diff options
author | wjv <wjv@FreeBSD.org> | 2002-07-05 10:09:32 +0000 |
---|---|---|
committer | wjv <wjv@FreeBSD.org> | 2002-07-05 10:09:32 +0000 |
commit | 2052caae32c8973aae094c82e0ef4a1702abeeac (patch) | |
tree | a1531a77fa3cf160286f7563a18d2319b86c101c /biology | |
parent | 7dfd41ca0aa47c21480bdf680d9551c7fb1fb999 (diff) | |
download | FreeBSD-ports-2052caae32c8973aae094c82e0ef4a1702abeeac.zip FreeBSD-ports-2052caae32c8973aae094c82e0ef4a1702abeeac.tar.gz |
- Update to version 2.4.1
- Unmark BROKEN
- Start adding support for Jemboss Java-based GUI (not active yet)
PR: 40198 ; many private requests
Submitted by: Tilman Linneweh <tilman@arved.de> (2.4.1 update)
Diffstat (limited to 'biology')
-rw-r--r-- | biology/emboss/Makefile | 32 | ||||
-rw-r--r-- | biology/emboss/distinfo | 14 | ||||
-rw-r--r-- | biology/emboss/files/patch-ajax::ajjava.c | 11 | ||||
-rw-r--r-- | biology/emboss/pkg-plist | 237 |
4 files changed, 183 insertions, 111 deletions
diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index c47492c..1bdd97d 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -6,7 +6,7 @@ # PORTNAME= emboss -PORTVERSION= 2.2.0 +PORTVERSION= 2.4.1 CATEGORIES= biology MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \ ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \ @@ -19,8 +19,6 @@ MAINTAINER= wjv@FreeBSD.org LIB_DEPENDS= gd.2:${PORTSDIR}/graphics/gd -BROKEN= "Incorrect checksums" - USE_SUBMAKE= yes USE_GMAKE= yes GNU_CONFIGURE= yes @@ -63,6 +61,17 @@ PLIST_${app}= "@comment " PLIST_SUB+= PLIST_${app}=${PLIST_${app}} .endfor +# Jemboss support is a work in progress. +# +#.if defined(WITH_JEMBOSS) +#USE_JAVA= 1.3+ +#CONFIGURE_ARGS+= --with-java=${JAVA_HOME}/include \ +# --with-javaos=${JAVA_HOME}/include/${JAVA_OS:L} +#CONFIGURE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin +#MAKE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin +#JEMBOSS_WRKSRC= ${WRKSRC}/jemboss +#.endif + pre-fetch: @ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME} @@ -86,28 +95,33 @@ post-patch: post-configure: .for app in ${APPLIST} - @ (cd ${${app}_WRKSRC} && \ + @ cd ${${app}_WRKSRC} && \ ${SETENV} CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" \ CXXFLAGS="${CXXFLAGS}" \ INSTALL="/usr/bin/install -c -o ${BINOWN} -g ${BINGRP}" \ INSTALL_DATA="${INSTALL_DATA}" \ INSTALL_PROGRAM="${INSTALL_PROGRAM}" \ INSTALL_SCRIPT="${INSTALL_SCRIPT}" \ - ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}) + ${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS} .endfor post-build: .for app in ${APPLIST} - @ (cd ${${app}_WRKSRC} && \ + @ cd ${${app}_WRKSRC} && \ ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ - ${MAKE_ARGS}) + ${MAKE_ARGS} .endfor +#.if defined(WITH_JEMBOSS) +# @ cd ${JEMBOSS_WRKSRC} && \ +# ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ +# ${MAKE_ARGS} +#.endif post-install: .for app in ${APPLIST} - @ (cd ${${app}_WRKSRC} && \ + @ cd ${${app}_WRKSRC} && \ ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \ - ${MAKE_ARGS} ${INSTALL_TARGET}) + ${MAKE_ARGS} ${INSTALL_TARGET} .endfor @ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \ ${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \ diff --git a/biology/emboss/distinfo b/biology/emboss/distinfo index 977a664..46e569a 100644 --- a/biology/emboss/distinfo +++ b/biology/emboss/distinfo @@ -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 diff --git a/biology/emboss/files/patch-ajax::ajjava.c b/biology/emboss/files/patch-ajax::ajjava.c new file mode 100644 index 0000000..76189b9 --- /dev/null +++ b/biology/emboss/files/patch-ajax::ajjava.c @@ -0,0 +1,11 @@ +--- ajax/ajjava.c.orig Thu May 2 22:06:08 2002 ++++ ajax/ajjava.c Sun May 26 09:14:20 2002 +@@ -75,7 +75,7 @@ + #endif + + #ifndef __ppc__ +-#include <crypt.h> ++#include <unistd.h> + #endif + + diff --git a/biology/emboss/pkg-plist b/biology/emboss/pkg-plist index 8556bf0..c3364d5 100644 --- a/biology/emboss/pkg-plist +++ b/biology/emboss/pkg-plist @@ -188,7 +188,6 @@ bin/polydot bin/preg bin/prettyplot bin/prettyseq -bin/primer3 bin/primersearch bin/printsextract bin/profit @@ -210,9 +209,6 @@ bin/scope 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/emma.acd 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/hmoment.acd 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/pasteseq.acd 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/preg.acd 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/restover.acd 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/tfextract.acd 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/PROSITE/dummyfile 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/package-list 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/Jemboss_logo_small.gif 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/jalview.jar 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/SetUpMenuBar.java 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/ParseAcd.java 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/ResultList.java 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/JembossRun.java 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.nbrf 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/acnum.trg 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/entrynam.idx 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/prettyplot.html 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/wobble0.gif 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/polydot.txt 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/wobble.txt 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 @@ share/doc/EMBOSS/tutorials/tmap.ps.gz @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 @@ share/doc/EMBOSS/tutorials/tmap.ps.gz @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 |