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Date:      Sat, 28 May 2005 10:07:54 GMT
From:      "Choe, Cheng-Dae" <whitekid@gmail.com>
To:        freebsd-gnats-submit@FreeBSD.org
Subject:   ports/81579: update biology/emboss to 2.10.0
Message-ID:  <200505281007.j4SA7sOg030702@www.freebsd.org>
Resent-Message-ID: <200505281010.j4SAA27I010882@freefall.freebsd.org>

---

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---

>Number:         81579
>Category:       ports
>Synopsis:       update biology/emboss to 2.10.0
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Sat May 28 10:10:02 GMT 2005
>Closed-Date:
>Last-Modified:
>Originator:     "Choe, Cheng-Dae"
>Release:        FreeBSD 4.10-STABLE i386
>Organization:
>Environment:
System: FreeBSD w.comdongin.com 5.4-RELEASE FreeBSD 5.4-RELEASE #0: Wed May 11 18:48:47 KST 2005 root@w.comdongin.com:/usr/obj/data/src/sys/CDI i386

>Description:
      update biology/emboss to 2.10.0
>How-To-Repeat:
      N/A
>Fix:
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
-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/domainatrix.doc
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-%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt
-%%PORTDOCS%%%%DOCSDIR%%/manuals/emboss_qg.pdf
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.html
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-%%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
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-%%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
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqboot.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/showfeat.html
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-%%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
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/transeq.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/trimseq.html
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-%%PORTDOCS%%%%DOCSDIR%%/programs/html/utils_misc_group.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/vectorstrip.html
-%%PORTDOCS%%%%DOCSDIR%%/programs/html/water.html
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 %%DATADIR%%/acd/aaindexextract.acd
 %%DATADIR%%/acd/abiview.acd
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 %%DATADIR%%/acd/ajbad.acd
 %%DATADIR%%/acd/ajfeatest.acd
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@@ -900,6 +294,7 @@
 %%DATADIR%%/acd/cirdna.acd
 %%DATADIR%%/acd/codcmp.acd
 %%DATADIR%%/acd/coderet.acd
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 %%DATADIR%%/acd/complex.acd
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 %%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
+%%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
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+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fdrawtree.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffactor.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffitch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ffreqboot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fgendist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/findkm.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fitch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fkitsch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmix.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fmove.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fneighbor.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpars.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpenny.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fproml.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fpromlk.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotdist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fprotpars.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/freak.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestboot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestdist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/frestml.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fretree.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqboot.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/fseqbootall.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedist.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/ftreedistpair.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/hmoment.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/interface.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/isochore.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/jembossctl.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/kitsch.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/libgen.txt
+%%PORTDOCS%%%%DOCSDIR%%/programs/text/libscan.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/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
 @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%%
>Release-Note:
>Audit-Trail:
>Unformatted:

---

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