FreeBSD Bugzilla – Attachment 53919 Details for
Bug 81579
update biology/emboss to 2.10.0
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[patch]
file.diff
file.diff (text/plain), 115.13 KB, created by
Choe, Cheng-Dae
on 2005-05-28 11:10:02 UTC
(
hide
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Description:
file.diff
Filename:
MIME Type:
Creator:
Choe, Cheng-Dae
Created:
2005-05-28 11:10:02 UTC
Size:
115.13 KB
patch
obsolete
>diff -ruN emboss.orig/Makefile emboss/Makefile >--- emboss.orig/Makefile Sat Feb 12 06:11:51 2005 >+++ emboss/Makefile Sat May 28 14:59:25 2005 >@@ -6,7 +6,7 @@ > # > > PORTNAME= emboss >-PORTVERSION= 2.9.0 >+PORTVERSION= 2.10.0 > CATEGORIES= biology > MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ > ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \ >diff -ruN emboss.orig/distinfo emboss/distinfo >--- emboss.orig/distinfo Fri Nov 26 10:11:42 2004 >+++ emboss/distinfo Sat May 28 14:59:34 2005 >@@ -1,2 +1,2 @@ >-MD5 (EMBOSS-2.9.0.tar.gz) = c6facfd1750e88a0c8b7bb7ac826d472 >-SIZE (EMBOSS-2.9.0.tar.gz) = 14479274 >+MD5 (EMBOSS-2.10.0.tar.gz) = 4a48388ced7021a8ffece5166c40a364 >+SIZE (EMBOSS-2.10.0.tar.gz) = 16262124 >diff -ruN emboss.orig/pkg-plist emboss/pkg-plist >--- emboss.orig/pkg-plist Fri Nov 26 10:11:42 2004 >+++ emboss/pkg-plist Sat May 28 16:42:31 2005 >@@ -82,8 +82,8 @@ > bin/newcpgreport > bin/newcpgseek > bin/newseq >-bin/notseq > bin/noreturn >+bin/notseq > bin/nthseq > bin/octanol > bin/oddcomp >@@ -119,6 +119,7 @@ > bin/restover > bin/restrict > bin/revseq >+bin/runJemboss.csh > bin/seealso > bin/seqmatchall > bin/seqret >@@ -159,31 +160,18 @@ > bin/wordmatch > bin/wossname > bin/yank >-bin/runJemboss.csh > etc/emboss.default.sample >-include/drivers.h >-include/pdf.h >-include/plcore.h >-include/plevent.h >-include/plplotP.h >-include/plxwd.h >-include/metadefs.h >-include/plConfig.h >-include/pldebug.h >-include/plplot.h >-include/plstrm.h >-include/plDevs.h >-include/ajax.h >-include/ajarch.h >-include/ajdefine.h > include/ajacd.h > include/ajalign.h >+include/ajarch.h > include/ajarr.h > include/ajassert.h >+include/ajax.h > include/ajbase.h > include/ajcall.h > include/ajcod.h > include/ajdan.h >+include/ajdefine.h > include/ajdmx.h > include/ajdomain.h > include/ajexcept.h >@@ -192,9 +180,10 @@ > include/ajfile.h > include/ajfmt.h > include/ajgraph.h >-include/ajgraphxml.h > include/ajgraphstruct.h >+include/ajgraphxml.h > include/ajhist.h >+include/ajindex.h > include/ajjava.h > include/ajlist.h > include/ajmath.h >@@ -225,23 +214,16 @@ > include/ajtree.h > include/ajutil.h > include/ajvector.h >-include/pcre.h >-include/pcre_chartables.c >-include/pcre_config.h >-include/pcre_get.c >-include/pcre_printint.c >-include/pcre_internal.h >-include/pcreposix.h >-include/emboss.h >+include/drivers.h > include/embaln.h > include/embcom.h > include/embcons.h > include/embdata.h > include/embdbi.h > include/embdmx.h >+include/embdomain.h > include/embest.h > include/embexit.h >-include/embgotoh.h > include/embgroup.h > include/embiep.h > include/embindex.h >@@ -250,640 +232,52 @@ > include/embmisc.h > include/embmol.h > include/embnmer.h >+include/emboss.h > include/embpat.h >-include/embprop.h > include/embpdb.h >-include/embdomain.h >-include/embsig.h >+include/embprop.h > include/embread.h > include/embshow.h >+include/embsig.h > include/embword.h >-lib/libplplot.so.5 >-lib/libplplot.so >-lib/libplplot.a 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>-%%PORTDOCS%%%%DOCSDIR%%/programs/html/hetparse.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/hmmgen.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/hmoment.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/iep.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/index.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/infoalign.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/information_group.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/infoseq.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/interface.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/html/kitsch.html >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/kitsch.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/lindna.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/listor.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/marscan.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskfeat.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/maskseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/matcher.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/megamerger.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/merger.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mix.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/msbar.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mse.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwcontam.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/mwfilter.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/needle.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/neighbor.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgreport.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newcpgseek.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/newseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/noreturn.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/notseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/nthseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/octanol.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/oddcomp.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/palindrome.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pasteseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatdb.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/patmatmotifs.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/penny.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepcoil.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepinfo.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepnet.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepstats.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwheel.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindow.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pepwindowall.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pestfind.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotcon.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/plotorf.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/polydot.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/preg.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyplot.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prettyseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/primersearch.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/printsextract.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/profit.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophecy.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prophet.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/prosextract.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/protdist.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/pscan.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/rebaseextract.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/recoder.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/redata.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/remap.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restml.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restover.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/restrict.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/revseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/scope.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seealso.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqboot.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqmatchall.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqret.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqretsplit.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showdb.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showalign.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showfeat.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showorf.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/showseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/shuffleseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigcleave.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/silent.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sirna.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/sixpack.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/skipseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/splitter.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/stretcher.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/stssearch.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/supermatcher.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/syco.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tcode.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/textsearch.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfextract.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfm.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tfscan.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tmap.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/topo.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/tranalign.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/transeq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimest.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/twofeat.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/union.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/vectorstrip.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/water.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/whichdb.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wobble.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/SITE-DIRECTED.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/aaindexextract.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/abiview.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/antigenic.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/backtranseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/banana.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/biosed.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/btwisted.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/chaos.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/charge.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/checktrans.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/chips.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cirdna.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/clique.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/codcmp.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/coderet.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/complex.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/compseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cons.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/consense.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contacts.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contml.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/contrast.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgplot.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cpgreport.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cusp.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutgextract.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/cutseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dan.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiblast.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbifasta.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbiflat.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dbigcg.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/degapseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/descseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/diffseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/digest.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/distmat.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnacomp.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnadist.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnainvar.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnaml.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnamlk.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnapars.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dnapenny.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dollop.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dolpenny.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/domainer.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotmatcher.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dotpath.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dottup.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/dreg.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eclique.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/econsense.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtml.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/econtrast.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednaml.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednacomp.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednadist.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednainvar.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednamlk.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapars.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapenny.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/edollop.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/edolpenny.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/efactor.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/efitch.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/egendist.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/einverted.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/ekitsch.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossdata.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/embossversion.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emix.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emma.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/emowse.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eneighbor.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/entret.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/epenny.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/epestfind.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/erestml.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprimer3.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotdist.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eprotpars.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/equicktandem.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/eseqboot.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/est2genome.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/etandem.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractfeat.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/extractseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/factor.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fitch.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/freak.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzznuc.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzzpro.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/fuzztran.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/garnier.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/geecee.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/gendist.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/getorf.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/helixturnhelix.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hetparse.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmmgen.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt >-%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt >-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt >-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt >-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt >-%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz >-%%DATADIR%%/plstnd5.fnt >-%%DATADIR%%/plxtnd5.fnt >-%%DATADIR%%/acd/megamerger.acd >-%%DATADIR%%/acd/merger.acd >-%%DATADIR%%/acd/msbar.acd >-%%DATADIR%%/acd/mwcontam.acd >-%%DATADIR%%/acd/mwfilter.acd >-%%DATADIR%%/acd/needle.acd >-%%DATADIR%%/acd/newcoils.acd >-%%DATADIR%%/acd/newcpgreport.acd >-%%DATADIR%%/acd/newcpgseek.acd >-%%DATADIR%%/acd/newseq.acd >-%%DATADIR%%/acd/noreturn.acd >-%%DATADIR%%/acd/notseq.acd >-%%DATADIR%%/acd/nthseq.acd >-%%DATADIR%%/acd/octanol.acd >-%%DATADIR%%/acd/oddcomp.acd >-%%DATADIR%%/acd/palindrome.acd >-%%DATADIR%%/acd/pasteseq.acd >-%%DATADIR%%/acd/patmatdb.acd >-%%DATADIR%%/acd/patmatmotifs.acd >-%%DATADIR%%/acd/patmattest.acd >-%%DATADIR%%/acd/pepcoil.acd >-%%DATADIR%%/acd/pepinfo.acd >-%%DATADIR%%/acd/pepnet.acd >-%%DATADIR%%/acd/pepstats.acd >-%%DATADIR%%/acd/pepwheel.acd >-%%DATADIR%%/acd/pepwindow.acd >-%%DATADIR%%/acd/pepwindowall.acd >-%%DATADIR%%/acd/plotcon.acd >-%%DATADIR%%/acd/plotorf.acd >-%%DATADIR%%/acd/polydot.acd >-%%DATADIR%%/acd/preg.acd >-%%DATADIR%%/acd/prettyplot.acd >-%%DATADIR%%/acd/prettyseq.acd >-%%DATADIR%%/acd/prima.acd >-%%DATADIR%%/acd/primers.acd >-%%DATADIR%%/acd/primersearch.acd >-%%DATADIR%%/acd/printsextract.acd >-%%DATADIR%%/acd/profit.acd >-%%DATADIR%%/acd/prophecy.acd >-%%DATADIR%%/acd/prophet.acd >-%%DATADIR%%/acd/prosextract.acd >-%%DATADIR%%/acd/pscan.acd >-%%DATADIR%%/acd/rebaseextract.acd >-%%DATADIR%%/acd/recoder.acd >-%%DATADIR%%/acd/redata.acd >-%%DATADIR%%/acd/remap.acd >-%%DATADIR%%/acd/restover.acd >-%%DATADIR%%/acd/restrict.acd >-%%DATADIR%%/acd/revseq.acd >-%%DATADIR%%/acd/seealso.acd >-%%DATADIR%%/acd/seqinfo.acd >-%%DATADIR%%/acd/seqmatchall.acd >-%%DATADIR%%/acd/seqret.acd >-%%DATADIR%%/acd/seqretall.acd >-%%DATADIR%%/acd/seqretallfeat.acd >-%%DATADIR%%/acd/seqretset.acd >-%%DATADIR%%/acd/seqretsingle.acd >-%%DATADIR%%/acd/seqretsplit.acd >-%%DATADIR%%/acd/seqrettype.acd >-%%DATADIR%%/acd/showalign.acd >-%%DATADIR%%/acd/showdb.acd >-%%DATADIR%%/acd/showfeat.acd >-%%DATADIR%%/acd/showorf.acd >-%%DATADIR%%/acd/showseq.acd >-%%DATADIR%%/acd/shuffleseq.acd >-%%DATADIR%%/acd/tfm.acd >-%%DATADIR%%/acd/sigcleave.acd >-%%DATADIR%%/acd/silent.acd >-%%DATADIR%%/acd/sirna.acd >-%%DATADIR%%/acd/sixpack.acd >-%%DATADIR%%/acd/skipseq.acd >-%%DATADIR%%/acd/splitter.acd >-%%DATADIR%%/acd/stretcher.acd >-%%DATADIR%%/acd/stssearch.acd >-%%DATADIR%%/acd/supermatcher.acd >-%%DATADIR%%/acd/syco.acd >-%%DATADIR%%/acd/tcode.acd >-%%DATADIR%%/acd/testplot.acd >-%%DATADIR%%/acd/textsearch.acd >-%%DATADIR%%/acd/tfextract.acd >-%%DATADIR%%/acd/tfscan.acd >-%%DATADIR%%/acd/tmap.acd >-%%DATADIR%%/acd/tranalign.acd >-%%DATADIR%%/acd/transeq.acd >-%%DATADIR%%/acd/treetypedisplay.acd >-%%DATADIR%%/acd/trimest.acd >-%%DATADIR%%/acd/trimseq.acd >-%%DATADIR%%/acd/twofeat.acd >-%%DATADIR%%/acd/union.acd >-%%DATADIR%%/acd/vectorstrip.acd >-%%DATADIR%%/acd/water.acd >-%%DATADIR%%/acd/whichdb.acd >-%%DATADIR%%/acd/wobble.acd >-%%DATADIR%%/acd/wordcount.acd >-%%DATADIR%%/acd/wordmatch.acd >-%%DATADIR%%/acd/wossname.acd >-%%DATADIR%%/acd/yank.acd >-%%DATADIR%%/acd/codes.english >-%%DATADIR%%/acd/groups.standard >-%%DATADIR%%/acd/sections.standard >+lib/libnucleus.so >+lib/libnucleus.so.1 >+lib/libplplot.a >+lib/libplplot.so >+lib/libplplot.so.5 > %%DATADIR%%/acd/aaindexextract.acd > %%DATADIR%%/acd/abiview.acd >+%%DATADIR%%/acd/acdc.acd >+%%DATADIR%%/acd/acdlog.acd >+%%DATADIR%%/acd/acdpretty.acd >+%%DATADIR%%/acd/acdtable.acd >+%%DATADIR%%/acd/acdtrace.acd >+%%DATADIR%%/acd/acdvalid.acd > %%DATADIR%%/acd/ajbad.acd > %%DATADIR%%/acd/ajfeatest.acd > %%DATADIR%%/acd/ajtest.acd >@@ -900,6 +294,7 @@ > %%DATADIR%%/acd/cirdna.acd > %%DATADIR%%/acd/codcmp.acd > %%DATADIR%%/acd/coderet.acd >+%%DATADIR%%/acd/codes.english > %%DATADIR%%/acd/complex.acd > %%DATADIR%%/acd/compseq.acd > %%DATADIR%%/acd/cons.acd >@@ -917,7 +312,6 @@ > %%DATADIR%%/acd/degapseq.acd > %%DATADIR%%/acd/demoalign.acd > %%DATADIR%%/acd/demofeatures.acd >-%%DATADIR%%/acd/iep.acd > %%DATADIR%%/acd/demolist.acd > %%DATADIR%%/acd/demoreport.acd > %%DATADIR%%/acd/demosequence.acd >@@ -943,8 +337,8 @@ > %%DATADIR%%/acd/equicktandem.acd > %%DATADIR%%/acd/est2genome.acd > %%DATADIR%%/acd/etandem.acd >-%%DATADIR%%/acd/extractseq.acd > %%DATADIR%%/acd/extractfeat.acd >+%%DATADIR%%/acd/extractseq.acd > %%DATADIR%%/acd/findkm.acd > %%DATADIR%%/acd/freak.acd > %%DATADIR%%/acd/fuzznuc.acd >@@ -953,18 +347,125 @@ > %%DATADIR%%/acd/garnier.acd > %%DATADIR%%/acd/geecee.acd > %%DATADIR%%/acd/getorf.acd >+%%DATADIR%%/acd/giep.acd >+%%DATADIR%%/acd/groups.standard > %%DATADIR%%/acd/helixturnhelix.acd >-%%DATADIR%%/acd/hmoment.acd > %%DATADIR%%/acd/histogramtest.acd >+%%DATADIR%%/acd/hmoment.acd >+%%DATADIR%%/acd/iep.acd > %%DATADIR%%/acd/infoalign.acd > %%DATADIR%%/acd/infoseq.acd >+%%DATADIR%%/acd/intconv.acd > %%DATADIR%%/acd/isochore.acd >+%%DATADIR%%/acd/kmrsplitter.acd >+%%DATADIR%%/acd/kmrunion.acd >+%%DATADIR%%/acd/knowntypes.standard > %%DATADIR%%/acd/lindna.acd > %%DATADIR%%/acd/listor.acd > %%DATADIR%%/acd/marscan.acd > %%DATADIR%%/acd/maskfeat.acd > %%DATADIR%%/acd/maskseq.acd > %%DATADIR%%/acd/matcher.acd >+%%DATADIR%%/acd/megamerger.acd >+%%DATADIR%%/acd/merger.acd >+%%DATADIR%%/acd/msbar.acd >+%%DATADIR%%/acd/mwcontam.acd >+%%DATADIR%%/acd/mwfilter.acd >+%%DATADIR%%/acd/needle.acd >+%%DATADIR%%/acd/newcoils.acd >+%%DATADIR%%/acd/newcpgreport.acd >+%%DATADIR%%/acd/newcpgseek.acd >+%%DATADIR%%/acd/newseq.acd >+%%DATADIR%%/acd/noreturn.acd >+%%DATADIR%%/acd/notseq.acd >+%%DATADIR%%/acd/nthseq.acd >+%%DATADIR%%/acd/octanol.acd >+%%DATADIR%%/acd/oddcomp.acd >+%%DATADIR%%/acd/palindrome.acd >+%%DATADIR%%/acd/pasteseq.acd >+%%DATADIR%%/acd/patmatdb.acd >+%%DATADIR%%/acd/patmatmotifs.acd >+%%DATADIR%%/acd/patmattest.acd >+%%DATADIR%%/acd/pepcoil.acd >+%%DATADIR%%/acd/pepinfo.acd >+%%DATADIR%%/acd/pepnet.acd >+%%DATADIR%%/acd/pepstats.acd >+%%DATADIR%%/acd/pepwheel.acd >+%%DATADIR%%/acd/pepwindow.acd >+%%DATADIR%%/acd/pepwindowall.acd >+%%DATADIR%%/acd/plotcon.acd >+%%DATADIR%%/acd/plotorf.acd >+%%DATADIR%%/acd/polydot.acd >+%%DATADIR%%/acd/preg.acd >+%%DATADIR%%/acd/prettyplot.acd >+%%DATADIR%%/acd/prettyseq.acd >+%%DATADIR%%/acd/prima.acd >+%%DATADIR%%/acd/primers.acd >+%%DATADIR%%/acd/primersearch.acd >+%%DATADIR%%/acd/printsextract.acd >+%%DATADIR%%/acd/profit.acd >+%%DATADIR%%/acd/prophecy.acd >+%%DATADIR%%/acd/prophet.acd >+%%DATADIR%%/acd/prosextract.acd >+%%DATADIR%%/acd/pscan.acd >+%%DATADIR%%/acd/psiphi.acd >+%%DATADIR%%/acd/rebaseextract.acd >+%%DATADIR%%/acd/recoder.acd >+%%DATADIR%%/acd/redata.acd >+%%DATADIR%%/acd/remap.acd >+%%DATADIR%%/acd/restover.acd >+%%DATADIR%%/acd/restrict.acd >+%%DATADIR%%/acd/revseq.acd >+%%DATADIR%%/acd/sections.standard >+%%DATADIR%%/acd/seealso.acd >+%%DATADIR%%/acd/seqinfo.acd >+%%DATADIR%%/acd/seqmatchall.acd >+%%DATADIR%%/acd/seqret.acd >+%%DATADIR%%/acd/seqretall.acd >+%%DATADIR%%/acd/seqretallfeat.acd >+%%DATADIR%%/acd/seqretset.acd >+%%DATADIR%%/acd/seqretsingle.acd >+%%DATADIR%%/acd/seqretsplit.acd >+%%DATADIR%%/acd/seqrettype.acd >+%%DATADIR%%/acd/showalign.acd >+%%DATADIR%%/acd/showdb.acd >+%%DATADIR%%/acd/showfeat.acd >+%%DATADIR%%/acd/showorf.acd >+%%DATADIR%%/acd/showseq.acd >+%%DATADIR%%/acd/shuffleseq.acd >+%%DATADIR%%/acd/sigcleave.acd >+%%DATADIR%%/acd/silent.acd >+%%DATADIR%%/acd/sirna.acd >+%%DATADIR%%/acd/sixpack.acd >+%%DATADIR%%/acd/skipseq.acd >+%%DATADIR%%/acd/splitter.acd >+%%DATADIR%%/acd/stretcher.acd >+%%DATADIR%%/acd/stssearch.acd >+%%DATADIR%%/acd/supermatcher.acd >+%%DATADIR%%/acd/syco.acd >+%%DATADIR%%/acd/tcode.acd >+%%DATADIR%%/acd/testplot.acd >+%%DATADIR%%/acd/textsearch.acd >+%%DATADIR%%/acd/tfextract.acd >+%%DATADIR%%/acd/tfm.acd >+%%DATADIR%%/acd/tfscan.acd >+%%DATADIR%%/acd/tmap.acd >+%%DATADIR%%/acd/tranalign.acd >+%%DATADIR%%/acd/transeq.acd >+%%DATADIR%%/acd/treetypedisplay.acd >+%%DATADIR%%/acd/trimest.acd >+%%DATADIR%%/acd/trimseq.acd >+%%DATADIR%%/acd/twofeat.acd >+%%DATADIR%%/acd/union.acd >+%%DATADIR%%/acd/variables.standard >+%%DATADIR%%/acd/vectorstrip.acd >+%%DATADIR%%/acd/water.acd >+%%DATADIR%%/acd/whichdb.acd >+%%DATADIR%%/acd/wobble.acd >+%%DATADIR%%/acd/wordcount.acd >+%%DATADIR%%/acd/wordmatch.acd >+%%DATADIR%%/acd/wossname.acd >+%%DATADIR%%/acd/yank.acd > %%DATADIR%%/data/AAINDEX/dummyfile > %%DATADIR%%/data/CODONS/Eacc.cut > %%DATADIR%%/data/CODONS/Eadenovirus5.cut >@@ -1013,10 +514,10 @@ > %%DATADIR%%/data/CODONS/Edro_h.cut > %%DATADIR%%/data/CODONS/Edrosophila.cut > %%DATADIR%%/data/CODONS/Eeca.cut >-%%DATADIR%%/data/CODONS/Ef1.cut > %%DATADIR%%/data/CODONS/Eeco.cut > %%DATADIR%%/data/CODONS/Eeco_h.cut > %%DATADIR%%/data/CODONS/Eecoli.cut >+%%DATADIR%%/data/CODONS/Ef1.cut > %%DATADIR%%/data/CODONS/Efish.cut > %%DATADIR%%/data/CODONS/Efmdvpolyp.cut > %%DATADIR%%/data/CODONS/Eham.cut >@@ -1117,9 +618,6 @@ > %%DATADIR%%/data/CODONS/Eysp.cut > %%DATADIR%%/data/CODONS/Ezebrafish.cut > %%DATADIR%%/data/CODONS/Ezma.cut >-%%DATADIR%%/data/REBASE/dummyfile >-%%DATADIR%%/data/PRINTS/dummyfile >-%%DATADIR%%/data/PROSITE/dummyfile > %%DATADIR%%/data/EBLOSUM30 > %%DATADIR%%/data/EBLOSUM35 > %%DATADIR%%/data/EBLOSUM40 >@@ -1227,233 +725,63 @@ > %%DATADIR%%/data/Efeatures.protein > %%DATADIR%%/data/Efeatures.swiss > %%DATADIR%%/data/Efreqs.dat >+%%DATADIR%%/data/Ehet.dat > %%DATADIR%%/data/Ehth.dat > %%DATADIR%%/data/Ehth87.dat >-%%DATADIR%%/data/Ememe.dat >-%%DATADIR%%/data/Enakai.dat >-%%DATADIR%%/data/Epepcoil.dat >-%%DATADIR%%/data/Epk.dat >-%%DATADIR%%/data/Epprofile >-%%DATADIR%%/data/Eprior1.plib >-%%DATADIR%%/data/Eprior30.plib >-%%DATADIR%%/data/Erna.melt >-%%DATADIR%%/data/Esig.euk >-%%DATADIR%%/data/Esig.pro >-%%DATADIR%%/data/Etags.embl >-%%DATADIR%%/data/Etags.emboss 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>-%%DATADIR%%/test/wormpep/wormpep >-%%DATADIR%%/test/wormpep/acnum.hit >-%%DATADIR%%/test/wormpep/acnum.trg >-%%DATADIR%%/test/wormpep/division.lkp >-%%DATADIR%%/test/wormpep/entrynam.idx >-%%DATADIR%%/test/wormpep/des.hit >-%%DATADIR%%/test/wormpep/des.trg >+%%DATADIR%%/data/Ememe.dat >+%%DATADIR%%/data/Emwfilter.dat >+%%DATADIR%%/data/Enakai.dat >+%%DATADIR%%/data/Epepcoil.dat >+%%DATADIR%%/data/Epk.dat >+%%DATADIR%%/data/Epprofile >+%%DATADIR%%/data/Eprior1.plib >+%%DATADIR%%/data/Eprior30.plib >+%%DATADIR%%/data/Erna.melt >+%%DATADIR%%/data/Esig.euk >+%%DATADIR%%/data/Esig.pro >+%%DATADIR%%/data/Etags.embl >+%%DATADIR%%/data/Etags.emboss >+%%DATADIR%%/data/Etags.gff >+%%DATADIR%%/data/Etags.pir >+%%DATADIR%%/data/Etags.protein >+%%DATADIR%%/data/Etags.swiss >+%%DATADIR%%/data/Etcode.dat >+%%DATADIR%%/data/Evdw.dat >+%%DATADIR%%/data/Ewhite-wimley.dat >+%%DATADIR%%/data/PRINTS/dummyfile >+%%DATADIR%%/data/PROSITE/dummyfile >+%%DATADIR%%/data/REBASE/dummyfile >+%%DATADIR%%/data/embossre.equ >+%%DATADIR%%/emboss.default.template >+%%DATADIR%%/jemboss/LICENSE >+%%DATADIR%%/jemboss/README >+%%DATADIR%%/jemboss/api/allclasses-frame.html >+%%DATADIR%%/jemboss/api/deprecated-list.html >+%%DATADIR%%/jemboss/api/getClasses.pl >+%%DATADIR%%/jemboss/api/help-doc.html >+%%DATADIR%%/jemboss/api/index-all.html >+%%DATADIR%%/jemboss/api/index.html >+%%DATADIR%%/jemboss/api/makeDocs.csh >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.winExit.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossLogo.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossParams.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/BuildProgramMenu.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ResultsMenuBar.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SetUpMenuBar.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowResultSet.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowSavedResults.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SwingWorker.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/DragTree.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.PopupListener.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileNode.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileSaving.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/BuildJembossForm.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.myComboUI.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/ListFilePanel.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SectionPanel.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SetInFileCard.html >@@ -1463,8 +791,6 @@ > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.WholeNumberDocument.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldSink.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.myComboUI.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/FileChooser.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.html >@@ -1475,19 +801,13 @@ > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/ProgList.HorizontalMenu.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/ProgList.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup/Splash.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/BuildProgramMenu.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ResultsMenuBar.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SetUpMenuBar.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowResultSet.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowSavedResults.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SwingWorker.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationFields.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationParam.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/AcdFunResolve.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/AcdVarResolve.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/Ajax.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/Dependent.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/ParseAcd.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationFields.html >+%%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd/ApplicationParam.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/JembossProcess.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/ListFile.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/ResultList.html >@@ -1500,17 +820,6 @@ > %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/PendingResults.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/PrivateRequest.html > %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap/ResListView.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.winExit.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossLogo.html >-%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossParams.html >-%%DATADIR%%/jemboss/api/allclasses-frame.html >-%%DATADIR%%/jemboss/api/deprecated-list.html >-%%DATADIR%%/jemboss/api/getClasses.pl >-%%DATADIR%%/jemboss/api/help-doc.html >-%%DATADIR%%/jemboss/api/index-all.html >-%%DATADIR%%/jemboss/api/index.html >-%%DATADIR%%/jemboss/api/makeDocs.csh > %%DATADIR%%/jemboss/api/overview-tree.html > %%DATADIR%%/jemboss/api/package-list > %%DATADIR%%/jemboss/api/packages.html >@@ -1526,6 +835,9 @@ > %%DATADIR%%/jemboss/images/Job_manager_button.gif > %%DATADIR%%/jemboss/images/Refresh_button.gif > %%DATADIR%%/jemboss/images/Refresh_button2.gif >+%%DATADIR%%/jemboss/lib/JembossPrintAlignment.jar >+%%DATADIR%%/jemboss/lib/README >+%%DATADIR%%/jemboss/lib/activation.jar > %%DATADIR%%/jemboss/lib/axis/axis-ant.jar > %%DATADIR%%/jemboss/lib/axis/axis.jar > %%DATADIR%%/jemboss/lib/axis/commons-discovery.jar >@@ -1535,83 +847,101 @@ > %%DATADIR%%/jemboss/lib/axis/saaj.jar > %%DATADIR%%/jemboss/lib/axis/servlet.jar > %%DATADIR%%/jemboss/lib/axis/wsdl4j.jar >-%%DATADIR%%/jemboss/lib/README >-%%DATADIR%%/jemboss/lib/activation.jar >+%%DATADIR%%/jemboss/lib/grout.jar > %%DATADIR%%/jemboss/lib/jakarta-regexp-1.2.jar >+%%DATADIR%%/jemboss/lib/jalview.jar > %%DATADIR%%/jemboss/lib/mail.jar > %%DATADIR%%/jemboss/lib/xerces.jar >-%%DATADIR%%/jemboss/lib/jalview.jar >-%%DATADIR%%/jemboss/lib/jcert.jar >-%%DATADIR%%/jemboss/lib/jnet.jar >-%%DATADIR%%/jemboss/lib/jsse.jar >-%%DATADIR%%/jemboss/lib/JembossPrintAlignment.jar >-%%DATADIR%%/jemboss/lib/grout.jar >+%%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/JembossParams.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Block.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/DNADraw.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/EmbossCirdnaReader.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/GeneticMarker.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/LineAttribute.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/PrintDNAImage.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/RestrictionEnzyme.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Ticks.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Wizard.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/AlignApplet.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequenceJPanel.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/AlignJFrame.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Matrix.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourJFrame.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/MatrixJFrame.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourMenu.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PatternJFrame.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/ColourPanel.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PlotConsensus.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/Consensus.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrettyPlotJFrame.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/ConsensusOptions.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignmentImage.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/GraphicSequenceCollection.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignment.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Paste.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameEvent.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Sequence.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrame.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceJPanel.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameEvent.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutAlignJFrameListener.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceNameJButton.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionEvent.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceProperties.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollection.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceReader.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionEvent.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutGraphicSequenceCollectionListener.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceSaver.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequence.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/GroutSequenceJPanel.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/IDTableJFrame.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Matrix.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/MatrixJFrame.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Paste.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PatternJFrame.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PlotConsensus.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrettyPlotJFrame.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignment.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintAlignmentImage.java > %%DATADIR%%/jemboss/org/emboss/jemboss/editor/PrintableJTable.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Block.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/PrintDNAImage.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/DNADraw.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/RestrictionEnzyme.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/EmbossCirdnaReader.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Ticks.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/GeneticMarker.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/Wizard.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/draw/LineAttribute.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/Sequence.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceJPanel.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceNameJButton.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceProperties.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceReader.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/editor/SequenceSaver.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/graphics/Graph2DPlot.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/graphics/PrintPlot.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Browser.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Favorites.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/KeywordSearch.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/LaunchJalView.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ScrollPanel.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceData.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceList.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowResultSet.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SplashThread.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SwingWorker.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSave.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/FileSaving.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalAndRemoteFileTreeFrame.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalTreeToolBar.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteDragTree.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileNode.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/RemoteFileTreePanel.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree/LocalAndRemoteFileTreeFrame.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ApplicationNamePanel.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/BuildJembossForm.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/JembossComboPopup.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/LabelTextBox.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ListFilePanel.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/MultiLineToolTipUI.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/PlafMacros.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SectionPanel.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/Separator.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetInFileCard.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/SetOutFileCard.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldFloat.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldInt.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/TextFieldSink.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/JembossComboPopup.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/MultiLineToolTipUI.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/PlafMacros.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ReportFormat.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/ApplicationNamePanel.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/LabelTextBox.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/Separator.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/FileChooser.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.java >@@ -1620,30 +950,15 @@ > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser/TextAreaSink.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/Database.java > %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup/ProgList.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ResultsMenuBar.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowResultSet.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceData.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/LaunchJalView.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SequenceList.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SwingWorker.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SetUpMenuBar.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/Browser.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/SplashThread.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ScrollPanel.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/gui/ImageIconJPanel.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java > %%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdFunResolve.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java > %%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVarResolve.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java > %%DATADIR%%/jemboss/org/emboss/jemboss/parser/Ajax.java > %%DATADIR%%/jemboss/org/emboss/jemboss/parser/AjaxUtil.java > %%DATADIR%%/jemboss/org/emboss/jemboss/parser/Dependent.java > %%DATADIR%%/jemboss/org/emboss/jemboss/parser/ParseAcd.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java >+%%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java > %%DATADIR%%/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java > %%DATADIR%%/jemboss/org/emboss/jemboss/programs/JembossProcess.java > %%DATADIR%%/jemboss/org/emboss/jemboss/programs/ListFile.java >@@ -1651,106 +966,1017 @@ > %%DATADIR%%/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java > %%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java > %%DATADIR%%/jemboss/org/emboss/jemboss/programs/RunEmbossApplication2.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossServer.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileServer.java >-%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossThread.java 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>+%%PORTDOCS%%%%DOCSDIR%%/programs/text/trimseq.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/twofeat.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/union.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/vectorstrip.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/water.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/whichdb.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wobble.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordcount.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wordmatch.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/wossname.txt >+%%PORTDOCS%%%%DOCSDIR%%/programs/text/yank.txt >+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt >+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt >+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt >+%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz >+%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials > %%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/text >+%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html > %%PORTDOCS%%@dirrm %%DOCSDIR%%/programs >-%%PORTDOCS%%@dirrm %%DOCSDIR%%/tutorials >+%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals > %%PORTDOCS%%@dirrm %%DOCSDIR%% >-@dirrm %%DATADIR%%/acd >-@dirrm %%DATADIR%%/data/AAINDEX >-@dirrm %%DATADIR%%/data/CODONS >-@dirrm %%DATADIR%%/data/REBASE >-@dirrm %%DATADIR%%/data/PRINTS >-@dirrm %%DATADIR%%/data/PROSITE >-@dirrm %%DATADIR%%/data >-@dirrm %%DATADIR%%/test/data >-@dirrm %%DATADIR%%/test/embl >+@dirrm %%DATADIR%%/test/wormpep >+@dirrm %%DATADIR%%/test/swnew >+@dirrm %%DATADIR%%/test/swiss >+@dirrm %%DATADIR%%/test/pir > @dirrm %%DATADIR%%/test/genbank > @dirrm %%DATADIR%%/test/gb >-@dirrm %%DATADIR%%/test/pir >-@dirrm %%DATADIR%%/test/swiss >-@dirrm %%DATADIR%%/test/swnew >-@dirrm %%DATADIR%%/test/wormpep >+@dirrm %%DATADIR%%/test/embl >+@dirrm %%DATADIR%%/test/data > @dirrm %%DATADIR%%/test >-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree >-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form >-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser >-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup >-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui >+@dirrm %%DATADIR%%/jemboss/utils >+@dirrm %%DATADIR%%/jemboss/resources >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/graphics >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw >+@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss >+@dirrm %%DATADIR%%/jemboss/org/emboss >+@dirrm %%DATADIR%%/jemboss/org >+@dirrm %%DATADIR%%/jemboss/lib/axis >+@dirrm %%DATADIR%%/jemboss/lib >+@dirrm %%DATADIR%%/jemboss/images >+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap >+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs > @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser/acd > @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/parser >-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/programs >-@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/soap >+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/startup >+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser >+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form >+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree >+@dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui > @dirrm %%DATADIR%%/jemboss/api/org/emboss/jemboss > @dirrm %%DATADIR%%/jemboss/api/org/emboss > @dirrm %%DATADIR%%/jemboss/api/org > @dirrm %%DATADIR%%/jemboss/api >-@dirrm %%DATADIR%%/jemboss/images >-@dirrm %%DATADIR%%/jemboss/lib/axis >-@dirrm %%DATADIR%%/jemboss/lib >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/editor >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/draw >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/filetree >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/form >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/sequenceChooser >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui/startup >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser/acd >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/parser >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/programs >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/server >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/soap >-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss >-@dirrm %%DATADIR%%/jemboss/org/emboss >-@dirrm %%DATADIR%%/jemboss/org >-@dirrm %%DATADIR%%/jemboss/resources >-@dirrm %%DATADIR%%/jemboss/utils > @dirrm %%DATADIR%%/jemboss >+@dirrm %%DATADIR%%/data/REBASE >+@dirrm %%DATADIR%%/data/PROSITE >+@dirrm %%DATADIR%%/data/PRINTS >+@dirrm %%DATADIR%%/data/CODONS >+@dirrm %%DATADIR%%/data/AAINDEX >+@dirrm %%DATADIR%%/data >+@dirrm %%DATADIR%%/acd > @dirrm %%DATADIR%%
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