diff options
| author | Pav Lucistnik <pav@FreeBSD.org> | 2005-05-29 18:26:05 +0000 |
|---|---|---|
| committer | Pav Lucistnik <pav@FreeBSD.org> | 2005-05-29 18:26:05 +0000 |
| commit | 947a8e30b5438862a3f77ab891752442359045d2 (patch) | |
| tree | 5c93ab5c7c5d87210d14aab2b28c72e62827db40 /biology | |
| parent | 75c04032898be9de1a513cd689b64ec4aa57bb7e (diff) | |
| download | ports-947a8e30b5438862a3f77ab891752442359045d2.tar.gz ports-947a8e30b5438862a3f77ab891752442359045d2.zip | |
Notes
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/emboss/Makefile | 2 | ||||
| -rw-r--r-- | biology/emboss/distinfo | 4 | ||||
| -rw-r--r-- | biology/emboss/pkg-plist | 2210 |
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 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-%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmmgen.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/hmoment.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoalign.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/infoseq.txt -%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-gcg.ppt -%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-interfaces.ppt -%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss-talk.ppt -%%PORTDOCS%%%%DOCSDIR%%/tutorials/emboss_tut.tar.gz -%%DATADIR%%/plstnd5.fnt -%%DATADIR%%/plxtnd5.fnt +lib/libnucleus.so +lib/libnucleus.so.1 +lib/libplplot.a +lib/libplplot.so +lib/libplplot.so.5 +%%DATADIR%%/acd/aaindexextract.acd +%%DATADIR%%/acd/abiview.acd +%%DATADIR%%/acd/acdc.acd +%%DATADIR%%/acd/acdlog.acd +%%DATADIR%%/acd/acdpretty.acd +%%DATADIR%%/acd/acdtable.acd +%%DATADIR%%/acd/acdtrace.acd +%%DATADIR%%/acd/acdvalid.acd +%%DATADIR%%/acd/ajbad.acd +%%DATADIR%%/acd/ajfeatest.acd +%%DATADIR%%/acd/ajtest.acd +%%DATADIR%%/acd/antigenic.acd +%%DATADIR%%/acd/backtranseq.acd 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+%%DATADIR%%/acd/descseq.acd +%%DATADIR%%/acd/diffseq.acd +%%DATADIR%%/acd/digest.acd +%%DATADIR%%/acd/distmat.acd +%%DATADIR%%/acd/dotmatcher.acd +%%DATADIR%%/acd/dotpath.acd +%%DATADIR%%/acd/dottup.acd +%%DATADIR%%/acd/dreg.acd +%%DATADIR%%/acd/einverted.acd +%%DATADIR%%/acd/embossdata.acd +%%DATADIR%%/acd/embossversion.acd +%%DATADIR%%/acd/emma.acd +%%DATADIR%%/acd/emowse.acd +%%DATADIR%%/acd/entrails.acd +%%DATADIR%%/acd/entret.acd +%%DATADIR%%/acd/epestfind.acd +%%DATADIR%%/acd/eprimer3.acd +%%DATADIR%%/acd/equicktandem.acd +%%DATADIR%%/acd/est2genome.acd +%%DATADIR%%/acd/etandem.acd +%%DATADIR%%/acd/extractfeat.acd +%%DATADIR%%/acd/extractseq.acd +%%DATADIR%%/acd/findkm.acd +%%DATADIR%%/acd/freak.acd +%%DATADIR%%/acd/fuzznuc.acd +%%DATADIR%%/acd/fuzzpro.acd +%%DATADIR%%/acd/fuzztran.acd +%%DATADIR%%/acd/garnier.acd +%%DATADIR%%/acd/geecee.acd +%%DATADIR%%/acd/getorf.acd +%%DATADIR%%/acd/giep.acd +%%DATADIR%%/acd/groups.standard +%%DATADIR%%/acd/helixturnhelix.acd +%%DATADIR%%/acd/histogramtest.acd +%%DATADIR%%/acd/hmoment.acd +%%DATADIR%%/acd/iep.acd +%%DATADIR%%/acd/infoalign.acd +%%DATADIR%%/acd/infoseq.acd +%%DATADIR%%/acd/intconv.acd +%%DATADIR%%/acd/isochore.acd +%%DATADIR%%/acd/kmrsplitter.acd +%%DATADIR%%/acd/kmrunion.acd +%%DATADIR%%/acd/knowntypes.standard +%%DATADIR%%/acd/lindna.acd +%%DATADIR%%/acd/listor.acd +%%DATADIR%%/acd/marscan.acd +%%DATADIR%%/acd/maskfeat.acd +%%DATADIR%%/acd/maskseq.acd +%%DATADIR%%/acd/matcher.acd %%DATADIR%%/acd/megamerger.acd %%DATADIR%%/acd/merger.acd %%DATADIR%%/acd/msbar.acd @@ -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 %%DATADIR%%/acd/recoder.acd %%DATADIR%%/acd/redata.acd @@ -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 %%DATADIR%%/acd/showseq.acd %%DATADIR%%/acd/shuffleseq.acd -%%DATADIR%%/acd/tfm.acd %%DATADIR%%/acd/sigcleave.acd %%DATADIR%%/acd/silent.acd %%DATADIR%%/acd/sirna.acd @@ -862,6 +447,7 @@ lib/libnucleus.a %%DATADIR%%/acd/testplot.acd %%DATADIR%%/acd/textsearch.acd %%DATADIR%%/acd/tfextract.acd +%%DATADIR%%/acd/tfm.acd %%DATADIR%%/acd/tfscan.acd %%DATADIR%%/acd/tmap.acd %%DATADIR%%/acd/tranalign.acd @@ -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 %%DATADIR%%/acd/whichdb.acd @@ -879,92 +466,6 @@ lib/libnucleus.a %%DATADIR%%/acd/wordmatch.acd %%DATADIR%%/acd/wossname.acd %%DATADIR%%/acd/yank.acd -%%DATADIR%%/acd/codes.english -%%DATADIR%%/acd/groups.standard -%%DATADIR%%/acd/sections.standard 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%%DATADIR%%/data/CODONS/Eham.cut @@ -1117,9 +618,6 @@ lib/libnucleus.a %%DATADIR%%/data/CODONS/Eysp.cut %%DATADIR%%/data/CODONS/Ezebrafish.cut %%DATADIR%%/data/CODONS/Ezma.cut -%%DATADIR%%/data/REBASE/dummyfile -%%DATADIR%%/data/PRINTS/dummyfile -%%DATADIR%%/data/PROSITE/dummyfile %%DATADIR%%/data/EBLOSUM30 %%DATADIR%%/data/EBLOSUM35 %%DATADIR%%/data/EBLOSUM40 @@ -1227,9 +725,13 @@ lib/libnucleus.a %%DATADIR%%/data/Efeatures.protein %%DATADIR%%/data/Efeatures.swiss %%DATADIR%%/data/Efreqs.dat +%%DATADIR%%/data/Ehet.dat %%DATADIR%%/data/Ehth.dat %%DATADIR%%/data/Ehth87.dat +%%DATADIR%%/data/Emass.dat +%%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 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%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.PopupListener.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileNode.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileSaving.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/BuildJembossForm.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.myComboUI.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/ListFilePanel.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SectionPanel.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SetInFileCard.html @@ -1463,8 +791,6 @@ lib/libnucleus.a %%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/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 @@ lib/libnucleus.a %%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 @@ 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 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