Attachment 23344 Details for Bug 40198 – file.diff

[patch] file.diff

file.diff (text/plain), 21.71 KB, created by Tilman Linneweh on 2002-07-04 21:50:01 UTC

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Creator: Tilman Linneweh

Created: 2002-07-04 21:50:01 UTC

Size: 21.71 KB

patch

obsolete

>Index: distinfo
>===================================================================
>RCS file: /home/ncvs/ports/biology/emboss/distinfo,v
>retrieving revision 1.20
>diff -u -r1.20 distinfo
>--- distinfo    18 Jan 2002 14:04:03 -0000      1.20
>+++ distinfo    4 Jul 2002 19:54:55 -0000
>@@ -1,7 +1,7 @@
>-MD5 (emboss/EMBOSS-2.2.0.tar.gz) = c6d755f98f558f9f98649c1d1cca44a6
>-MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66
>-MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21
>-MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c
>-MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9
>-MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084
>-MD5 (emboss/TOPO-0.1.tar.gz) = 96fced0b0979157e344fd9b08dc2aa64
>+MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad
>+MD5 (emboss/EMNU-1.0.5.tar.gz) = 628f28b24762e75a9546b608cc60f179
>+MD5 (emboss/HMMER-2.1.1.tar.gz) = 1bce29d9f215076c90d2b95b9ba6942f
>+MD5 (emboss/MEME-2.3.1.tar.gz) = 6961f0308b122d170a5e8d27f02edbc3
>+MD5 (emboss/MSE-0.0.4.tar.gz) = 067952daa34ce4af71e88d9e87136257
>+MD5 (emboss/PHYLIP-3.573c.tar.gz) = 4e69bc86f429d95f99b5e9d3f83036ab
>+MD5 (emboss/TOPO-0.1.tar.gz) = 8ca248a5cf0ad230d3959fbcce013942
>Index: pkg-plist
>===================================================================
>RCS file: /home/ncvs/ports/biology/emboss/pkg-plist,v
>retrieving revision 1.17
>diff -u -r1.17 pkg-plist
>--- pkg-plist   18 Jan 2002 14:04:03 -0000      1.17
>+++ pkg-plist   4 Jul 2002 20:29:46 -0000
>@@ -188,7 +188,6 @@
> bin/preg
> bin/prettyplot
> bin/prettyseq
>-bin/primer3
> bin/primersearch
> bin/printsextract
> bin/profit
>@@ -210,9 +209,6 @@
> bin/seealso
> bin/seqmatchall
> bin/seqret
>-bin/seqretall
>-bin/seqretallfeat
>-bin/seqretset
> bin/seqretsplit
> bin/showalign
> bin/showdb
>@@ -320,6 +316,7 @@
> share/EMBOSS/acd/emowse.acd
> share/EMBOSS/acd/entrails.acd
> share/EMBOSS/acd/entret.acd
>+share/EMBOSS/acd/eprimer3.acd
> share/EMBOSS/acd/equicktandem.acd
> share/EMBOSS/acd/est2genome.acd
> share/EMBOSS/acd/etandem.acd
>@@ -339,6 +336,7 @@
> share/EMBOSS/acd/iep.acd
> share/EMBOSS/acd/infoalign.acd
> share/EMBOSS/acd/infoseq.acd
>+share/EMBOSS/acd/interface.acd
> share/EMBOSS/acd/isochore.acd
> share/EMBOSS/acd/lindna.acd
> share/EMBOSS/acd/listor.acd
>@@ -365,6 +363,7 @@
> share/EMBOSS/acd/patmatdb.acd
> share/EMBOSS/acd/patmatmotifs.acd
> share/EMBOSS/acd/patmattest.acd
>+share/EMBOSS/acd/pdbtosp.acd
> share/EMBOSS/acd/pepcoil.acd
> share/EMBOSS/acd/pepinfo.acd
> share/EMBOSS/acd/pepnet.acd
>@@ -379,7 +378,6 @@
> share/EMBOSS/acd/prettyplot.acd
> share/EMBOSS/acd/prettyseq.acd
> share/EMBOSS/acd/prima.acd
>-share/EMBOSS/acd/primer3.acd
> share/EMBOSS/acd/primers.acd
> share/EMBOSS/acd/primersearch.acd
> share/EMBOSS/acd/printsextract.acd
>@@ -397,16 +395,19 @@
> share/EMBOSS/acd/restrict.acd
> share/EMBOSS/acd/revseq.acd
> share/EMBOSS/acd/scopalign.acd
>+share/EMBOSS/acd/scopparse.acd
> share/EMBOSS/acd/scope.acd
> share/EMBOSS/acd/seealso.acd
> share/EMBOSS/acd/seqinfo.acd
> share/EMBOSS/acd/seqmatchall.acd
>+share/EMBOSS/acd/seqnr.acd
> share/EMBOSS/acd/seqret.acd
> share/EMBOSS/acd/seqretall.acd
> share/EMBOSS/acd/seqretallfeat.acd
> share/EMBOSS/acd/seqretset.acd
> share/EMBOSS/acd/seqretsingle.acd
> share/EMBOSS/acd/seqretsplit.acd
>+share/EMBOSS/acd/seqsort.acd
> share/EMBOSS/acd/showalign.acd
> share/EMBOSS/acd/showdb.acd
> share/EMBOSS/acd/showfeat.acd
>@@ -429,16 +430,20 @@
> share/EMBOSS/acd/tfm.acd
> share/EMBOSS/acd/tfscan.acd
> share/EMBOSS/acd/tmap.acd
>+share/EMBOSS/acd/tranalign.acd
> share/EMBOSS/acd/transeq.acd
> share/EMBOSS/acd/treetypedisplay.acd
> share/EMBOSS/acd/trimest.acd
> share/EMBOSS/acd/trimseq.acd
>+share/EMBOSS/acd/union.acd
> share/EMBOSS/acd/vectorstrip.acd
> share/EMBOSS/acd/water.acd
>+share/EMBOSS/acd/whichdb.acd
> share/EMBOSS/acd/wobble.acd
> share/EMBOSS/acd/wordcount.acd
> share/EMBOSS/acd/wordmatch.acd
> share/EMBOSS/acd/wossname.acd
>+share/EMBOSS/acd/yank.acd
> share/EMBOSS/data/CODONS/Eacc.cut
> share/EMBOSS/data/CODONS/Eadenovirus5.cut
> share/EMBOSS/data/CODONS/Eadenovirus7.cut
>@@ -721,6 +726,7 @@
> share/EMBOSS/data/REBASE/dummyfile
> share/EMBOSS/data/embossre.equ
> share/EMBOSS/emboss.default.template
>+share/EMBOSS/jemboss/README
> share/EMBOSS/jemboss/LICENSE
> share/EMBOSS/jemboss/api/allclasses-frame.html
> share/EMBOSS/jemboss/api/deprecated-list.html
>@@ -791,79 +797,6 @@
> share/EMBOSS/jemboss/api/packages.html
> share/EMBOSS/jemboss/api/serialized-form.html
> share/EMBOSS/jemboss/api/stylesheet.css
>-share/EMBOSS/jemboss/embreo/LICENSE
>-share/EMBOSS/jemboss/embreo/Modules/EmbossSoap.pm
>-share/EMBOSS/jemboss/embreo/Modules/EmbreoFile.pm
>-share/EMBOSS/jemboss/embreo/Modules/ParseSoapOptions.pm
>-share/EMBOSS/jemboss/embreo/Modules/README
>-share/EMBOSS/jemboss/embreo/PROBLEMS
>-share/EMBOSS/jemboss/embreo/README
>-share/EMBOSS/jemboss/embreo/README.macos
>-share/EMBOSS/jemboss/embreo/README.properties
>-share/EMBOSS/jemboss/embreo/api-docs/allclasses-frame.html
>-share/EMBOSS/jemboss/embreo/api-docs/deprecated-list.html
>-share/EMBOSS/jemboss/embreo/api-docs/help-doc.html
>-share/EMBOSS/jemboss/embreo/api-docs/index-all.html
>-share/EMBOSS/jemboss/embreo/api-docs/index.html
>-share/EMBOSS/jemboss/embreo/api-docs/overview-tree.html
>-share/EMBOSS/jemboss/embreo/api-docs/package-list
>-share/EMBOSS/jemboss/embreo/api-docs/serialized-form.html
>-share/EMBOSS/jemboss/embreo/api-docs/stylesheet.css
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoACD.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAnnotate.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAppList.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthException.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthPopup.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthPrompt.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoException.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoFrame.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoGroupList.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoGroupTree.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoHelp.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoHelpView.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoJList.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoListFile.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoMakeFileSafe.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoParams.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPendingResults.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPrivateRequest.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPublicRequest.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResList.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResListView.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResSave.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResView.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResult.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoRun.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoServiceDesc.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoShowDB.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoStartup.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoTreeCellRenderer.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoUtils.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFile.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileGet.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileLaunch.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileList.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileListView.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileMgr.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileNode.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFilePut.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileRequest.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileRoots.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileSave.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileTree.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileTreePanel.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileView.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileViewPanel.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalGet.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalRoots.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalTree.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalTreePanel.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalView.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoLocalViewPanel.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/FileNode.html
>-share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/WindowsAltFileSystemView.html
>-share/EMBOSS/jemboss/embreo/cgi-bin/soap.cgi
>-share/EMBOSS/jemboss/embreo/embreo-full.jar
> share/EMBOSS/jemboss/images/Backward_arrow_button.gif
> share/EMBOSS/jemboss/images/Forward_arrow_button.gif
> share/EMBOSS/jemboss/images/Go_button.gif
>@@ -874,7 +807,6 @@
> share/EMBOSS/jemboss/images/Job_manager_button.gif
> share/EMBOSS/jemboss/images/Refresh_button.gif
> share/EMBOSS/jemboss/images/Refresh_button2.gif
>-share/EMBOSS/jemboss/interface.html
> share/EMBOSS/jemboss/lib/README
> share/EMBOSS/jemboss/lib/activation.jar
> share/EMBOSS/jemboss/lib/jakarta-regexp-1.2.jar
>@@ -882,9 +814,13 @@
> share/EMBOSS/jemboss/lib/mail.jar
> share/EMBOSS/jemboss/lib/soap.jar
> share/EMBOSS/jemboss/lib/xerces.jar
>+share/EMBOSS/jemboss/lib/jcert.jar
>+share/EMBOSS/jemboss/lib/jnet.jar
>+share/EMBOSS/jemboss/lib/jsse.jar
> share/EMBOSS/jemboss/org/emboss/jemboss/Jemboss.java
> share/EMBOSS/jemboss/org/emboss/jemboss/JembossLogo.java
> share/EMBOSS/jemboss/org/emboss/jemboss/JembossParams.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/JembossJarUtil.java
> share/EMBOSS/jemboss/org/emboss/jemboss/gui/AdvancedOptions.java
> share/EMBOSS/jemboss/org/emboss/jemboss/gui/BuildProgramMenu.java
> share/EMBOSS/jemboss/org/emboss/jemboss/gui/LaunchJalView.java
>@@ -893,6 +829,9 @@
> share/EMBOSS/jemboss/org/emboss/jemboss/gui/ShowResultSet.java
> share/EMBOSS/jemboss/org/emboss/jemboss/gui/ShowSavedResults.java
> share/EMBOSS/jemboss/org/emboss/jemboss/gui/SwingWorker.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceData.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/gui/SequenceList.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/gui/MemoryComboBox.java
> share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/DragTree.java
> share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileEditorDisplay.java
> share/EMBOSS/jemboss/org/emboss/jemboss/gui/filetree/FileNode.java
>@@ -929,6 +868,8 @@
> share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/Application.java
> share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/ApplicationFields.java
> share/EMBOSS/jemboss/org/emboss/jemboss/parser/acd/ApplicationParam.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/parser/AcdVariableResolve.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/parser/AjaxUtil.java
> share/EMBOSS/jemboss/org/emboss/jemboss/programs/BatchUpdateTimer.java
> share/EMBOSS/jemboss/org/emboss/jemboss/programs/JembossProcess.java
> share/EMBOSS/jemboss/org/emboss/jemboss/programs/ListFile.java
>@@ -936,6 +877,12 @@
> share/EMBOSS/jemboss/org/emboss/jemboss/programs/ResultsUpdateTimer.java
> share/EMBOSS/jemboss/org/emboss/jemboss/programs/RunEmbossApplication.java
> share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossServer.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileServer.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossThread.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossAuthServer.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossAuthThread.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/server/JembossFileAuthServer.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/server/TestPublicServer.java
> share/EMBOSS/jemboss/org/emboss/jemboss/soap/AuthPopup.java
> share/EMBOSS/jemboss/org/emboss/jemboss/soap/CallAjax.java
> share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetWossname.java
>@@ -943,13 +890,25 @@
> share/EMBOSS/jemboss/org/emboss/jemboss/soap/JembossSoapException.java
> share/EMBOSS/jemboss/org/emboss/jemboss/soap/PendingResults.java
> share/EMBOSS/jemboss/org/emboss/jemboss/soap/PrivateRequest.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/soap/ServerSetup.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileRoots.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/soap/FileList.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/soap/PublicRequest.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetACD.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/soap/GetHelp.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/soap/ShowDB.java
>+share/EMBOSS/jemboss/org/emboss/jemboss/soap/MakeFileSafe.java
>+share/EMBOSS/jemboss/utils/install-jemboss-server.sh
>+share/EMBOSS/jemboss/utils/keys.sh
>+share/EMBOSS/jemboss/utils/makeJNLP.sh
>+share/EMBOSS/jemboss/utils/template.html
>+share/EMBOSS/jemboss/utils/README
>+share/EMBOSS/jemboss/utils/makeJar.csh
> share/EMBOSS/jemboss/readme.html
> share/EMBOSS/jemboss/resources/jemboss.properties
> share/EMBOSS/jemboss/resources/readme.txt
> share/EMBOSS/jemboss/resources/version
> share/EMBOSS/jemboss/runJemboss.csh
>-share/EMBOSS/jemboss/setup.html
>-share/EMBOSS/jemboss/utils/makeJar.csh
> share/EMBOSS/plstnd5.fnt
> share/EMBOSS/plxtnd5.fnt
> share/EMBOSS/test/data/aligna.dna
>@@ -1005,25 +964,79 @@
> share/EMBOSS/test/data/prot.ncbi
> share/EMBOSS/test/data/prot.swiss
> share/EMBOSS/test/data/prot.text
>+share/EMBOSS/test/data/tranalign.pep
>+share/EMBOSS/test/data/tranalign.seq
> share/EMBOSS/test/data/z83307.seq
> share/EMBOSS/test/embl/acnum.hit
> share/EMBOSS/test/embl/acnum.trg
>+share/EMBOSS/test/embl/des.hit
>+share/EMBOSS/test/embl/des.trg
> share/EMBOSS/test/embl/division.lkp
> share/EMBOSS/test/embl/entrynam.idx
> share/EMBOSS/test/embl/est.dat
> share/EMBOSS/test/embl/fun.dat
> share/EMBOSS/test/embl/hum1.dat
> share/EMBOSS/test/embl/inv.dat
>+share/EMBOSS/test/embl/keyword.hit
>+share/EMBOSS/test/embl/keyword.trg
> share/EMBOSS/test/embl/pln.dat
> share/EMBOSS/test/embl/pro.dat
> share/EMBOSS/test/embl/rod.dat
>+share/EMBOSS/test/embl/seqvn.hit
>+share/EMBOSS/test/embl/seqvn.trg
> share/EMBOSS/test/embl/sts.dat
>+share/EMBOSS/test/embl/taxon.hit
>+share/EMBOSS/test/embl/taxon.trg
> share/EMBOSS/test/embl/vrl.dat
> share/EMBOSS/test/embl/vrt.dat
>+share/EMBOSS/test/genbank/acnum.hit
>+share/EMBOSS/test/genbank/acnum.trg
>+share/EMBOSS/test/genbank/division.lkp
>+share/EMBOSS/test/genbank/entrynam.idx
>+share/EMBOSS/test/genbank/seqvn.hit
>+share/EMBOSS/test/genbank/seqvn.trg
>+share/EMBOSS/test/genbank/des.hit
>+share/EMBOSS/test/genbank/des.trg
>+share/EMBOSS/test/genbank/keyword.hit
>+share/EMBOSS/test/genbank/keyword.trg
>+share/EMBOSS/test/genbank/taxon.hit
>+share/EMBOSS/test/genbank/taxon.trg
>+share/EMBOSS/test/genbank/gbbct1.seq
>+share/EMBOSS/test/genbank/gbest1.seq
>+share/EMBOSS/test/genbank/gbinv1.seq
>+share/EMBOSS/test/genbank/gbpln1.seq
>+share/EMBOSS/test/genbank/gbpln2.seq
>+share/EMBOSS/test/genbank/gbpri1.seq
>+share/EMBOSS/test/genbank/gbrod1.seq
>+share/EMBOSS/test/genbank/gbsts1.seq
>+share/EMBOSS/test/genbank/gbvrl1.seq
>+share/EMBOSS/test/genbank/gbvrt.seq
>+share/EMBOSS/test/gb/acnum.hit
>+share/EMBOSS/test/gb/acnum.trg
>+share/EMBOSS/test/gb/division.lkp
>+share/EMBOSS/test/gb/entrynam.idx
>+share/EMBOSS/test/gb/seqvn.hit
>+share/EMBOSS/test/gb/seqvn.trg
>+share/EMBOSS/test/gb/des.hit
>+share/EMBOSS/test/gb/des.trg
>+share/EMBOSS/test/gb/keyword.hit
>+share/EMBOSS/test/gb/keyword.trg
>+share/EMBOSS/test/gb/taxon.hit
>+share/EMBOSS/test/gb/taxon.trg
>+share/EMBOSS/test/gb/ba.ref
>+share/EMBOSS/test/gb/ba.seq
>+share/EMBOSS/test/gb/htg.ref
>+share/EMBOSS/test/gb/htg.seq
> share/EMBOSS/test/pir/acnum.hit
> share/EMBOSS/test/pir/acnum.trg
>+share/EMBOSS/test/pir/des.hit
>+share/EMBOSS/test/pir/des.trg
> share/EMBOSS/test/pir/division.lkp
> share/EMBOSS/test/pir/entrynam.idx
>+share/EMBOSS/test/pir/keyword.hit
>+share/EMBOSS/test/pir/keyword.trg
>+share/EMBOSS/test/pir/taxon.hit
>+share/EMBOSS/test/pir/taxon.trg
> share/EMBOSS/test/pir/pir1.header
> share/EMBOSS/test/pir/pir1.names
> share/EMBOSS/test/pir/pir1.numbers
>@@ -1053,6 +1066,14 @@
> share/EMBOSS/test/swiss/division.lkp
> share/EMBOSS/test/swiss/entrynam.idx
> share/EMBOSS/test/swiss/seq.dat
>+share/EMBOSS/test/swiss/seqvn.hit
>+share/EMBOSS/test/swiss/seqvn.trg
>+share/EMBOSS/test/swiss/des.hit
>+share/EMBOSS/test/swiss/des.trg
>+share/EMBOSS/test/swiss/keyword.hit
>+share/EMBOSS/test/swiss/keyword.trg
>+share/EMBOSS/test/swiss/taxon.hit
>+share/EMBOSS/test/swiss/taxon.trg
> share/EMBOSS/test/swnew/acnum.hit
> share/EMBOSS/test/swnew/acnum.trg
> share/EMBOSS/test/swnew/division.lkp
>@@ -1060,11 +1081,21 @@
> share/EMBOSS/test/swnew/new_seq.dat
> share/EMBOSS/test/swnew/upd_ann.dat
> share/EMBOSS/test/swnew/upd_seq.dat
>+share/EMBOSS/test/swnew/seqvn.hit
>+share/EMBOSS/test/swnew/seqvn.trg
>+share/EMBOSS/test/swnew/des.hit
>+share/EMBOSS/test/swnew/des.trg
>+share/EMBOSS/test/swnew/keyword.hit
>+share/EMBOSS/test/swnew/keyword.trg
>+share/EMBOSS/test/swnew/taxon.hit
>+share/EMBOSS/test/swnew/taxon.trg
> share/EMBOSS/test/wormpep/acnum.hit
> share/EMBOSS/test/wormpep/acnum.trg
> share/EMBOSS/test/wormpep/division.lkp
> share/EMBOSS/test/wormpep/entrynam.idx
> share/EMBOSS/test/wormpep/wormpep
>+share/EMBOSS/test/wormpep/des.hit
>+share/EMBOSS/test/wormpep/des.trg
> share/doc/EMBOSS/manuals/EMBOSS-FreeBSD-HOWTO.txt
> share/doc/EMBOSS/manuals/admin.aux
> share/doc/EMBOSS/manuals/admin.dvi
>@@ -1272,8 +1303,6 @@
> share/doc/EMBOSS/programs/html/prettyplot3.gif
> share/doc/EMBOSS/programs/html/prettyplot4.gif
> share/doc/EMBOSS/programs/html/prettyseq.html
>-share/doc/EMBOSS/programs/html/prima.html
>-share/doc/EMBOSS/programs/html/primer3.html
> share/doc/EMBOSS/programs/html/primersearch.html
> share/doc/EMBOSS/programs/html/printsextract.html
> share/doc/EMBOSS/programs/html/profit.html
>@@ -1350,6 +1379,20 @@
> share/doc/EMBOSS/programs/html/wordcount.html
> share/doc/EMBOSS/programs/html/wordmatch.html
> share/doc/EMBOSS/programs/html/wossname.html
>+share/doc/EMBOSS/programs/html/pdbtosp.html
>+share/doc/EMBOSS/programs/html/psiblasts.html
>+share/doc/EMBOSS/programs/html/scopparse.html
>+share/doc/EMBOSS/programs/html/seqnr.html
>+share/doc/EMBOSS/programs/html/seqsort.html
>+share/doc/EMBOSS/programs/html/tranalign.html
>+share/doc/EMBOSS/programs/html/union.html
>+share/doc/EMBOSS/programs/html/whichdb.html
>+share/doc/EMBOSS/programs/html/yank.html
>+share/doc/EMBOSS/programs/html/alignwrap.html
>+share/doc/EMBOSS/programs/html/dichet.html
>+share/doc/EMBOSS/programs/html/eprimer3.html
>+share/doc/EMBOSS/programs/html/interface.html
>+share/doc/EMBOSS/programs/html/jembossctl.html
> share/doc/EMBOSS/programs/text/SITE-DIRECTED.txt
> share/doc/EMBOSS/programs/text/abiview.txt
> share/doc/EMBOSS/programs/text/ajtest.txt
>@@ -1497,8 +1540,6 @@
> share/doc/EMBOSS/programs/text/preg.txt
> share/doc/EMBOSS/programs/text/prettyplot.txt
> share/doc/EMBOSS/programs/text/prettyseq.txt
>-share/doc/EMBOSS/programs/text/prima.txt
>-share/doc/EMBOSS/programs/text/primer3.txt
> share/doc/EMBOSS/programs/text/primersearch.txt
> share/doc/EMBOSS/programs/text/printsextract.txt
> share/doc/EMBOSS/programs/text/profit.txt
>@@ -1559,6 +1600,20 @@
> share/doc/EMBOSS/programs/text/wordcount.txt
> share/doc/EMBOSS/programs/text/wordmatch.txt
> share/doc/EMBOSS/programs/text/wossname.txt
>+share/doc/EMBOSS/programs/text/jembossctl.txt
>+share/doc/EMBOSS/programs/text/pdbtosp.txt
>+share/doc/EMBOSS/programs/text/psiblasts.txt
>+share/doc/EMBOSS/programs/text/scopparse.txt
>+share/doc/EMBOSS/programs/text/seqnr.txt
>+share/doc/EMBOSS/programs/text/seqsort.txt
>+share/doc/EMBOSS/programs/text/tranalign.txt
>+share/doc/EMBOSS/programs/text/union.txt
>+share/doc/EMBOSS/programs/text/whichdb.txt
>+share/doc/EMBOSS/programs/text/yank.txt
>+share/doc/EMBOSS/programs/text/alignwrap.txt
>+share/doc/EMBOSS/programs/text/dichet.txt
>+share/doc/EMBOSS/programs/text/eprimer3.txt
>+share/doc/EMBOSS/programs/text/interface.txt
> share/doc/EMBOSS/tutorials/biblio.bib
> share/doc/EMBOSS/tutorials/dottup.ps.gz
> share/doc/EMBOSS/tutorials/emboss-gcg.ppt
>@@ -1580,6 +1635,8 @@
> @dirrm share/EMBOSS/test/swnew
> @dirrm share/EMBOSS/test/swiss
> @dirrm share/EMBOSS/test/pir
>+@dirrm share/EMBOSS/test/genbank
>+@dirrm share/EMBOSS/test/gb
> @dirrm share/EMBOSS/test/embl
> @dirrm share/EMBOSS/test/data
> @dirrm share/EMBOSS/test
>@@ -1600,16 +1657,6 @@
> @dirrm share/EMBOSS/jemboss/org
> @dirrm share/EMBOSS/jemboss/lib
> @dirrm share/EMBOSS/jemboss/images
>-@dirrm share/EMBOSS/jemboss/embreo/cgi-bin
>-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr
>-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo
>-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp
>-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc
>-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk/ac
>-@dirrm share/EMBOSS/jemboss/embreo/api-docs/uk
>-@dirrm share/EMBOSS/jemboss/embreo/api-docs
>-@dirrm share/EMBOSS/jemboss/embreo/Modules
>-@dirrm share/EMBOSS/jemboss/embreo
> @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/soap
> @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/programs
> @dirrm share/EMBOSS/jemboss/api/org/emboss/jemboss/parser/acd
>cvs diff: Diffing files

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Attachments on bug 40198: 23343 | 23344