From 17d59dbeca8ab77b5998b68066120758b6a90811 Mon Sep 17 00:00:00 2001 From: rafan Date: Sun, 13 Apr 2008 07:21:16 +0000 Subject: - Sort pkg-plist before updating to 5.0.0 PR: ports/122437 Submitted by: Fernan Aguero (maintainer) --- biology/emboss/pkg-plist | 2882 +++++++++++++++++++++++----------------------- 1 file changed, 1441 insertions(+), 1441 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 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%%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 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+%%DATADIR%%/jemboss/api/makeDocs.csh +%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/Jemboss.winExit.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossLogo.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/JembossParams.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/BuildProgramMenu.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ResultsMenuBar.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SetUpMenuBar.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowResultSet.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/ShowSavedResults.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/SwingWorker.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/DragTree.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.PopupListener.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileEditorDisplay.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileNode.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/filetree/FileSaving.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/BuildJembossForm.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.html +%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.myComboUI.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/ListFilePanel.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SectionPanel.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/SetInFileCard.html @@ -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 -%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.html -%%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/form/JembossComboPopup.myComboUI.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/CutNPasteTextArea.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/FileChooser.html %%DATADIR%%/jemboss/api/org/emboss/jemboss/gui/sequenceChooser/InputSequenceAttributes.html @@ -1782,19 +1604,13 @@ lib/libnucleus.a %%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 @@ -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 %%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 @@ -1842,117 +1650,118 @@ 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/JembossPrintAlignment.jar -%%DATADIR%%/jemboss/lib/grout.jar +%%DATADIR%%/jemboss/org/emboss/jemboss/Jemboss.java +%%DATADIR%%/jemboss/org/emboss/jemboss/JembossJarUtil.java 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