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authorPav Lucistnik <pav@FreeBSD.org>2005-05-29 18:26:05 +0000
committerPav Lucistnik <pav@FreeBSD.org>2005-05-29 18:26:05 +0000
commit947a8e30b5438862a3f77ab891752442359045d2 (patch)
tree5c93ab5c7c5d87210d14aab2b28c72e62827db40 /biology
parent75c04032898be9de1a513cd689b64ec4aa57bb7e (diff)
downloadports-947a8e30b5438862a3f77ab891752442359045d2.tar.gz
ports-947a8e30b5438862a3f77ab891752442359045d2.zip
Notes
Diffstat (limited to 'biology')
-rw-r--r--biology/emboss/Makefile2
-rw-r--r--biology/emboss/distinfo4
-rw-r--r--biology/emboss/pkg-plist2210
3 files changed, 1221 insertions, 995 deletions
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile
index b0e4759f5025..ec6b750a313b 100644
--- a/biology/emboss/Makefile
+++ b/biology/emboss/Makefile
@@ -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 --git a/biology/emboss/distinfo b/biology/emboss/distinfo
index 5c53ea980ba9..7d6f55577cb6 100644
--- a/biology/emboss/distinfo
+++ b/biology/emboss/distinfo
@@ -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 --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist
index ce1ef92d70f0..fc8d17cca9f2 100644
--- a/biology/emboss/pkg-plist
+++ b/biology/emboss/pkg-plist
@@ -82,8 +82,8 @@ bin/needle
bin/newcpgreport
bin/newcpgseek
bin/newseq
-bin/notseq
bin/noreturn
+bin/notseq
bin/nthseq
bin/octanol
bin/oddcomp
@@ -119,6 +119,7 @@ bin/remap
bin/restover
bin/restrict
bin/revseq
+bin/runJemboss.csh
bin/seealso
bin/seqmatchall
bin/seqret
@@ -159,31 +160,18 @@ bin/wordcount
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/ajfeatdata.h
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/ajtranslate.h
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
@@ -250,538 +232,140 @@ include/embmat.h
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
-lib/libajax.so.1
-lib/libajax.so
+include/metadefs.h
+include/pcre.h
+include/pcre_chartables.c
+include/pcre_config.h
+include/pcre_get.c
+include/pcre_internal.h
+include/pcre_printint.c
+include/pcreposix.h
+include/pdf.h
+include/plConfig.h
+include/plDevs.h
+include/plcore.h
+include/pldebug.h
+include/plevent.h
+include/plplot.h
+include/plplotP.h
+include/plstrm.h
+include/plxwd.h
lib/libajax.a
-lib/libajaxg.so.1
-lib/libajaxg.so
+lib/libajax.so
+lib/libajax.so.1
lib/libajaxg.a
-lib/libnucleus.so.1
-lib/libnucleus.so
+lib/libajaxg.so
+lib/libajaxg.so.1
lib/libnucleus.a
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-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.aux
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.dvi
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.log
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.toc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/adminguide.tar.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/domainatrix.doc
-%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz
-%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.ps
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss.sty
-%%PORTDOCS%%%%DOCSDIR%%/manuals/fdl.txt
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/listor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/marscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/maskseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/matcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mix.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/msbar.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mse.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwcontam.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/mwfilter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/neighbor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgreport.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newcpgseek.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/newseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/noreturn.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/notseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nthseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/penny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_codon_usage_nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_cpg_islands_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_gene_finding_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_primers_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_repeats_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_restriction_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_transcription_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/oddcomp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/palindrome.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pasteseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/patmatmotifs.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepcoil.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepstats.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pestfind.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/preg.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/primersearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/printsextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/profit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophecy.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prophet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prosextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protdist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_2d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_3d_structure_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_composition_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_motifs_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_mutation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_profiles_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/rebaseextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/recoder.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/redata.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/remap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restover.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqboot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showorf.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/shuffleseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigcleave.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/textsearch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfm.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tfscan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/tranalign.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimest.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/twofeat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/union.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_creation_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_database_indexing_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/whichdb.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordcount.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wordmatch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wossname.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/yank.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.jpg
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.1.abiview.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.1.chaos.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.1.cirdna.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.2.dan.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.1.cpgplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.1.dotmatcher.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.1.dotpath.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dottup.1.dottup.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emboss_icon.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/findkm.1.findkm.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/isochore.1.isochore.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/lindna.1.lindna.gif
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotcon.1.plotcon.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.1.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/plotorf.2.plotorf.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/polydot.1.polydot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.1.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/prettyplot.2.prettyplot.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.1.syco.gif
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.1.wobble.gif
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/aaindexextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_consensus_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_differences_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_dot_plots_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_global_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_local_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/antigenic.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_multiple_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/backtranseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/banana.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/biosed.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/btwisted.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cai.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/charge.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/checktrans.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/chips.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/clique.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/codcmp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/coderet.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/compseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cons.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/consense.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/contacts.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/contml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/contrast.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgreport.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cusp.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutgextract.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/cutseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiblast.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbifasta.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dbigcg.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/degapseq.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/descseq.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/digest.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/display_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/distmat.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnacomp.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/dnapenny.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/econtml.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/edit_group.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednadist.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednainvar.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednaml.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednamlk.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednapars.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ednapenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/edollop.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/edolpenny.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/efactor.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/efitch.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/einverted.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/ekitsch.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossdata.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/embossversion.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/emma.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/entret.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/enzyme_kinetics_group.html
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%%DATADIR%%/acd/megamerger.acd
%%DATADIR%%/acd/merger.acd
%%DATADIR%%/acd/msbar.acd
@@ -824,6 +408,7 @@ lib/libnucleus.a
%%DATADIR%%/acd/prophet.acd
%%DATADIR%%/acd/prosextract.acd
%%DATADIR%%/acd/pscan.acd
+%%DATADIR%%/acd/psiphi.acd
%%DATADIR%%/acd/rebaseextract.acd
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@@ -831,6 +416,7 @@ lib/libnucleus.a
%%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
@@ -847,7 +433,6 @@ lib/libnucleus.a
%%DATADIR%%/acd/showorf.acd
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%%DATADIR%%/acd/shuffleseq.acd
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%%DATADIR%%/acd/sigcleave.acd
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@@ -862,6 +447,7 @@ lib/libnucleus.a
%%DATADIR%%/acd/testplot.acd
%%DATADIR%%/acd/textsearch.acd
%%DATADIR%%/acd/tfextract.acd
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%%DATADIR%%/acd/tfscan.acd
%%DATADIR%%/acd/tmap.acd
%%DATADIR%%/acd/tranalign.acd
@@ -871,6 +457,7 @@ lib/libnucleus.a
%%DATADIR%%/acd/trimseq.acd
%%DATADIR%%/acd/twofeat.acd
%%DATADIR%%/acd/union.acd
+%%DATADIR%%/acd/variables.standard
%%DATADIR%%/acd/vectorstrip.acd
%%DATADIR%%/acd/water.acd
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-%%DATADIR%%/acd/freak.acd
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-%%DATADIR%%/acd/isochore.acd
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%%DATADIR%%/data/AAINDEX/dummyfile
%%DATADIR%%/data/CODONS/Eacc.cut
%%DATADIR%%/data/CODONS/Eadenovirus5.cut
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%%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 @@ lib/libnucleus.a
%%DATADIR%%/data/CODONS/Eysp.cut
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%%DATADIR%%/data/EBLOSUM30
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@@ -1227,9 +725,13 @@ lib/libnucleus.a
%%DATADIR%%/data/Efeatures.protein
%%DATADIR%%/data/Efeatures.swiss
%%DATADIR%%/data/Efreqs.dat
+%%DATADIR%%/data/Ehet.dat
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%%DATADIR%%/data/Ehth87.dat
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+%%DATADIR%%/data/Emassmod.dat
%%DATADIR%%/data/Ememe.dat
+%%DATADIR%%/data/Emwfilter.dat
%%DATADIR%%/data/Enakai.dat
%%DATADIR%%/data/Epepcoil.dat
%%DATADIR%%/data/Epk.dat
@@ -1248,212 +750,38 @@ lib/libnucleus.a
%%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%%/data/Emwfilter.dat
-%%DATADIR%%/data/Emass.dat
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-%%DATADIR%%/test/data/withrefm
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-%%DATADIR%%/test/data/dna.gcg
-%%DATADIR%%/test/data/dna.gcg8
-%%DATADIR%%/test/data/dna.genbank
-%%DATADIR%%/test/data/dna.ig
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-%%DATADIR%%/test/data/dna.m-ncbi
-%%DATADIR%%/test/data/dna.m-strider
-%%DATADIR%%/test/data/dna.msf
-%%DATADIR%%/test/data/dna.msf8
-%%DATADIR%%/test/data/dna.ncbi
-%%DATADIR%%/test/data/dna.phylip
-%%DATADIR%%/test/data/dna.phylip3
-%%DATADIR%%/test/data/dna.staden
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-%%DATADIR%%/test/data/dna.text
-%%DATADIR%%/test/data/feat.emft
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-%%DATADIR%%/test/data/z83307.seq
-%%DATADIR%%/test/data/aligna.dna
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-%%DATADIR%%/test/data/alignb.dna
-%%DATADIR%%/test/data/aligna.prot
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-%%DATADIR%%/test/wormpep/des.hit
-%%DATADIR%%/test/wormpep/des.trg
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+%%DATADIR%%/jemboss/api/index.html
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+%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.html
+%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.winExit.html
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+%%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
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%%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
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%%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
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%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SetInFileCard.html
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%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.WholeNumberDocument.html
%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.html
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%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.html
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%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.html
@@ -1475,19 +801,13 @@ lib/libnucleus.a
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%%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
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%%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/JembossProcess.html
%%DATADIR%%/jemboss/api/org/emboss/jemboss/programs/ListFile.html
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@@ -1500,17 +820,6 @@ lib/libnucleus.a
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-%%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 @@ lib/libnucleus.a
%%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 @@ lib/libnucleus.a
%%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 @@ lib/libnucleus.a
%%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 @@ lib/libnucleus.a
%%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
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPublicServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossFileServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossServer.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/JembossThread.java
%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPrivateServer.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/server/AppendToLogFileThread.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/server/TestPublicServer.java
%%DATADIR%%/jemboss/org/emboss/jemboss/soap/AuthPopup.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossSoapException.java
%%DATADIR%%/jemboss/org/emboss/jemboss/soap/CallAjax.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PendingResults.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetWossname.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossRun.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ServerSetup.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java
%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileList.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PublicRequest.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/FileRoots.java
%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetACD.java
%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetHelp.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ShowDB.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/GetWossname.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossRun.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/JembossSoapException.java
%%DATADIR%%/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/JembossLogo.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/JembossParams.java
-%%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PendingResults.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/PublicRequest.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ServerSetup.java
+%%DATADIR%%/jemboss/org/emboss/jemboss/soap/ShowDB.java
+%%DATADIR%%/jemboss/readme.html
+%%DATADIR%%/jemboss/resources/filemgr.html
%%DATADIR%%/jemboss/resources/jemboss.properties
%%DATADIR%%/jemboss/resources/readme.html
%%DATADIR%%/jemboss/resources/readmeAlign.html
%%DATADIR%%/jemboss/resources/readmeDNADraw.html
%%DATADIR%%/jemboss/resources/results.html
-%%DATADIR%%/jemboss/resources/version
-%%DATADIR%%/jemboss/resources/filemgr.html
%%DATADIR%%/jemboss/resources/seqList.html
+%%DATADIR%%/jemboss/resources/version
+%%DATADIR%%/jemboss/runJemboss.sh
+%%DATADIR%%/jemboss/utils/README
%%DATADIR%%/jemboss/utils/install-jemboss-server.sh
%%DATADIR%%/jemboss/utils/keys.sh
-%%DATADIR%%/jemboss/utils/makeJar.csh
-%%DATADIR%%/jemboss/utils/makeJNLP.sh
%%DATADIR%%/jemboss/utils/makeFileManagerJNLP.sh
+%%DATADIR%%/jemboss/utils/makeJNLP.sh
+%%DATADIR%%/jemboss/utils/makeJar.csh
%%DATADIR%%/jemboss/utils/template.html
-%%DATADIR%%/jemboss/utils/README
-%%DATADIR%%/jemboss/LICENSE
-%%DATADIR%%/jemboss/readme.html
-%%DATADIR%%/jemboss/runJemboss.sh
-%%DATADIR%%/jemboss/README
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/manuals
-%%PORTDOCS%%@dirrm %%DOCSDIR%%/programs/html
+%%DATADIR%%/plstnd5.fnt
+%%DATADIR%%/plxtnd5.fnt
+%%DATADIR%%/test/data/aaindex1.test
+%%DATADIR%%/test/data/aligna.dna
+%%DATADIR%%/test/data/aligna.prot
+%%DATADIR%%/test/data/alignapart.dna
+%%DATADIR%%/test/data/alignapart.prot
+%%DATADIR%%/test/data/alignb.dna
+%%DATADIR%%/test/data/alignb.prot
+%%DATADIR%%/test/data/cutg.codon
+%%DATADIR%%/test/data/dna.acedb
+%%DATADIR%%/test/data/dna.aln
+%%DATADIR%%/test/data/dna.asn1
+%%DATADIR%%/test/data/dna.codata
+%%DATADIR%%/test/data/dna.embl
+%%DATADIR%%/test/data/dna.fasta
+%%DATADIR%%/test/data/dna.fitch
+%%DATADIR%%/test/data/dna.gcg
+%%DATADIR%%/test/data/dna.gcg8
+%%DATADIR%%/test/data/dna.genbank
+%%DATADIR%%/test/data/dna.ig
+%%DATADIR%%/test/data/dna.m-acedb
+%%DATADIR%%/test/data/dna.m-codata
+%%DATADIR%%/test/data/dna.m-embl
+%%DATADIR%%/test/data/dna.m-fasta
+%%DATADIR%%/test/data/dna.m-fasta-long
+%%DATADIR%%/test/data/dna.m-ncbi
+%%DATADIR%%/test/data/dna.m-strider
+%%DATADIR%%/test/data/dna.msf
+%%DATADIR%%/test/data/dna.msf8
+%%DATADIR%%/test/data/dna.ncbi
+%%DATADIR%%/test/data/dna.phylip
+%%DATADIR%%/test/data/dna.phylip3
+%%DATADIR%%/test/data/dna.staden
+%%DATADIR%%/test/data/dna.strider
+%%DATADIR%%/test/data/dna.text
+%%DATADIR%%/test/data/feat.emft
+%%DATADIR%%/test/data/feat.fasta
+%%DATADIR%%/test/data/feat.pir
+%%DATADIR%%/test/data/mw1.dat
+%%DATADIR%%/test/data/mw2.dat
+%%DATADIR%%/test/data/mw3.dat
+%%DATADIR%%/test/data/paamir.pep
+%%DATADIR%%/test/data/pax6_cdna.fasta
+%%DATADIR%%/test/data/prints.test
+%%DATADIR%%/test/data/prosite.dat
+%%DATADIR%%/test/data/prosite.doc
+%%DATADIR%%/test/data/prot.acedb
+%%DATADIR%%/test/data/prot.codata
+%%DATADIR%%/test/data/prot.fasta
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+%%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/meme.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/myseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/nawalignrunner.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/needle.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/needlerunner.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/pdbparse.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbplus.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/pdbtosp.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/psiphi.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/rocon.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/rocplot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scope.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scopparse.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorer.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/scorerrunner.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seealso.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqboot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqfraggle.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqmatchall.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqnr.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqret.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqretsplit.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsearch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqsort.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/seqwords.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/showdb.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/siggen.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscan.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/silent.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sirna.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sites.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/sixpack.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/skipseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/splitter.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ssematch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/stretcher.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/stssearch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/substitute.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/substituterunner.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%%/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
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-@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
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-@dirrm %%DATADIR%%/jemboss/org/emboss/jemboss/gui
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-@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%%