logfile. If this is uncommented and set to a file
-+# that any user can append to, EMBOSS applications
-+# will automatically log usage information.
-+#
-+#SET emboss_logfile /var/log/emboss.log
-+
-+
-+###########################################
-+### Configuration options for databases ###
-+###########################################
-
- # swissprot (Puffer fish entries)
- # =========
diff -ruN emboss.orig/pkg-plist emboss/pkg-plist
--- emboss.orig/pkg-plist Fri Jul 2 13:13:59 2004
+++ emboss/pkg-plist Mon Jul 12 02:02:33 2004
@@ -1,94 +1,9 @@
-%%PLIST_EMNU%%bin/emnu
-%%PLIST_EMNU%%share/EMBOSS/acd/emnu.acd
-%%PLIST_HMMER%%bin/ealistat
-%%PLIST_HMMER%%bin/ehmmalign
-%%PLIST_HMMER%%bin/ehmmbuild
-%%PLIST_HMMER%%bin/ehmmcalibrate
-%%PLIST_HMMER%%bin/ehmmconvert
-%%PLIST_HMMER%%bin/ehmmemit
-%%PLIST_HMMER%%bin/ehmmfetch
-%%PLIST_HMMER%%bin/ehmmindex
-%%PLIST_HMMER%%bin/ehmmpfam
-%%PLIST_HMMER%%bin/ehmmsearch
-%%PLIST_HMMER%%lib/libhmmer.a
-%%PLIST_HMMER%%lib/libhmmer.la
-%%PLIST_HMMER%%lib/libhmmer.so
-%%PLIST_HMMER%%lib/libhmmer.so.2
-%%PLIST_HMMER%%share/EMBOSS/acd/ealistat.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmalign.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmbuild.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmcalibrate.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmconvert.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmemit.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmfetch.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmindex.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmpfam.acd
-%%PLIST_HMMER%%share/EMBOSS/acd/ehmmsearch.acd
-%%PLIST_MEME%%bin/meme
-%%PLIST_MEME%%lib/libmeme.a
-%%PLIST_MEME%%lib/libmeme.la
-%%PLIST_MEME%%lib/libmeme.so
-%%PLIST_MEME%%lib/libmeme.so.2
-%%PLIST_MEME%%share/EMBOSS/acd/meme.acd
-%%PLIST_MSE%%bin/mse
-%%PLIST_MSE%%lib/libckit.a
-%%PLIST_MSE%%lib/libckit.la
-%%PLIST_MSE%%lib/libckit.so
-%%PLIST_MSE%%lib/libckit.so.1
-%%PLIST_MSE%%share/EMBOSS/acd/mse.acd
-%%PLIST_PHYLIP%%bin/eclique
-%%PLIST_PHYLIP%%bin/econsense
-%%PLIST_PHYLIP%%bin/econtml
-%%PLIST_PHYLIP%%bin/econtrast
-%%PLIST_PHYLIP%%bin/ednacomp
-%%PLIST_PHYLIP%%bin/ednadist
-%%PLIST_PHYLIP%%bin/ednainvar
-%%PLIST_PHYLIP%%bin/ednaml
-%%PLIST_PHYLIP%%bin/ednamlk
-%%PLIST_PHYLIP%%bin/ednapars
-%%PLIST_PHYLIP%%bin/ednapenny
-%%PLIST_PHYLIP%%bin/edollop
-%%PLIST_PHYLIP%%bin/edolpenny
-%%PLIST_PHYLIP%%bin/efactor
-%%PLIST_PHYLIP%%bin/efitch
-%%PLIST_PHYLIP%%bin/egendist
-%%PLIST_PHYLIP%%bin/ekitsch
-%%PLIST_PHYLIP%%bin/emix
-%%PLIST_PHYLIP%%bin/eneighbor
-%%PLIST_PHYLIP%%bin/epenny
-%%PLIST_PHYLIP%%bin/eprotdist
-%%PLIST_PHYLIP%%bin/eprotpars
-%%PLIST_PHYLIP%%bin/erestml
-%%PLIST_PHYLIP%%bin/eseqboot
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eclique.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/econsense.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/econtml.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/econtrast.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednacomp.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednadist.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednainvar.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednaml.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednamlk.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapars.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ednapenny.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/edollop.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/edolpenny.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/efactor.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/efitch.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/egendist.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/ekitsch.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/emix.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eneighbor.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/epenny.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotdist.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eprotpars.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/erestml.acd
-%%PLIST_PHYLIP%%share/EMBOSS/acd/eseqboot.acd
-%%PLIST_TOPO%%bin/topo
-%%PLIST_TOPO%%share/EMBOSS/acd/topo.acd
+bin/aaindexextract
bin/abiview
bin/acdc
-bin/alignwrap
+bin/acdpretty
+bin/acdtable
+bin/acdvalid
bin/antigenic
bin/backtranseq
bin/banana
@@ -104,7 +19,6 @@
bin/coderet
bin/compseq
bin/cons
-bin/contacts
bin/cpgplot
bin/cpgreport
bin/cusp
@@ -117,11 +31,9 @@
bin/dbigcg
bin/degapseq
bin/descseq
-bin/dichet
bin/diffseq
bin/digest
bin/distmat
-bin/domainer
bin/dotmatcher
bin/dotpath
bin/dottup
@@ -132,6 +44,8 @@
bin/emma
bin/emowse
bin/entret
+bin/epestfind
+bin/eprimer3
bin/equicktandem
bin/est2genome
bin/etandem
@@ -151,6 +65,7 @@
bin/infoalign
bin/infoseq
bin/isochore
+bin/jembossctl
bin/lindna
bin/listor
bin/marscan
@@ -160,6 +75,7 @@
bin/megamerger
bin/merger
bin/msbar
+bin/mwcontam
bin/mwfilter
bin/needle
bin/newcpgreport
@@ -167,7 +83,6 @@
bin/newseq
bin/noreturn
bin/notseq
-bin/nrscope
bin/nthseq
bin/octanol
bin/oddcomp
@@ -195,7 +110,6 @@
bin/prophet
bin/prosextract
bin/pscan
-bin/psiblasts
bin/rebaseextract
bin/recoder
bin/redata
@@ -204,8 +118,6 @@
bin/restrict
bin/revseq
bin/runJemboss.csh
-bin/scopalign
-bin/scope
bin/seealso
bin/seqmatchall
bin/seqret
@@ -217,29 +129,35 @@
bin/showseq
bin/shuffleseq
bin/sigcleave
-bin/siggen
-bin/sigscan
bin/silent
+bin/sirna
+bin/sixpack
+bin/skipseq
bin/splitter
bin/stretcher
bin/stssearch
bin/supermatcher
-bin/swissparse
bin/syco
+bin/tcode
bin/textsearch
bin/tfextract
bin/tfm
bin/tfscan
bin/tmap
+bin/tranalign
bin/transeq
bin/trimest
bin/trimseq
+bin/twofeat
+bin/union
bin/vectorstrip
bin/water
+bin/whichdb
bin/wobble
bin/wordcount
bin/wordmatch
bin/wossname
+bin/yank
etc/emboss.default.sample
lib/libajax.a
lib/libajax.la
@@ -257,11 +175,11 @@
lib/libplplot.la
lib/libplplot.so
lib/libplplot.so.5
+share/EMBOSS/acd/aaindexextract.acd
share/EMBOSS/acd/abiview.acd
share/EMBOSS/acd/ajbad.acd
share/EMBOSS/acd/ajfeatest.acd
share/EMBOSS/acd/ajtest.acd
-share/EMBOSS/acd/alignwrap.acd
share/EMBOSS/acd/antigenic.acd
share/EMBOSS/acd/backtranseq.acd
share/EMBOSS/acd/banana.acd
@@ -279,7 +197,6 @@
share/EMBOSS/acd/complex.acd
share/EMBOSS/acd/compseq.acd
share/EMBOSS/acd/cons.acd
-share/EMBOSS/acd/contacts.acd
share/EMBOSS/acd/corbatest.acd
share/EMBOSS/acd/cpgplot.acd
share/EMBOSS/acd/cpgreport.acd
@@ -300,11 +217,9 @@
share/EMBOSS/acd/demostring.acd
share/EMBOSS/acd/demotable.acd
share/EMBOSS/acd/descseq.acd
-share/EMBOSS/acd/dichet.acd
share/EMBOSS/acd/diffseq.acd
share/EMBOSS/acd/digest.acd
share/EMBOSS/acd/distmat.acd
-share/EMBOSS/acd/domainer.acd
share/EMBOSS/acd/dotmatcher.acd
share/EMBOSS/acd/dotpath.acd
share/EMBOSS/acd/dottup.acd
@@ -316,6 +231,7 @@
share/EMBOSS/acd/emowse.acd
share/EMBOSS/acd/entrails.acd
share/EMBOSS/acd/entret.acd
+share/EMBOSS/acd/epestfind.acd
share/EMBOSS/acd/eprimer3.acd
share/EMBOSS/acd/equicktandem.acd
share/EMBOSS/acd/est2genome.acd
@@ -330,13 +246,13 @@
share/EMBOSS/acd/garnier.acd
share/EMBOSS/acd/geecee.acd
share/EMBOSS/acd/getorf.acd
+share/EMBOSS/acd/groups.standard
share/EMBOSS/acd/helixturnhelix.acd
share/EMBOSS/acd/histogramtest.acd
share/EMBOSS/acd/hmoment.acd
share/EMBOSS/acd/iep.acd
share/EMBOSS/acd/infoalign.acd
share/EMBOSS/acd/infoseq.acd
-share/EMBOSS/acd/interface.acd
share/EMBOSS/acd/isochore.acd
share/EMBOSS/acd/lindna.acd
share/EMBOSS/acd/listor.acd
@@ -347,14 +263,15 @@
share/EMBOSS/acd/megamerger.acd
share/EMBOSS/acd/merger.acd
share/EMBOSS/acd/msbar.acd
+share/EMBOSS/acd/mwcontam.acd
share/EMBOSS/acd/mwfilter.acd
share/EMBOSS/acd/needle.acd
+share/EMBOSS/acd/newcoils.acd
share/EMBOSS/acd/newcpgreport.acd
share/EMBOSS/acd/newcpgseek.acd
share/EMBOSS/acd/newseq.acd
share/EMBOSS/acd/noreturn.acd
share/EMBOSS/acd/notseq.acd
-share/EMBOSS/acd/nrscope.acd
share/EMBOSS/acd/nthseq.acd
share/EMBOSS/acd/octanol.acd
share/EMBOSS/acd/oddcomp.acd
@@ -363,7 +280,6 @@
share/EMBOSS/acd/patmatdb.acd
share/EMBOSS/acd/patmatmotifs.acd
share/EMBOSS/acd/patmattest.acd
-share/EMBOSS/acd/pdbtosp.acd
share/EMBOSS/acd/pepcoil.acd
share/EMBOSS/acd/pepinfo.acd
share/EMBOSS/acd/pepnet.acd
@@ -386,7 +302,6 @@
share/EMBOSS/acd/prophet.acd
share/EMBOSS/acd/prosextract.acd
share/EMBOSS/acd/pscan.acd
-share/EMBOSS/acd/psiblasts.acd
share/EMBOSS/acd/rebaseextract.acd
share/EMBOSS/acd/recoder.acd
share/EMBOSS/acd/redata.acd
@@ -394,20 +309,17 @@
share/EMBOSS/acd/restover.acd
share/EMBOSS/acd/restrict.acd
share/EMBOSS/acd/revseq.acd
-share/EMBOSS/acd/scopalign.acd
-share/EMBOSS/acd/scopparse.acd
-share/EMBOSS/acd/scope.acd
+share/EMBOSS/acd/sections.standard
share/EMBOSS/acd/seealso.acd
share/EMBOSS/acd/seqinfo.acd
share/EMBOSS/acd/seqmatchall.acd
-share/EMBOSS/acd/seqnr.acd
share/EMBOSS/acd/seqret.acd
share/EMBOSS/acd/seqretall.acd
share/EMBOSS/acd/seqretallfeat.acd
share/EMBOSS/acd/seqretset.acd
share/EMBOSS/acd/seqretsingle.acd
share/EMBOSS/acd/seqretsplit.acd
-share/EMBOSS/acd/seqsort.acd
+share/EMBOSS/acd/seqrettype.acd
share/EMBOSS/acd/showalign.acd
share/EMBOSS/acd/showdb.acd
share/EMBOSS/acd/showfeat.acd
@@ -415,15 +327,16 @@
share/EMBOSS/acd/showseq.acd
share/EMBOSS/acd/shuffleseq.acd
share/EMBOSS/acd/sigcleave.acd
-share/EMBOSS/acd/siggen.acd
-share/EMBOSS/acd/sigscan.acd
share/EMBOSS/acd/silent.acd
+share/EMBOSS/acd/sirna.acd
+share/EMBOSS/acd/sixpack.acd
+share/EMBOSS/acd/skipseq.acd
share/EMBOSS/acd/splitter.acd
share/EMBOSS/acd/stretcher.acd
share/EMBOSS/acd/stssearch.acd
share/EMBOSS/acd/supermatcher.acd
-share/EMBOSS/acd/swissparse.acd
share/EMBOSS/acd/syco.acd
+share/EMBOSS/acd/tcode.acd
share/EMBOSS/acd/testplot.acd
share/EMBOSS/acd/textsearch.acd
share/EMBOSS/acd/tfextract.acd
@@ -435,6 +348,7 @@
share/EMBOSS/acd/treetypedisplay.acd
share/EMBOSS/acd/trimest.acd
share/EMBOSS/acd/trimseq.acd
+share/EMBOSS/acd/twofeat.acd
share/EMBOSS/acd/union.acd
share/EMBOSS/acd/vectorstrip.acd
share/EMBOSS/acd/water.acd
@@ -444,6 +358,7 @@
share/EMBOSS/acd/wordmatch.acd
share/EMBOSS/acd/wossname.acd
share/EMBOSS/acd/yank.acd
+share/EMBOSS/data/AAINDEX/dummyfile
share/EMBOSS/data/CODONS/Eacc.cut
share/EMBOSS/data/CODONS/Eadenovirus5.cut
share/EMBOSS/data/CODONS/Eadenovirus7.cut
@@ -704,7 +619,10 @@
share/EMBOSS/data/Efreqs.dat
share/EMBOSS/data/Ehth.dat
share/EMBOSS/data/Ehth87.dat
+share/EMBOSS/data/Emass.dat
+share/EMBOSS/data/Emassmod.dat
share/EMBOSS/data/Ememe.dat
+share/EMBOSS/data/Emwfilter.dat
share/EMBOSS/data/Enakai.dat
share/EMBOSS/data/Epepcoil.dat
share/EMBOSS/data/Epk.dat
@@ -720,14 +638,15 @@
share/EMBOSS/data/Etags.pir
share/EMBOSS/data/Etags.protein
share/EMBOSS/data/Etags.swiss
+share/EMBOSS/data/Etcode.dat
share/EMBOSS/data/Ewhite-wimley.dat
share/EMBOSS/data/PRINTS/dummyfile
share/EMBOSS/data/PROSITE/dummyfile
share/EMBOSS/data/REBASE/dummyfile
share/EMBOSS/data/embossre.equ
share/EMBOSS/emboss.default.template
-share/EMBOSS/jemboss/README
share/EMBOSS/jemboss/LICENSE
+share/EMBOSS/jemboss/README
share/EMBOSS/jemboss/api/allclasses-frame.html
share/EMBOSS/jemboss/api/deprecated-list.html
share/EMBOSS/jemboss/api/getClasses.pl
@@ -751,6 +670,8 @@
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/filetree/FileNode.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/filetree/FileSaving.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/BuildJembossForm.html
+share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.html
+share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.myComboUI.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/ListFilePanel.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/SectionPanel.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/SetInFileCard.html
@@ -760,8 +681,6 @@
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.WholeNumberDocument.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/TextFieldSink.html
-share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/myComboPopup.html
-share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/form/myComboPopup.myComboUI.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/FileChooser.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.html
@@ -777,7 +696,6 @@
share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/Ajax.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/Dependent.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/ParseAcd.html
-share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd/Application.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationFields.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationParam.html
share/EMBOSS/jemboss/api/org/emboss/jemboss/programs/JembossProcess.html
@@ -807,43 +725,94 @@
share/EMBOSS/jemboss/images/Job_manager_button.gif
share/EMBOSS/jemboss/images/Refresh_button.gif
share/EMBOSS/jemboss/images/Refresh_button2.gif
+share/EMBOSS/jemboss/lib/JembossPrintAlignment.jar
share/EMBOSS/jemboss/lib/README
share/EMBOSS/jemboss/lib/activation.jar
+share/EMBOSS/jemboss/lib/axis/axis-ant.jar
+share/EMBOSS/jemboss/lib/axis/axis.jar
+share/EMBOSS/jemboss/lib/axis/commons-discovery.jar
+share/EMBOSS/jemboss/lib/axis/commons-logging.jar
+share/EMBOSS/jemboss/lib/axis/jaxrpc.jar
+share/EMBOSS/jemboss/lib/axis/log4j-1.2.8.jar
+share/EMBOSS/jemboss/lib/axis/saaj.jar
+share/EMBOSS/jemboss/lib/axis/servlet.jar
+share/EMBOSS/jemboss/lib/axis/wsdl4j.jar
+share/EMBOSS/jemboss/lib/grout.jar
share/EMBOSS/jemboss/lib/jakarta-regexp-1.2.jar
share/EMBOSS/jemboss/lib/jalview.jar
-share/EMBOSS/jemboss/lib/mail.jar
-share/EMBOSS/jemboss/lib/soap.jar
-share/EMBOSS/jemboss/lib/xerces.jar
share/EMBOSS/jemboss/lib/jcert.jar
share/EMBOSS/jemboss/lib/jnet.jar
share/EMBOSS/jemboss/lib/jsse.jar
+share/EMBOSS/jemboss/lib/mail.jar
+share/EMBOSS/jemboss/lib/xerces.jar
share/EMBOSS/jemboss/org/emboss/jemboss/Jemboss.java
+share/EMBOSS/jemboss/org/emboss/jemboss/JembossJarUtil.java
share/EMBOSS/jemboss/org/emboss/jemboss/JembossLogo.java
share/EMBOSS/jemboss/org/emboss/jemboss/JembossParams.java
-share/EMBOSS/jemboss/org/emboss/jemboss/JembossJarUtil.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/AlignApplet.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/AlignJFrame.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/ColourJFrame.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/ColourMenu.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/ColourPanel.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/Consensus.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/ConsensusOptions.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/GraphicSequenceCollection.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/GroutAlignJFrame.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameEvent.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameListener.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollection.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionEvent.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionListener.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/GroutSequence.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/GroutSequenceJPanel.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/IDTableJFrame.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/Matrix.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/MatrixJFrame.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/PatternJFrame.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/PlotConsensus.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/PrettyPlotJFrame.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/PrintAlignment.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/PrintAlignmentImage.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/PrintableJTable.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/Sequence.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/SequenceJPanel.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/SequenceNameJButton.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/SequenceProperties.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/SequenceReader.java
+share/EMBOSS/jemboss/org/emboss/jemboss/editor/SequenceSaver.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/Browser.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/LaunchJalView.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/ScrollPanel.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceData.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceList.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/SplashThread.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/SwingWorker.java
-share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceData.java
-share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceList.java
-share/EMBOSS/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileSave.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileSaving.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/LocalAndRemoteFileTreeFrame.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileNode.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileTreePanel.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/ApplicationNamePanel.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/JembossComboPopup.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/LabelTextBox.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/ListFilePanel.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/MultiLineToolTipUI.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/PlafMacros.java
+share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/SectionPanel.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/Separator.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/SetInFileCard.java
@@ -851,7 +820,6 @@
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/TextFieldFloat.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/TextFieldInt.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/TextFieldSink.java
-share/EMBOSS/jemboss/org/emboss/jemboss/gui/form/myComboPopup.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/sequenceChooser/FileChooser.java
share/EMBOSS/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java
@@ -862,61 +830,69 @@
share/EMBOSS/jemboss/org/emboss/jemboss/gui/startup/ProgList.java
share/EMBOSS/jemboss/org/emboss/jemboss/parser/AcdFunResolve.java
share/EMBOSS/jemboss/org/emboss/jemboss/parser/AcdVarResolve.java
+share/EMBOSS/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java
share/EMBOSS/jemboss/org/emboss/jemboss/parser/Ajax.java
+share/EMBOSS/jemboss/org/emboss/jemboss/parser/AjaxUtil.java
share/EMBOSS/jemboss/org/emboss/jemboss/parser/Dependent.java
share/EMBOSS/jemboss/org/emboss/jemboss/parser/ParseAcd.java
-share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/Application.java
share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java
share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java
-share/EMBOSS/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java
-share/EMBOSS/jemboss/org/emboss/jemboss/parser/AjaxUtil.java
share/EMBOSS/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java
share/EMBOSS/jemboss/org/emboss/jemboss/programs/JembossProcess.java
share/EMBOSS/jemboss/org/emboss/jemboss/programs/ListFile.java
share/EMBOSS/jemboss/org/emboss/jemboss/programs/ResultList.java
share/EMBOSS/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java
share/EMBOSS/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java
-share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossServer.java
-share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileServer.java
-share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossThread.java
+share/EMBOSS/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java
+share/EMBOSS/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
-share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossAuthThread.java
share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java
+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileServer.java
+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossServer.java
+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossThread.java
+share/EMBOSS/jemboss/org/emboss/jemboss/server/TestPrivateServer.java
share/EMBOSS/jemboss/org/emboss/jemboss/server/TestPublicServer.java
share/EMBOSS/jemboss/org/emboss/jemboss/soap/AuthPopup.java
share/EMBOSS/jemboss/org/emboss/jemboss/soap/CallAjax.java
+share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileList.java
+share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileRoots.java
+share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetACD.java
+share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetHelp.java
share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetWossname.java
share/EMBOSS/jemboss/org/emboss/jemboss/soap/JembossRun.java
share/EMBOSS/jemboss/org/emboss/jemboss/soap/JembossSoapException.java
+share/EMBOSS/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
share/EMBOSS/jemboss/org/emboss/jemboss/soap/PendingResults.java
share/EMBOSS/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
-share/EMBOSS/jemboss/org/emboss/jemboss/soap/ServerSetup.java
-share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileRoots.java
-share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileList.java
share/EMBOSS/jemboss/org/emboss/jemboss/soap/PublicRequest.java
-share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetACD.java
-share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetHelp.java
+share/EMBOSS/jemboss/org/emboss/jemboss/soap/ServerSetup.java
share/EMBOSS/jemboss/org/emboss/jemboss/soap/ShowDB.java
-share/EMBOSS/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
+share/EMBOSS/jemboss/readme.html
+share/EMBOSS/jemboss/resources/filemgr.html
+share/EMBOSS/jemboss/resources/jemboss.properties
+share/EMBOSS/jemboss/resources/readme.html
+share/EMBOSS/jemboss/resources/readmeAlign.html
+share/EMBOSS/jemboss/resources/results.html
+share/EMBOSS/jemboss/resources/seqList.html
+share/EMBOSS/jemboss/resources/version
+share/EMBOSS/jemboss/runJemboss.sh
+share/EMBOSS/jemboss/utils/README
share/EMBOSS/jemboss/utils/install-jemboss-server.sh
share/EMBOSS/jemboss/utils/keys.sh
+share/EMBOSS/jemboss/utils/makeFileManagerJNLP.sh
share/EMBOSS/jemboss/utils/makeJNLP.sh
-share/EMBOSS/jemboss/utils/template.html
-share/EMBOSS/jemboss/utils/README
share/EMBOSS/jemboss/utils/makeJar.csh
-share/EMBOSS/jemboss/readme.html
-share/EMBOSS/jemboss/resources/jemboss.properties
-share/EMBOSS/jemboss/resources/readme.txt
-share/EMBOSS/jemboss/resources/version
-share/EMBOSS/jemboss/runJemboss.csh
+share/EMBOSS/jemboss/utils/template.html
share/EMBOSS/plstnd5.fnt
share/EMBOSS/plxtnd5.fnt
+share/EMBOSS/test/data/aaindex1.test
share/EMBOSS/test/data/aligna.dna
share/EMBOSS/test/data/aligna.prot
share/EMBOSS/test/data/alignapart.dna
share/EMBOSS/test/data/alignapart.prot
share/EMBOSS/test/data/alignb.dna
share/EMBOSS/test/data/alignb.prot
+share/EMBOSS/test/data/cutg.codon
share/EMBOSS/test/data/dna.acedb
share/EMBOSS/test/data/dna.aln
share/EMBOSS/test/data/dna.asn1
@@ -946,8 +922,14 @@
share/EMBOSS/test/data/feat.emft
share/EMBOSS/test/data/feat.fasta
share/EMBOSS/test/data/feat.pir
+share/EMBOSS/test/data/mw1.dat
+share/EMBOSS/test/data/mw2.dat
+share/EMBOSS/test/data/mw3.dat
share/EMBOSS/test/data/paamir.pep
share/EMBOSS/test/data/pax6_cdna.fasta
+share/EMBOSS/test/data/prints.test
+share/EMBOSS/test/data/prosite.dat
+share/EMBOSS/test/data/prosite.doc
share/EMBOSS/test/data/prot.acedb
share/EMBOSS/test/data/prot.codata
share/EMBOSS/test/data/prot.fasta
@@ -964,8 +946,10 @@
share/EMBOSS/test/data/prot.ncbi
share/EMBOSS/test/data/prot.swiss
share/EMBOSS/test/data/prot.text
+share/EMBOSS/test/data/site.dat
share/EMBOSS/test/data/tranalign.pep
share/EMBOSS/test/data/tranalign.seq
+share/EMBOSS/test/data/withrefm
share/EMBOSS/test/data/z83307.seq
share/EMBOSS/test/embl/acnum.hit
share/EMBOSS/test/embl/acnum.trg
@@ -989,18 +973,28 @@
share/EMBOSS/test/embl/taxon.trg
share/EMBOSS/test/embl/vrl.dat
share/EMBOSS/test/embl/vrt.dat
+share/EMBOSS/test/gb/acnum.hit
+share/EMBOSS/test/gb/acnum.trg
+share/EMBOSS/test/gb/ba.ref
+share/EMBOSS/test/gb/ba.seq
+share/EMBOSS/test/gb/des.hit
+share/EMBOSS/test/gb/des.trg
+share/EMBOSS/test/gb/division.lkp
+share/EMBOSS/test/gb/entrynam.idx
+share/EMBOSS/test/gb/htg.ref
+share/EMBOSS/test/gb/htg.seq
+share/EMBOSS/test/gb/keyword.hit
+share/EMBOSS/test/gb/keyword.trg
+share/EMBOSS/test/gb/seqvn.hit
+share/EMBOSS/test/gb/seqvn.trg
+share/EMBOSS/test/gb/taxon.hit
+share/EMBOSS/test/gb/taxon.trg
share/EMBOSS/test/genbank/acnum.hit
share/EMBOSS/test/genbank/acnum.trg
-share/EMBOSS/test/genbank/division.lkp
-share/EMBOSS/test/genbank/entrynam.idx
-share/EMBOSS/test/genbank/seqvn.hit
-share/EMBOSS/test/genbank/seqvn.trg
share/EMBOSS/test/genbank/des.hit
share/EMBOSS/test/genbank/des.trg
-share/EMBOSS/test/genbank/keyword.hit
-share/EMBOSS/test/genbank/keyword.trg
-share/EMBOSS/test/genbank/taxon.hit
-share/EMBOSS/test/genbank/taxon.trg
+share/EMBOSS/test/genbank/division.lkp
+share/EMBOSS/test/genbank/entrynam.idx
share/EMBOSS/test/genbank/gbbct1.seq
share/EMBOSS/test/genbank/gbest1.seq
share/EMBOSS/test/genbank/gbinv1.seq
@@ -1011,22 +1005,12 @@
share/EMBOSS/test/genbank/gbsts1.seq
share/EMBOSS/test/genbank/gbvrl1.seq
share/EMBOSS/test/genbank/gbvrt.seq
-share/EMBOSS/test/gb/acnum.hit
-share/EMBOSS/test/gb/acnum.trg
-share/EMBOSS/test/gb/division.lkp
-share/EMBOSS/test/gb/entrynam.idx
-share/EMBOSS/test/gb/seqvn.hit
-share/EMBOSS/test/gb/seqvn.trg
-share/EMBOSS/test/gb/des.hit
-share/EMBOSS/test/gb/des.trg
-share/EMBOSS/test/gb/keyword.hit
-share/EMBOSS/test/gb/keyword.trg
-share/EMBOSS/test/gb/taxon.hit
-share/EMBOSS/test/gb/taxon.trg
-share/EMBOSS/test/gb/ba.ref
-share/EMBOSS/test/gb/ba.seq
-share/EMBOSS/test/gb/htg.ref
-share/EMBOSS/test/gb/htg.seq
+share/EMBOSS/test/genbank/keyword.hit
+share/EMBOSS/test/genbank/keyword.trg
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+share/EMBOSS/test/genbank/seqvn.trg
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share/EMBOSS/test/pir/acnum.hit
share/EMBOSS/test/pir/acnum.trg
share/EMBOSS/test/pir/des.hit
@@ -1035,8 +1019,6 @@
share/EMBOSS/test/pir/entrynam.idx
share/EMBOSS/test/pir/keyword.hit
share/EMBOSS/test/pir/keyword.trg
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-share/EMBOSS/test/pir/taxon.trg
share/EMBOSS/test/pir/pir1.header
share/EMBOSS/test/pir/pir1.names
share/EMBOSS/test/pir/pir1.numbers
@@ -1061,41 +1043,43 @@
share/EMBOSS/test/pir/pir4.offset
share/EMBOSS/test/pir/pir4.ref
share/EMBOSS/test/pir/pir4.seq
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share/EMBOSS/test/swiss/acnum.hit
share/EMBOSS/test/swiss/acnum.trg
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share/EMBOSS/test/swiss/division.lkp
share/EMBOSS/test/swiss/entrynam.idx
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share/EMBOSS/test/swiss/seq.dat
share/EMBOSS/test/swiss/seqvn.hit
share/EMBOSS/test/swiss/seqvn.trg
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share/EMBOSS/test/swiss/taxon.hit
share/EMBOSS/test/swiss/taxon.trg
share/EMBOSS/test/swnew/acnum.hit
share/EMBOSS/test/swnew/acnum.trg
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share/EMBOSS/test/swnew/division.lkp
share/EMBOSS/test/swnew/entrynam.idx
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share/EMBOSS/test/swnew/new_seq.dat
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share/EMBOSS/test/swnew/seqvn.hit
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share/EMBOSS/test/swnew/taxon.hit
share/EMBOSS/test/swnew/taxon.trg
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share/EMBOSS/test/wormpep/acnum.hit
share/EMBOSS/test/wormpep/acnum.trg
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share/EMBOSS/test/wormpep/division.lkp
share/EMBOSS/test/wormpep/entrynam.idx
share/EMBOSS/test/wormpep/wormpep
-share/EMBOSS/test/wormpep/des.hit
-share/EMBOSS/test/wormpep/des.trg
share/doc/EMBOSS/manuals/EMBOSS-FreeBSD-HOWTO.txt
share/doc/EMBOSS/manuals/admin.aux
share/doc/EMBOSS/manuals/admin.dvi
@@ -1106,12 +1090,15 @@
share/doc/EMBOSS/manuals/admin.tex
share/doc/EMBOSS/manuals/admin.toc
share/doc/EMBOSS/manuals/adminguide.tar.gz
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share/doc/EMBOSS/manuals/emboss_qg.pdf
share/doc/EMBOSS/manuals/emboss_qg.ps
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share/doc/EMBOSS/manuals/program.ps.gz
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share/doc/EMBOSS/programs/html/abiview.html
-share/doc/EMBOSS/programs/html/abiview0.gif
-share/doc/EMBOSS/programs/html/ajtest.html
share/doc/EMBOSS/programs/html/alignment_consensus_group.html
share/doc/EMBOSS/programs/html/alignment_differences_group.html
share/doc/EMBOSS/programs/html/alignment_dot_plots_group.html
@@ -1121,15 +1108,15 @@
share/doc/EMBOSS/programs/html/antigenic.html
share/doc/EMBOSS/programs/html/backtranseq.html
share/doc/EMBOSS/programs/html/banana.html
-share/doc/EMBOSS/programs/html/banana0.gif
share/doc/EMBOSS/programs/html/biosed.html
share/doc/EMBOSS/programs/html/btwisted.html
share/doc/EMBOSS/programs/html/cai.html
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share/doc/EMBOSS/programs/html/chaos.html
-share/doc/EMBOSS/programs/html/chaos0.gif
share/doc/EMBOSS/programs/html/charge.html
share/doc/EMBOSS/programs/html/checktrans.html
share/doc/EMBOSS/programs/html/chips.html
+share/doc/EMBOSS/programs/html/cirdna.1.cirdna.gif
share/doc/EMBOSS/programs/html/cirdna.html
share/doc/EMBOSS/programs/html/clique.html
share/doc/EMBOSS/programs/html/codcmp.html
@@ -1140,12 +1127,13 @@
share/doc/EMBOSS/programs/html/contacts.html
share/doc/EMBOSS/programs/html/contml.html
share/doc/EMBOSS/programs/html/contrast.html
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share/doc/EMBOSS/programs/html/cpgplot.html
-share/doc/EMBOSS/programs/html/cpgplot0.gif
share/doc/EMBOSS/programs/html/cpgreport.html
share/doc/EMBOSS/programs/html/cusp.html
share/doc/EMBOSS/programs/html/cutgextract.html
share/doc/EMBOSS/programs/html/cutseq.html
+share/doc/EMBOSS/programs/html/dan.2.dan.gif
share/doc/EMBOSS/programs/html/dan.html
share/doc/EMBOSS/programs/html/dbiblast.html
share/doc/EMBOSS/programs/html/dbifasta.html
@@ -1167,11 +1155,12 @@
share/doc/EMBOSS/programs/html/dollop.html
share/doc/EMBOSS/programs/html/dolpenny.html
share/doc/EMBOSS/programs/html/domainer.html
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share/doc/EMBOSS/programs/html/dotmatcher.html
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share/doc/EMBOSS/programs/html/dotpath.html
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share/doc/EMBOSS/programs/html/dottup.html
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share/doc/EMBOSS/programs/html/dreg.html
share/doc/EMBOSS/programs/html/eclique.html
share/doc/EMBOSS/programs/html/econsense.html
@@ -1193,6 +1182,7 @@
share/doc/EMBOSS/programs/html/einverted.html
share/doc/EMBOSS/programs/html/ekitsch.html
share/doc/EMBOSS/programs/html/emboss_icon.gif
+share/doc/EMBOSS/programs/html/emboss_icon.jpg
share/doc/EMBOSS/programs/html/embossdata.html
share/doc/EMBOSS/programs/html/embossversion.html
share/doc/EMBOSS/programs/html/emix.html
@@ -1202,6 +1192,8 @@
share/doc/EMBOSS/programs/html/entret.html
share/doc/EMBOSS/programs/html/enzyme_kinetics_group.html
share/doc/EMBOSS/programs/html/epenny.html
+share/doc/EMBOSS/programs/html/epestfind.html
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share/doc/EMBOSS/programs/html/eprotdist.html
share/doc/EMBOSS/programs/html/eprotpars.html
share/doc/EMBOSS/programs/html/equicktandem.html
@@ -1213,8 +1205,8 @@
share/doc/EMBOSS/programs/html/extractseq.html
share/doc/EMBOSS/programs/html/factor.html
share/doc/EMBOSS/programs/html/feature_tables_group.html
+share/doc/EMBOSS/programs/html/findkm.1.findkm.gif
share/doc/EMBOSS/programs/html/findkm.html
-share/doc/EMBOSS/programs/html/findkm0.gif
share/doc/EMBOSS/programs/html/fitch.html
share/doc/EMBOSS/programs/html/freak.html
share/doc/EMBOSS/programs/html/fuzznuc.html
@@ -1226,16 +1218,19 @@
share/doc/EMBOSS/programs/html/getorf.html
share/doc/EMBOSS/programs/html/groups.html
share/doc/EMBOSS/programs/html/helixturnhelix.html
+share/doc/EMBOSS/programs/html/hetparse.html
+share/doc/EMBOSS/programs/html/hmmgen.html
share/doc/EMBOSS/programs/html/hmoment.html
share/doc/EMBOSS/programs/html/iep.html
share/doc/EMBOSS/programs/html/index.html
share/doc/EMBOSS/programs/html/infoalign.html
share/doc/EMBOSS/programs/html/information_group.html
share/doc/EMBOSS/programs/html/infoseq.html
+share/doc/EMBOSS/programs/html/interface.html
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share/doc/EMBOSS/programs/html/isochore.html
-share/doc/EMBOSS/programs/html/isochore0.gif
share/doc/EMBOSS/programs/html/kitsch.html
-share/doc/EMBOSS/programs/html/lindna.gif
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share/doc/EMBOSS/programs/html/lindna.html
share/doc/EMBOSS/programs/html/listor.html
share/doc/EMBOSS/programs/html/marscan.html
@@ -1243,11 +1238,11 @@
share/doc/EMBOSS/programs/html/maskseq.html
share/doc/EMBOSS/programs/html/matcher.html
share/doc/EMBOSS/programs/html/megamerger.html
-share/doc/EMBOSS/programs/html/menus_group.html
share/doc/EMBOSS/programs/html/merger.html
share/doc/EMBOSS/programs/html/mix.html
share/doc/EMBOSS/programs/html/msbar.html
share/doc/EMBOSS/programs/html/mse.html
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share/doc/EMBOSS/programs/html/mwfilter.html
share/doc/EMBOSS/programs/html/needle.html
share/doc/EMBOSS/programs/html/neighbor.html
@@ -1256,10 +1251,10 @@
share/doc/EMBOSS/programs/html/newseq.html
share/doc/EMBOSS/programs/html/noreturn.html
share/doc/EMBOSS/programs/html/notseq.html
-share/doc/EMBOSS/programs/html/nrscope.html
share/doc/EMBOSS/programs/html/nthseq.html
share/doc/EMBOSS/programs/html/nucleic_2d_structure_group.html
share/doc/EMBOSS/programs/html/nucleic_codon_usage_group.html
+share/doc/EMBOSS/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
share/doc/EMBOSS/programs/html/nucleic_composition_group.html
share/doc/EMBOSS/programs/html/nucleic_cpg_islands_group.html
share/doc/EMBOSS/programs/html/nucleic_gene_finding_group.html
@@ -1271,8 +1266,8 @@
share/doc/EMBOSS/programs/html/nucleic_restriction_group.html
share/doc/EMBOSS/programs/html/nucleic_transcription_group.html
share/doc/EMBOSS/programs/html/nucleic_translation_group.html
+share/doc/EMBOSS/programs/html/octanol.1.octanol.gif
share/doc/EMBOSS/programs/html/octanol.html
-share/doc/EMBOSS/programs/html/octanol0.gif
share/doc/EMBOSS/programs/html/oddcomp.html
share/doc/EMBOSS/programs/html/palindrome.html
share/doc/EMBOSS/programs/html/pasteseq.html
@@ -1280,28 +1275,31 @@
share/doc/EMBOSS/programs/html/patmatmotifs.html
share/doc/EMBOSS/programs/html/penny.html
share/doc/EMBOSS/programs/html/pepcoil.html
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share/doc/EMBOSS/programs/html/pepinfo.html
-share/doc/EMBOSS/programs/html/pepinfo1.gif
-share/doc/EMBOSS/programs/html/pepinfo2.gif
+share/doc/EMBOSS/programs/html/pepnet.1.pepnet.gif
share/doc/EMBOSS/programs/html/pepnet.html
-share/doc/EMBOSS/programs/html/pepnet0.gif
share/doc/EMBOSS/programs/html/pepstats.html
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share/doc/EMBOSS/programs/html/pepwheel.html
-share/doc/EMBOSS/programs/html/pepwheel0.gif
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share/doc/EMBOSS/programs/html/pepwindow.html
-share/doc/EMBOSS/programs/html/pepwindow0.gif
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share/doc/EMBOSS/programs/html/pepwindowall.html
-share/doc/EMBOSS/programs/html/pepwindowall0.gif
+share/doc/EMBOSS/programs/html/pestfind.html
+share/doc/EMBOSS/programs/html/phylogeny_distance_matrix_group.html
share/doc/EMBOSS/programs/html/phylogeny_group.html
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share/doc/EMBOSS/programs/html/plotcon.html
+share/doc/EMBOSS/programs/html/plotorf.1.plotorf.gif
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share/doc/EMBOSS/programs/html/plotorf.html
-share/doc/EMBOSS/programs/html/plotorf0.gif
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share/doc/EMBOSS/programs/html/polydot.html
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share/doc/EMBOSS/programs/html/preg.html
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share/doc/EMBOSS/programs/html/prettyplot.html
-share/doc/EMBOSS/programs/html/prettyplot3.gif
-share/doc/EMBOSS/programs/html/prettyplot4.gif
share/doc/EMBOSS/programs/html/prettyseq.html
share/doc/EMBOSS/programs/html/primersearch.html
share/doc/EMBOSS/programs/html/printsextract.html
@@ -1316,10 +1314,8 @@
share/doc/EMBOSS/programs/html/protein_motifs_group.html
share/doc/EMBOSS/programs/html/protein_mutation_group.html
share/doc/EMBOSS/programs/html/protein_profiles_group.html
-share/doc/EMBOSS/programs/html/protein_structure_group.html
share/doc/EMBOSS/programs/html/pscan.html
share/doc/EMBOSS/programs/html/rebaseextract.html
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share/doc/EMBOSS/programs/html/recoder.html
share/doc/EMBOSS/programs/html/redata.html
share/doc/EMBOSS/programs/html/remap.html
@@ -1327,16 +1323,11 @@
share/doc/EMBOSS/programs/html/restover.html
share/doc/EMBOSS/programs/html/restrict.html
share/doc/EMBOSS/programs/html/revseq.html
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share/doc/EMBOSS/programs/html/scope.html
share/doc/EMBOSS/programs/html/seealso.html
share/doc/EMBOSS/programs/html/seqboot.html
share/doc/EMBOSS/programs/html/seqmatchall.html
share/doc/EMBOSS/programs/html/seqret.html
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share/doc/EMBOSS/programs/html/seqretsplit.html
share/doc/EMBOSS/programs/html/showalign.html
share/doc/EMBOSS/programs/html/showdb.html
@@ -1345,57 +1336,46 @@
share/doc/EMBOSS/programs/html/showseq.html
share/doc/EMBOSS/programs/html/shuffleseq.html
share/doc/EMBOSS/programs/html/sigcleave.html
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share/doc/EMBOSS/programs/html/silent.html
+share/doc/EMBOSS/programs/html/sirna.html
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+share/doc/EMBOSS/programs/html/skipseq.html
share/doc/EMBOSS/programs/html/splitter.html
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share/doc/EMBOSS/programs/html/stretcher.html
share/doc/EMBOSS/programs/html/stssearch.html
share/doc/EMBOSS/programs/html/supermatcher.html
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share/doc/EMBOSS/programs/html/syco.html
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share/doc/EMBOSS/programs/html/textsearch.html
share/doc/EMBOSS/programs/html/tfextract.html
share/doc/EMBOSS/programs/html/tfm.html
share/doc/EMBOSS/programs/html/tfscan.html
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share/doc/EMBOSS/programs/html/tmap.html
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share/doc/EMBOSS/programs/html/topo.gif
share/doc/EMBOSS/programs/html/topo.html
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share/doc/EMBOSS/programs/html/transeq.html
share/doc/EMBOSS/programs/html/trimest.html
share/doc/EMBOSS/programs/html/trimseq.html
+share/doc/EMBOSS/programs/html/twofeat.html
+share/doc/EMBOSS/programs/html/union.html
share/doc/EMBOSS/programs/html/utils_database_creation_group.html
share/doc/EMBOSS/programs/html/utils_database_indexing_group.html
share/doc/EMBOSS/programs/html/utils_misc_group.html
share/doc/EMBOSS/programs/html/vectorstrip.html
share/doc/EMBOSS/programs/html/water.html
+share/doc/EMBOSS/programs/html/whichdb.html
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share/doc/EMBOSS/programs/html/wobble.html
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share/doc/EMBOSS/programs/html/wordcount.html
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share/doc/EMBOSS/programs/text/SITE-DIRECTED.txt
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share/doc/EMBOSS/programs/text/abiview.txt
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share/doc/EMBOSS/programs/text/antigenic.txt
share/doc/EMBOSS/programs/text/backtranseq.txt
share/doc/EMBOSS/programs/text/banana.txt
@@ -1472,6 +1452,8 @@
share/doc/EMBOSS/programs/text/eneighbor.txt
share/doc/EMBOSS/programs/text/entret.txt
share/doc/EMBOSS/programs/text/epenny.txt
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share/doc/EMBOSS/programs/text/eprotdist.txt
share/doc/EMBOSS/programs/text/eprotpars.txt
share/doc/EMBOSS/programs/text/equicktandem.txt
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share/doc/EMBOSS/programs/text/gendist.txt
share/doc/EMBOSS/programs/text/getorf.txt
share/doc/EMBOSS/programs/text/helixturnhelix.txt
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share/doc/EMBOSS/programs/text/hmoment.txt
share/doc/EMBOSS/programs/text/iep.txt
share/doc/EMBOSS/programs/text/infoalign.txt
share/doc/EMBOSS/programs/text/infoseq.txt
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share/doc/EMBOSS/programs/text/isochore.txt
share/doc/EMBOSS/programs/text/kitsch.txt
share/doc/EMBOSS/programs/text/lindna.txt
@@ -1510,6 +1495,7 @@
share/doc/EMBOSS/programs/text/mix.txt
share/doc/EMBOSS/programs/text/msbar.txt
share/doc/EMBOSS/programs/text/mse.txt
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share/doc/EMBOSS/programs/text/mwfilter.txt
share/doc/EMBOSS/programs/text/needle.txt
share/doc/EMBOSS/programs/text/neighbor.txt
@@ -1518,7 +1504,6 @@
share/doc/EMBOSS/programs/text/newseq.txt
share/doc/EMBOSS/programs/text/noreturn.txt
share/doc/EMBOSS/programs/text/notseq.txt
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share/doc/EMBOSS/programs/text/nthseq.txt
share/doc/EMBOSS/programs/text/octanol.txt
share/doc/EMBOSS/programs/text/oddcomp.txt
@@ -1534,6 +1519,7 @@
share/doc/EMBOSS/programs/text/pepwheel.txt
share/doc/EMBOSS/programs/text/pepwindow.txt
share/doc/EMBOSS/programs/text/pepwindowall.txt
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share/doc/EMBOSS/programs/text/plotcon.txt
share/doc/EMBOSS/programs/text/plotorf.txt
share/doc/EMBOSS/programs/text/polydot.txt
@@ -1549,7 +1535,6 @@
share/doc/EMBOSS/programs/text/protdist.txt
share/doc/EMBOSS/programs/text/pscan.txt
share/doc/EMBOSS/programs/text/rebaseextract.txt
-share/doc/EMBOSS/programs/text/recode.txt
share/doc/EMBOSS/programs/text/recoder.txt
share/doc/EMBOSS/programs/text/redata.txt
share/doc/EMBOSS/programs/text/remap.txt
@@ -1557,16 +1542,11 @@
share/doc/EMBOSS/programs/text/restover.txt
share/doc/EMBOSS/programs/text/restrict.txt
share/doc/EMBOSS/programs/text/revseq.txt
-share/doc/EMBOSS/programs/text/scopalign.txt
share/doc/EMBOSS/programs/text/scope.txt
share/doc/EMBOSS/programs/text/seealso.txt
share/doc/EMBOSS/programs/text/seqboot.txt
share/doc/EMBOSS/programs/text/seqmatchall.txt
share/doc/EMBOSS/programs/text/seqret.txt
-share/doc/EMBOSS/programs/text/seqretall.txt
-share/doc/EMBOSS/programs/text/seqretallfeat.txt
-share/doc/EMBOSS/programs/text/seqretfeat.txt
-share/doc/EMBOSS/programs/text/seqretset.txt
share/doc/EMBOSS/programs/text/seqretsplit.txt
share/doc/EMBOSS/programs/text/showalign.txt
share/doc/EMBOSS/programs/text/showdb.txt
@@ -1575,56 +1555,40 @@
share/doc/EMBOSS/programs/text/showseq.txt
share/doc/EMBOSS/programs/text/shuffleseq.txt
share/doc/EMBOSS/programs/text/sigcleave.txt
-share/doc/EMBOSS/programs/text/siggen.txt
-share/doc/EMBOSS/programs/text/sigscan.txt
share/doc/EMBOSS/programs/text/silent.txt
+share/doc/EMBOSS/programs/text/sirna.txt
+share/doc/EMBOSS/programs/text/sixpack.txt
+share/doc/EMBOSS/programs/text/skipseq.txt
share/doc/EMBOSS/programs/text/splitter.txt
-share/doc/EMBOSS/programs/text/stamps.txt
share/doc/EMBOSS/programs/text/stretcher.txt
share/doc/EMBOSS/programs/text/stssearch.txt
share/doc/EMBOSS/programs/text/supermatcher.txt
-share/doc/EMBOSS/programs/text/swissparse.txt
share/doc/EMBOSS/programs/text/syco.txt
+share/doc/EMBOSS/programs/text/tcode.txt
share/doc/EMBOSS/programs/text/textsearch.txt
share/doc/EMBOSS/programs/text/tfextract.txt
share/doc/EMBOSS/programs/text/tfm.txt
share/doc/EMBOSS/programs/text/tfscan.txt
share/doc/EMBOSS/programs/text/tmap.txt
share/doc/EMBOSS/programs/text/topo.txt
+share/doc/EMBOSS/programs/text/tranalign.txt
share/doc/EMBOSS/programs/text/transeq.txt
share/doc/EMBOSS/programs/text/trimest.txt
share/doc/EMBOSS/programs/text/trimseq.txt
+share/doc/EMBOSS/programs/text/twofeat.txt
+share/doc/EMBOSS/programs/text/union.txt
share/doc/EMBOSS/programs/text/vectorstrip.txt
share/doc/EMBOSS/programs/text/water.txt
+share/doc/EMBOSS/programs/text/whichdb.txt
share/doc/EMBOSS/programs/text/wobble.txt
share/doc/EMBOSS/programs/text/wordcount.txt
share/doc/EMBOSS/programs/text/wordmatch.txt
share/doc/EMBOSS/programs/text/wossname.txt
-share/doc/EMBOSS/programs/text/jembossctl.txt
-share/doc/EMBOSS/programs/text/pdbtosp.txt
-share/doc/EMBOSS/programs/text/psiblasts.txt
-share/doc/EMBOSS/programs/text/scopparse.txt
-share/doc/EMBOSS/programs/text/seqnr.txt
-share/doc/EMBOSS/programs/text/seqsort.txt
-share/doc/EMBOSS/programs/text/tranalign.txt
-share/doc/EMBOSS/programs/text/union.txt
-share/doc/EMBOSS/programs/text/whichdb.txt
share/doc/EMBOSS/programs/text/yank.txt
-share/doc/EMBOSS/programs/text/alignwrap.txt
-share/doc/EMBOSS/programs/text/dichet.txt
-share/doc/EMBOSS/programs/text/eprimer3.txt
-share/doc/EMBOSS/programs/text/interface.txt
-share/doc/EMBOSS/tutorials/biblio.bib
-share/doc/EMBOSS/tutorials/dottup.ps.gz
share/doc/EMBOSS/tutorials/emboss-gcg.ppt
share/doc/EMBOSS/tutorials/emboss-interfaces.ppt
share/doc/EMBOSS/tutorials/emboss-talk.ppt
-share/doc/EMBOSS/tutorials/emboss_tutorial.ps.gz
-share/doc/EMBOSS/tutorials/emboss_tutorial.tex
-share/doc/EMBOSS/tutorials/pepinfo1.ps.gz
-share/doc/EMBOSS/tutorials/pepinfo2.ps.gz
-share/doc/EMBOSS/tutorials/plotorf.ps.gz
-share/doc/EMBOSS/tutorials/tmap.ps.gz
+share/doc/EMBOSS/tutorials/emboss_tut.tar.gz
@dirrm share/doc/EMBOSS/tutorials
@dirrm share/doc/EMBOSS/programs/text
@dirrm share/doc/EMBOSS/programs/html
@@ -1652,9 +1616,11 @@
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/form
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/gui
+@dirrm share/EMBOSS/jemboss/org/emboss/jemboss/editor
@dirrm share/EMBOSS/jemboss/org/emboss/jemboss
@dirrm share/EMBOSS/jemboss/org/emboss
@dirrm share/EMBOSS/jemboss/org
+@dirrm share/EMBOSS/jemboss/lib/axis
@dirrm share/EMBOSS/jemboss/lib
@dirrm share/EMBOSS/jemboss/images
@dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap
@@ -1675,6 +1641,7 @@
@dirrm share/EMBOSS/data/PROSITE
@dirrm share/EMBOSS/data/PRINTS
@dirrm share/EMBOSS/data/CODONS
+@dirrm share/EMBOSS/data/AAINDEX
@dirrm share/EMBOSS/data
@dirrm share/EMBOSS/acd
@dirrm share/EMBOSS
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>Audit-Trail:
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