diff options
| author | rafan <rafan@FreeBSD.org> | 2008-04-13 15:21:16 +0800 |
|---|---|---|
| committer | rafan <rafan@FreeBSD.org> | 2008-04-13 15:21:16 +0800 |
| commit | 17d59dbeca8ab77b5998b68066120758b6a90811 (patch) | |
| tree | 690b7be3d514f177155568ae97114c82e89d87ce | |
| parent | 893e716a078165df96285f1a5b02a92d6d228b3a (diff) | |
| download | freebsd-ports-graphics-17d59dbeca8ab77b5998b68066120758b6a90811.tar.gz freebsd-ports-graphics-17d59dbeca8ab77b5998b68066120758b6a90811.tar.zst freebsd-ports-graphics-17d59dbeca8ab77b5998b68066120758b6a90811.zip | |
- Sort pkg-plist before updating to 5.0.0
PR: ports/122437
Submitted by: Fernan Aguero <fernan@iib.unsam.edu.ar> (maintainer)
| -rw-r--r-- | biology/emboss/pkg-plist | 1776 |
1 files changed, 888 insertions, 888 deletions
diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index ea98778089e..12a1a5046e1 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -25,8 +25,8 @@ bin/cpgplot bin/cpgreport bin/cusp bin/cutgextract -bin/dan bin/cutseq +bin/dan bin/dbiblast bin/dbifasta bin/dbiflat @@ -123,6 +123,7 @@ bin/remap bin/restover bin/restrict bin/revseq +bin/runJemboss.csh bin/seealso bin/seqmatchall bin/seqret @@ -138,11 +139,11 @@ bin/silent bin/sirna bin/sixpack bin/skipseq -bin/syco bin/splitter bin/stretcher bin/stssearch bin/supermatcher +bin/syco bin/tcode bin/textsearch bin/tfextract @@ -163,30 +164,17 @@ bin/wordcount bin/wordmatch bin/wossname bin/yank -bin/runJemboss.csh -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 @@ -195,8 +183,8 @@ 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 @@ -229,14 +217,7 @@ 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 @@ -254,234 +235,66 @@ 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/embprop.h include/embread.h -include/embsig.h include/embshow.h +include/embsig.h include/embword.h -lib/libplplot.so.5 -lib/libplplot.so -lib/libplplot.la -lib/libplplot.a -lib/libajax.so.3 -lib/libajax.so -lib/libajax.la +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.3 -lib/libajaxg.so -lib/libajaxg.la +lib/libajax.la +lib/libajax.so +lib/libajax.so.3 lib/libajaxg.a -lib/libnucleus.so.3 -lib/libnucleus.so -lib/libnucleus.la +lib/libajaxg.la +lib/libajaxg.so +lib/libajaxg.so.3 lib/libnucleus.a -%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.sty -%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex +lib/libnucleus.la +lib/libnucleus.so +lib/libnucleus.so.3 +lib/libplplot.a +lib/libplplot.la +lib/libplplot.so +lib/libplplot.so.5 +%%PORTDOCS%%%%DOCSDIR%%/manuals/EMBOSS-FreeBSD-HOWTO.txt %%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.sty +%%PORTDOCS%%%%DOCSDIR%%/manuals/admin.tex %%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.sty %%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/matgen3d.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/megamerger.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/meme.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/menus_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/merger.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/myseq.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalign.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/nawalignrunner.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/needle.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/needlerunner.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/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/nucleic_transcription_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/nucleic_translation_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.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/pdbparse.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbplus.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/pdbtosp.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/phylogeny_consensus_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_continuous_characters_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_discrete_characters_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_distance_matrix_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_gene_frequencies_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_molecular_sequence_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/phylogeny_tree_drawing_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/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/protein_profiles_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/protein_sequence_alignment_group.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/pscan.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/psiphi.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/restover.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/restrict.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/revseq.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocon.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/rocplot.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/scope.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/scopparse.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorecmapdir.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorer.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/scorerrunner.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seealso.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqalign.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqfraggle.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqmatchall.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqnr.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqret.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqretsplit.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsearch.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqsort.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/seqwords.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/siggen.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/siggenlig.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscan.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/sigscanlig.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/silent.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/sirna.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/sites.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/sixpack.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/skipseq.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/splitter.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/ssematch.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/stretcher.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/stssearch.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/substitute.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/substituterunner.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/supermatcher.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/syco.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/tcode.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/template.html -%%PORTDOCS%%%%DOCSDIR%%/programs/html/test_group.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/cpgplot.1.cpgplot.gif -%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.2.dan.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 -%%PORTDOCS%%%%DOCSDIR%%/programs/html/octanol.1.octanol.gif -%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepinfo.1.pepinfo.gif -%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepnet.1.pepnet.gif -%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwheel.1.pepwheel.gif -%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindow.1.pepwindow.gif -%%PORTDOCS%%%%DOCSDIR%%/programs/html/pepwindowall.1.pepwindowall.gif -%%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 -%%PORTDOCS%%%%DOCSDIR%%/programs/html/tmap.1.tmap.gif -%%PORTDOCS%%%%DOCSDIR%%/programs/html/topo.gif -%%PORTDOCS%%%%DOCSDIR%%/programs/html/wobble.1.wobble.gif +%%PORTDOCS%%%%DOCSDIR%%/manuals/program.ps.gz %%PORTDOCS%%%%DOCSDIR%%/programs/html/aaindexextract.html +%%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.1.abiview.gif %%PORTDOCS%%%%DOCSDIR%%/programs/html/abiview.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/acd_group.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/acdc.html @@ -494,22 +307,24 @@ lib/libnucleus.a %%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/antigenic.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_global_group.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_local_group.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/alignment_multiple_group.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/alignrunner.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/allversusall.html +%%PORTDOCS%%%%DOCSDIR%%/programs/html/antigenic.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/cathparse.html +%%PORTDOCS%%%%DOCSDIR%%/programs/html/chaos.1.chaos.gif %%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.1.cirdna.gif %%PORTDOCS%%%%DOCSDIR%%/programs/html/cirdna.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/codcmp.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/codcopy.html @@ -519,12 +334,14 @@ lib/libnucleus.a %%PORTDOCS%%%%DOCSDIR%%/programs/html/cons.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/contactalign.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/contacts.html +%%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.1.cpgplot.gif %%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgplot.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/cpgreport.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/crystalball.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/cusp.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/cutgextract.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/cutseq.html +%%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.2.dan.gif %%PORTDOCS%%%%DOCSDIR%%/programs/html/dan.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/dbiblast.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/dbifasta.html @@ -547,8 +364,11 @@ lib/libnucleus.a %%PORTDOCS%%%%DOCSDIR%%/programs/html/domainreso.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/domainseqs.html %%PORTDOCS%%%%DOCSDIR%%/programs/html/domainsse.html +%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.1.dotmatcher.gif %%PORTDOCS%%%%DOCSDIR%%/programs/html/dotmatcher.html +%%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.1.dotpath.gif %%PORTDOCS%%%%DOCSDIR%%/programs/html/dotpath.html 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%%PORTDOCS%%%%DOCSDIR%%/programs/text/acdtrace.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/acdvalid.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/alignrunner.txt @@ -810,6 +682,7 @@ lib/libnucleus.a %%PORTDOCS%%%%DOCSDIR%%/programs/text/banana.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/biosed.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/btwisted.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/cai.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/cathparse.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/chaos.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/charge.txt @@ -869,7 +742,6 @@ lib/libnucleus.a %%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapars.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/ednapenny.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/edollop.txt -%%PORTDOCS%%%%DOCSDIR%%/programs/text/iep.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/edolpenny.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/efactor.txt %%PORTDOCS%%%%DOCSDIR%%/programs/text/efitch.txt @@ -957,114 +829,142 @@ lib/libnucleus.a 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+%%PORTDOCS%%%%DOCSDIR%%/programs/text/meme.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/merger.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/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/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/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/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/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/scorecmapdir.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/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/siggenlig.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscan.txt +%%PORTDOCS%%%%DOCSDIR%%/programs/text/sigscanlig.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 -%%DATADIR%%/plstnd5.fnt -%%DATADIR%%/plxtnd5.fnt -%%DATADIR%%/acd/needle.acd -%%DATADIR%%/acd/newcoils.acd -%%DATADIR%%/acd/newcpgreport.acd -%%DATADIR%%/acd/newcpgseek.acd -%%DATADIR%%/acd/newseq.acd -%%DATADIR%%/acd/noreturn.acd -%%DATADIR%%/acd/notseq.acd -%%DATADIR%%/acd/nthseq.acd -%%DATADIR%%/acd/octanol.acd -%%DATADIR%%/acd/oddcomp.acd -%%DATADIR%%/acd/palindrome.acd -%%DATADIR%%/acd/pasteseq.acd -%%DATADIR%%/acd/patmatdb.acd -%%DATADIR%%/acd/patmatmotifs.acd -%%DATADIR%%/acd/patmattest.acd -%%DATADIR%%/acd/pepcoil.acd -%%DATADIR%%/acd/pepinfo.acd -%%DATADIR%%/acd/pepnet.acd -%%DATADIR%%/acd/pepstats.acd -%%DATADIR%%/acd/pepwheel.acd -%%DATADIR%%/acd/pepwindow.acd -%%DATADIR%%/acd/pepwindowall.acd -%%DATADIR%%/acd/plotcon.acd -%%DATADIR%%/acd/plotorf.acd -%%DATADIR%%/acd/polydot.acd -%%DATADIR%%/acd/preg.acd -%%DATADIR%%/acd/prettyplot.acd -%%DATADIR%%/acd/prettyseq.acd -%%DATADIR%%/acd/prima.acd -%%DATADIR%%/acd/primers.acd -%%DATADIR%%/acd/primersearch.acd -%%DATADIR%%/acd/printsextract.acd -%%DATADIR%%/acd/profit.acd -%%DATADIR%%/acd/prophecy.acd -%%DATADIR%%/acd/prophet.acd -%%DATADIR%%/acd/prosextract.acd -%%DATADIR%%/acd/pscan.acd -%%DATADIR%%/acd/psiphi.acd -%%DATADIR%%/acd/rebaseextract.acd -%%DATADIR%%/acd/recoder.acd -%%DATADIR%%/acd/redata.acd -%%DATADIR%%/acd/remap.acd -%%DATADIR%%/acd/restover.acd -%%DATADIR%%/acd/revseq.acd -%%DATADIR%%/acd/restrict.acd -%%DATADIR%%/acd/seealso.acd -%%DATADIR%%/acd/seqinfo.acd -%%DATADIR%%/acd/seqmatchall.acd -%%DATADIR%%/acd/seqret.acd -%%DATADIR%%/acd/seqretall.acd -%%DATADIR%%/acd/seqretallfeat.acd -%%DATADIR%%/acd/seqretset.acd -%%DATADIR%%/acd/seqretsingle.acd -%%DATADIR%%/acd/seqretsplit.acd -%%DATADIR%%/acd/seqrettype.acd -%%DATADIR%%/acd/showalign.acd -%%DATADIR%%/acd/showdb.acd -%%DATADIR%%/acd/showfeat.acd -%%DATADIR%%/acd/showorf.acd -%%DATADIR%%/acd/showseq.acd -%%DATADIR%%/acd/shuffleseq.acd -%%DATADIR%%/acd/sigcleave.acd -%%DATADIR%%/acd/silent.acd -%%DATADIR%%/acd/sirna.acd -%%DATADIR%%/acd/sixpack.acd -%%DATADIR%%/acd/skipseq.acd -%%DATADIR%%/acd/tfm.acd -%%DATADIR%%/acd/splitter.acd -%%DATADIR%%/acd/stretcher.acd -%%DATADIR%%/acd/stssearch.acd -%%DATADIR%%/acd/supermatcher.acd -%%DATADIR%%/acd/syco.acd -%%DATADIR%%/acd/tcode.acd -%%DATADIR%%/acd/testplot.acd -%%DATADIR%%/acd/textsearch.acd -%%DATADIR%%/acd/tfextract.acd -%%DATADIR%%/acd/tfscan.acd -%%DATADIR%%/acd/tmap.acd -%%DATADIR%%/acd/tranalign.acd -%%DATADIR%%/acd/transeq.acd -%%DATADIR%%/acd/treetypedisplay.acd -%%DATADIR%%/acd/trimest.acd -%%DATADIR%%/acd/trimseq.acd -%%DATADIR%%/acd/twofeat.acd -%%DATADIR%%/acd/union.acd -%%DATADIR%%/acd/vectorstrip.acd -%%DATADIR%%/acd/water.acd -%%DATADIR%%/acd/whichdb.acd -%%DATADIR%%/acd/wobble.acd -%%DATADIR%%/acd/wordcount.acd -%%DATADIR%%/acd/wordmatch.acd -%%DATADIR%%/acd/wossname.acd -%%DATADIR%%/acd/yank.acd -%%DATADIR%%/acd/codes.english -%%DATADIR%%/acd/groups.standard -%%DATADIR%%/acd/knowntypes.standard -%%DATADIR%%/acd/sections.standard -%%DATADIR%%/acd/variables.standard %%DATADIR%%/acd/aaindexextract.acd %%DATADIR%%/acd/abiview.acd %%DATADIR%%/acd/acdc.acd @@ -1078,10 +978,10 @@ lib/libnucleus.a %%DATADIR%%/acd/ajtest.acd %%DATADIR%%/acd/antigenic.acd %%DATADIR%%/acd/backtranseq.acd -%%DATADIR%%/acd/cai.acd %%DATADIR%%/acd/banana.acd %%DATADIR%%/acd/biosed.acd %%DATADIR%%/acd/btwisted.acd +%%DATADIR%%/acd/cai.acd %%DATADIR%%/acd/chaos.acd %%DATADIR%%/acd/charge.acd %%DATADIR%%/acd/checktrans.acd @@ -1090,6 +990,7 @@ lib/libnucleus.a %%DATADIR%%/acd/codcmp.acd %%DATADIR%%/acd/codcopy.acd %%DATADIR%%/acd/coderet.acd +%%DATADIR%%/acd/codes.english %%DATADIR%%/acd/complex.acd %%DATADIR%%/acd/compseq.acd %%DATADIR%%/acd/cons.acd @@ -1125,7 +1026,6 @@ lib/libnucleus.a %%DATADIR%%/acd/dreg.acd %%DATADIR%%/acd/einverted.acd %%DATADIR%%/acd/embossdata.acd -%%DATADIR%%/acd/iep.acd %%DATADIR%%/acd/embossversion.acd %%DATADIR%%/acd/emma.acd %%DATADIR%%/acd/emowse.acd @@ -1147,15 +1047,18 @@ lib/libnucleus.a %%DATADIR%%/acd/geecee.acd %%DATADIR%%/acd/getorf.acd %%DATADIR%%/acd/giep.acd +%%DATADIR%%/acd/groups.standard %%DATADIR%%/acd/helixturnhelix.acd -%%DATADIR%%/acd/hmoment.acd %%DATADIR%%/acd/histogramtest.acd +%%DATADIR%%/acd/hmoment.acd +%%DATADIR%%/acd/iep.acd %%DATADIR%%/acd/infoalign.acd %%DATADIR%%/acd/infoseq.acd %%DATADIR%%/acd/intconv.acd %%DATADIR%%/acd/isochore.acd %%DATADIR%%/acd/kmrsplitter.acd %%DATADIR%%/acd/kmrunion.acd +%%DATADIR%%/acd/knowntypes.standard %%DATADIR%%/acd/lindna.acd %%DATADIR%%/acd/listor.acd %%DATADIR%%/acd/marscan.acd @@ -1167,177 +1070,218 @@ lib/libnucleus.a %%DATADIR%%/acd/msbar.acd %%DATADIR%%/acd/mwcontam.acd %%DATADIR%%/acd/mwfilter.acd +%%DATADIR%%/acd/needle.acd +%%DATADIR%%/acd/newcoils.acd +%%DATADIR%%/acd/newcpgreport.acd +%%DATADIR%%/acd/newcpgseek.acd +%%DATADIR%%/acd/newseq.acd +%%DATADIR%%/acd/noreturn.acd +%%DATADIR%%/acd/notseq.acd +%%DATADIR%%/acd/nthseq.acd +%%DATADIR%%/acd/octanol.acd +%%DATADIR%%/acd/oddcomp.acd +%%DATADIR%%/acd/palindrome.acd +%%DATADIR%%/acd/pasteseq.acd +%%DATADIR%%/acd/patmatdb.acd +%%DATADIR%%/acd/patmatmotifs.acd +%%DATADIR%%/acd/patmattest.acd +%%DATADIR%%/acd/pepcoil.acd +%%DATADIR%%/acd/pepinfo.acd +%%DATADIR%%/acd/pepnet.acd +%%DATADIR%%/acd/pepstats.acd +%%DATADIR%%/acd/pepwheel.acd +%%DATADIR%%/acd/pepwindow.acd +%%DATADIR%%/acd/pepwindowall.acd +%%DATADIR%%/acd/plotcon.acd +%%DATADIR%%/acd/plotorf.acd +%%DATADIR%%/acd/polydot.acd +%%DATADIR%%/acd/preg.acd +%%DATADIR%%/acd/prettyplot.acd +%%DATADIR%%/acd/prettyseq.acd +%%DATADIR%%/acd/prima.acd +%%DATADIR%%/acd/primers.acd +%%DATADIR%%/acd/primersearch.acd +%%DATADIR%%/acd/printsextract.acd +%%DATADIR%%/acd/profit.acd +%%DATADIR%%/acd/prophecy.acd +%%DATADIR%%/acd/prophet.acd +%%DATADIR%%/acd/prosextract.acd +%%DATADIR%%/acd/pscan.acd +%%DATADIR%%/acd/psiphi.acd +%%DATADIR%%/acd/rebaseextract.acd +%%DATADIR%%/acd/recoder.acd +%%DATADIR%%/acd/redata.acd +%%DATADIR%%/acd/remap.acd +%%DATADIR%%/acd/restover.acd +%%DATADIR%%/acd/restrict.acd +%%DATADIR%%/acd/revseq.acd +%%DATADIR%%/acd/sections.standard +%%DATADIR%%/acd/seealso.acd +%%DATADIR%%/acd/seqinfo.acd +%%DATADIR%%/acd/seqmatchall.acd +%%DATADIR%%/acd/seqret.acd +%%DATADIR%%/acd/seqretall.acd +%%DATADIR%%/acd/seqretallfeat.acd +%%DATADIR%%/acd/seqretset.acd +%%DATADIR%%/acd/seqretsingle.acd +%%DATADIR%%/acd/seqretsplit.acd +%%DATADIR%%/acd/seqrettype.acd +%%DATADIR%%/acd/showalign.acd +%%DATADIR%%/acd/showdb.acd +%%DATADIR%%/acd/showfeat.acd +%%DATADIR%%/acd/showorf.acd +%%DATADIR%%/acd/showseq.acd +%%DATADIR%%/acd/shuffleseq.acd +%%DATADIR%%/acd/sigcleave.acd +%%DATADIR%%/acd/silent.acd +%%DATADIR%%/acd/sirna.acd +%%DATADIR%%/acd/sixpack.acd +%%DATADIR%%/acd/skipseq.acd +%%DATADIR%%/acd/splitter.acd +%%DATADIR%%/acd/stretcher.acd +%%DATADIR%%/acd/stssearch.acd +%%DATADIR%%/acd/supermatcher.acd +%%DATADIR%%/acd/syco.acd +%%DATADIR%%/acd/tcode.acd +%%DATADIR%%/acd/testplot.acd +%%DATADIR%%/acd/textsearch.acd +%%DATADIR%%/acd/tfextract.acd +%%DATADIR%%/acd/tfm.acd +%%DATADIR%%/acd/tfscan.acd +%%DATADIR%%/acd/tmap.acd +%%DATADIR%%/acd/tranalign.acd +%%DATADIR%%/acd/transeq.acd +%%DATADIR%%/acd/treetypedisplay.acd +%%DATADIR%%/acd/trimest.acd +%%DATADIR%%/acd/trimseq.acd +%%DATADIR%%/acd/twofeat.acd +%%DATADIR%%/acd/union.acd +%%DATADIR%%/acd/variables.standard +%%DATADIR%%/acd/vectorstrip.acd +%%DATADIR%%/acd/water.acd +%%DATADIR%%/acd/whichdb.acd +%%DATADIR%%/acd/wobble.acd +%%DATADIR%%/acd/wordcount.acd +%%DATADIR%%/acd/wordmatch.acd +%%DATADIR%%/acd/wossname.acd +%%DATADIR%%/acd/yank.acd %%DATADIR%%/data/AAINDEX/dummyfile %%DATADIR%%/data/CODONS/Cut.index -%%DATADIR%%/data/CODONS/Eacica.cut -%%DATADIR%%/data/CODONS/Eagrtu.cut -%%DATADIR%%/data/CODONS/Eanasp.cut -%%DATADIR%%/data/CODONS/Earath.cut -%%DATADIR%%/data/CODONS/Eazovi.cut -%%DATADIR%%/data/CODONS/Ebacme.cut -%%DATADIR%%/data/CODONS/Ebacst.cut -%%DATADIR%%/data/CODONS/Ebacsu.cut -%%DATADIR%%/data/CODONS/Ebacsu_high.cut -%%DATADIR%%/data/CODONS/Ebommo.cut -%%DATADIR%%/data/CODONS/Ebovin.cut -%%DATADIR%%/data/CODONS/Ebpphx.cut -%%DATADIR%%/data/CODONS/Ebraja.cut -%%DATADIR%%/data/CODONS/Ebrana.cut -%%DATADIR%%/data/CODONS/Ebrare.cut -%%DATADIR%%/data/CODONS/Ecaeel.cut -%%DATADIR%%/data/CODONS/Ecanal.cut -%%DATADIR%%/data/CODONS/Ecanfa.cut -%%DATADIR%%/data/CODONS/Ecaucr.cut -%%DATADIR%%/data/CODONS/Echick.cut -%%DATADIR%%/data/CODONS/Echlre.cut -%%DATADIR%%/data/CODONS/Echltr.cut -%%DATADIR%%/data/CODONS/Ecloab.cut -%%DATADIR%%/data/CODONS/Ecrigr.cut -%%DATADIR%%/data/CODONS/Ecyapa.cut -%%DATADIR%%/data/CODONS/Edayhoff.cut -%%DATADIR%%/data/CODONS/Edicdi.cut -%%DATADIR%%/data/CODONS/Edicdi_high.cut -%%DATADIR%%/data/CODONS/Edrome.cut -%%DATADIR%%/data/CODONS/Edrome_high.cut -%%DATADIR%%/data/CODONS/Eecoli.cut -%%DATADIR%%/data/CODONS/Eecoli_high.cut -%%DATADIR%%/data/CODONS/Eemeni.cut -%%DATADIR%%/data/CODONS/Eemeni_mit.cut -%%DATADIR%%/data/CODONS/Eemeni_high.cut -%%DATADIR%%/data/CODONS/Eerwct.cut -%%DATADIR%%/data/CODONS/Ehaein.cut -%%DATADIR%%/data/CODONS/Ehalma.cut -%%DATADIR%%/data/CODONS/Ehalsa.cut -%%DATADIR%%/data/CODONS/Ehorvu.cut -%%DATADIR%%/data/CODONS/Ehuman.cut -%%DATADIR%%/data/CODONS/Eklepn.cut -%%DATADIR%%/data/CODONS/Eklula.cut -%%DATADIR%%/data/CODONS/Elacdl.cut -%%DATADIR%%/data/CODONS/Elyces.cut -%%DATADIR%%/data/CODONS/Emacfa.cut -%%DATADIR%%/data/CODONS/Emaize.cut -%%DATADIR%%/data/CODONS/Emaize_chl.cut -%%DATADIR%%/data/CODONS/Emammal_high.cut -%%DATADIR%%/data/CODONS/Emanse.cut -%%DATADIR%%/data/CODONS/Emarpo_chl.cut -%%DATADIR%%/data/CODONS/Emedsa.cut -%%DATADIR%%/data/CODONS/Emetth.cut -%%DATADIR%%/data/CODONS/Emouse.cut 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+%%DATADIR%%/data/CODONS/Emarpo_chl.cut +%%DATADIR%%/data/CODONS/Emedsa.cut +%%DATADIR%%/data/CODONS/Emetth.cut %%DATADIR%%/data/CODONS/Emixlg.cut +%%DATADIR%%/data/CODONS/Emouse.cut %%DATADIR%%/data/CODONS/Emsa.cut %%DATADIR%%/data/CODONS/Emse.cut %%DATADIR%%/data/CODONS/Emta.cut @@ -1345,40 +1289,69 @@ lib/libnucleus.a %%DATADIR%%/data/CODONS/Emus.cut %%DATADIR%%/data/CODONS/Emussp.cut %%DATADIR%%/data/CODONS/Emva.cut +%%DATADIR%%/data/CODONS/Emyctu.cut %%DATADIR%%/data/CODONS/Emze.cut %%DATADIR%%/data/CODONS/Emzecp.cut %%DATADIR%%/data/CODONS/Encr.cut +%%DATADIR%%/data/CODONS/Eneigo.cut %%DATADIR%%/data/CODONS/Eneu.cut +%%DATADIR%%/data/CODONS/Eneucr.cut %%DATADIR%%/data/CODONS/Engo.cut +%%DATADIR%%/data/CODONS/Eoncmy.cut %%DATADIR%%/data/CODONS/Eoncsp.cut +%%DATADIR%%/data/CODONS/Eorysa.cut +%%DATADIR%%/data/CODONS/Eorysa_chl.cut %%DATADIR%%/data/CODONS/Epae.cut +%%DATADIR%%/data/CODONS/Epea.cut %%DATADIR%%/data/CODONS/Epet.cut +%%DATADIR%%/data/CODONS/Epethy.cut %%DATADIR%%/data/CODONS/Epfa.cut +%%DATADIR%%/data/CODONS/Ephavu.cut %%DATADIR%%/data/CODONS/Ephix174.cut %%DATADIR%%/data/CODONS/Ephv.cut %%DATADIR%%/data/CODONS/Ephy.cut +%%DATADIR%%/data/CODONS/Epig.cut +%%DATADIR%%/data/CODONS/Eplafa.cut %%DATADIR%%/data/CODONS/Epolyomaa2.cut %%DATADIR%%/data/CODONS/Epombe.cut %%DATADIR%%/data/CODONS/Epombecai.cut %%DATADIR%%/data/CODONS/Epot.cut %%DATADIR%%/data/CODONS/Eppu.cut +%%DATADIR%%/data/CODONS/Eprovu.cut %%DATADIR%%/data/CODONS/Epse.cut +%%DATADIR%%/data/CODONS/Epseae.cut +%%DATADIR%%/data/CODONS/Epsepu.cut +%%DATADIR%%/data/CODONS/Epsesm.cut %%DATADIR%%/data/CODONS/Epsy.cut %%DATADIR%%/data/CODONS/Epvu.cut %%DATADIR%%/data/CODONS/Erab.cut %%DATADIR%%/data/CODONS/Erabbit.cut +%%DATADIR%%/data/CODONS/Erabit.cut %%DATADIR%%/data/CODONS/Erabsp.cut +%%DATADIR%%/data/CODONS/Erat.cut %%DATADIR%%/data/CODONS/Eratsp.cut %%DATADIR%%/data/CODONS/Erca.cut +%%DATADIR%%/data/CODONS/Erhile.cut +%%DATADIR%%/data/CODONS/Erhime.cut %%DATADIR%%/data/CODONS/Erhm.cut +%%DATADIR%%/data/CODONS/Erhoca.cut +%%DATADIR%%/data/CODONS/Erhosh.cut %%DATADIR%%/data/CODONS/Eric.cut %%DATADIR%%/data/CODONS/Erle.cut %%DATADIR%%/data/CODONS/Erme.cut %%DATADIR%%/data/CODONS/Ersp.cut +%%DATADIR%%/data/CODONS/Esalsa.cut %%DATADIR%%/data/CODONS/Esalsp.cut +%%DATADIR%%/data/CODONS/Esalty.cut %%DATADIR%%/data/CODONS/Esau.cut +%%DATADIR%%/data/CODONS/Eschma.cut +%%DATADIR%%/data/CODONS/Eschpo.cut +%%DATADIR%%/data/CODONS/Eschpo_cai.cut +%%DATADIR%%/data/CODONS/Eschpo_high.cut %%DATADIR%%/data/CODONS/Esco.cut +%%DATADIR%%/data/CODONS/Eserma.cut %%DATADIR%%/data/CODONS/Esgi.cut +%%DATADIR%%/data/CODONS/Esheep.cut %%DATADIR%%/data/CODONS/Eshp.cut %%DATADIR%%/data/CODONS/Eshpsp.cut %%DATADIR%%/data/CODONS/Esli.cut @@ -1386,41 +1359,63 @@ lib/libnucleus.a %%DATADIR%%/data/CODONS/Esma.cut %%DATADIR%%/data/CODONS/Esmi.cut %%DATADIR%%/data/CODONS/Esmu.cut +%%DATADIR%%/data/CODONS/Esoltu.cut %%DATADIR%%/data/CODONS/Esoy.cut +%%DATADIR%%/data/CODONS/Esoybn.cut %%DATADIR%%/data/CODONS/Espi.cut +%%DATADIR%%/data/CODONS/Espiol.cut %%DATADIR%%/data/CODONS/Espn.cut %%DATADIR%%/data/CODONS/Espo.cut %%DATADIR%%/data/CODONS/Espo_h.cut %%DATADIR%%/data/CODONS/Espu.cut %%DATADIR%%/data/CODONS/Esta.cut +%%DATADIR%%/data/CODONS/Estaau.cut +%%DATADIR%%/data/CODONS/Estrco.cut +%%DATADIR%%/data/CODONS/Estrmu.cut +%%DATADIR%%/data/CODONS/Estrpn.cut +%%DATADIR%%/data/CODONS/Estrpu.cut %%DATADIR%%/data/CODONS/Esty.cut %%DATADIR%%/data/CODONS/Esus.cut %%DATADIR%%/data/CODONS/Esv40.cut %%DATADIR%%/data/CODONS/Esyhsp.cut +%%DATADIR%%/data/CODONS/Esynco.cut +%%DATADIR%%/data/CODONS/Esyncy.cut %%DATADIR%%/data/CODONS/Esynsp.cut %%DATADIR%%/data/CODONS/Etbr.cut %%DATADIR%%/data/CODONS/Etcr.cut %%DATADIR%%/data/CODONS/Eter.cut %%DATADIR%%/data/CODONS/Etetsp.cut +%%DATADIR%%/data/CODONS/Etetth.cut +%%DATADIR%%/data/CODONS/Etheth.cut %%DATADIR%%/data/CODONS/Etob.cut +%%DATADIR%%/data/CODONS/Etobac.cut +%%DATADIR%%/data/CODONS/Etobac_chl.cut %%DATADIR%%/data/CODONS/Etobcp.cut %%DATADIR%%/data/CODONS/Etom.cut %%DATADIR%%/data/CODONS/Etrb.cut +%%DATADIR%%/data/CODONS/Etrybr.cut +%%DATADIR%%/data/CODONS/Etrycr.cut %%DATADIR%%/data/CODONS/Evco.cut +%%DATADIR%%/data/CODONS/Evibch.cut +%%DATADIR%%/data/CODONS/Ewheat.cut %%DATADIR%%/data/CODONS/Ewht.cut %%DATADIR%%/data/CODONS/Exel.cut +%%DATADIR%%/data/CODONS/Exenla.cut %%DATADIR%%/data/CODONS/Exenopus.cut +%%DATADIR%%/data/CODONS/Eyeast.cut +%%DATADIR%%/data/CODONS/Eyeast_cai.cut +%%DATADIR%%/data/CODONS/Eyeast_high.cut +%%DATADIR%%/data/CODONS/Eyeast_mit.cut %%DATADIR%%/data/CODONS/Eyeastcai.cut %%DATADIR%%/data/CODONS/Eyen.cut +%%DATADIR%%/data/CODONS/Eyeren.cut +%%DATADIR%%/data/CODONS/Eyerpe.cut %%DATADIR%%/data/CODONS/Eysc.cut %%DATADIR%%/data/CODONS/Eysc_h.cut %%DATADIR%%/data/CODONS/Eyscmt.cut %%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 @@ -1533,7 +1528,10 @@ lib/libnucleus.a %%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 @@ -1552,215 +1550,41 @@ lib/libnucleus.a %%DATADIR%%/data/Etcode.dat %%DATADIR%%/data/Evdw.dat %%DATADIR%%/data/Ewhite-wimley.dat -%%DATADIR%%/data/embossre.equ -%%DATADIR%%/data/Emwfilter.dat -%%DATADIR%%/data/Emass.dat -%%DATADIR%%/data/Emassmod.dat %%DATADIR%%/data/Matrices.nucleotide %%DATADIR%%/data/Matrices.protein %%DATADIR%%/data/Matrices.proteinstructure +%%DATADIR%%/data/PRINTS/dummyfile +%%DATADIR%%/data/PROSITE/dummyfile +%%DATADIR%%/data/REBASE/dummyfile +%%DATADIR%%/data/embossre.equ 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%%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 @@ -1770,8 +1594,6 @@ lib/libnucleus.a %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.WholeNumberDocument.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldInt.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/TextFieldSink.html 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-%%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 @@ -1807,17 +1623,6 @@ 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 @@ -1833,6 +1638,9 @@ lib/libnucleus.a %%DATADIR%%/jemboss/images/Job_manager_button.gif 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%%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/filetree/LocalTreeToolBar.java +%%DATADIR%%/jemboss/org/emboss/jemboss/gui/form/AlignFormat.java 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%%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 @@ -1927,32 +1753,15 @@ 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/gui/Favorites.java -%%DATADIR%%/jemboss/org/emboss/jemboss/gui/KeywordSearch.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 @@ -1960,52 +1769,243 @@ 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 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