mirror of
https://git.FreeBSD.org/ports.git
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- 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)
This commit is contained in:
Johann Visagie
parent
650e6590fe
commit
cd4c80ae90
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=62472
@ -6,7 +6,7 @@
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#
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PORTNAME= emboss
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PORTVERSION= 2.2.0
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PORTVERSION= 2.4.1
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CATEGORIES= biology
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MASTER_SITES= ftp://ftp.uk.embnet.org/pub/EMBOSS/ \
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ftp://ftp.es.embnet.org/pub/software/emboss/EMBOSS/ \
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@ -19,8 +19,6 @@ MAINTAINER= wjv@FreeBSD.org
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LIB_DEPENDS= gd.2:${PORTSDIR}/graphics/gd
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BROKEN= "Incorrect checksums"
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USE_SUBMAKE= yes
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USE_GMAKE= yes
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GNU_CONFIGURE= yes
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@ -63,6 +61,17 @@ PLIST_${app}= "@comment "
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PLIST_SUB+= PLIST_${app}=${PLIST_${app}}
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.endfor
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# Jemboss support is a work in progress.
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#
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#.if defined(WITH_JEMBOSS)
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#USE_JAVA= 1.3+
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#CONFIGURE_ARGS+= --with-java=${JAVA_HOME}/include \
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# --with-javaos=${JAVA_HOME}/include/${JAVA_OS:L}
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#CONFIGURE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin
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#MAKE_ENV+= PATH=${PATH}:${JAVA_HOME}/bin
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#JEMBOSS_WRKSRC= ${WRKSRC}/jemboss
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#.endif
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pre-fetch:
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@ ${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/configure.${PORTNAME}
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@ -86,28 +95,33 @@ post-patch:
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post-configure:
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.for app in ${APPLIST}
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@ (cd ${${app}_WRKSRC} && \
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@ cd ${${app}_WRKSRC} && \
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${SETENV} CC="${CC}" CXX="${CXX}" CFLAGS="${CFLAGS}" \
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CXXFLAGS="${CXXFLAGS}" \
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INSTALL="/usr/bin/install -c -o ${BINOWN} -g ${BINGRP}" \
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INSTALL_DATA="${INSTALL_DATA}" \
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INSTALL_PROGRAM="${INSTALL_PROGRAM}" \
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INSTALL_SCRIPT="${INSTALL_SCRIPT}" \
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${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS})
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${CONFIGURE_ENV} ./${CONFIGURE_SCRIPT} ${CONFIGURE_ARGS}
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.endfor
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post-build:
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.for app in ${APPLIST}
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@ (cd ${${app}_WRKSRC} && \
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@ cd ${${app}_WRKSRC} && \
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${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
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${MAKE_ARGS})
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${MAKE_ARGS}
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.endfor
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#.if defined(WITH_JEMBOSS)
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# @ cd ${JEMBOSS_WRKSRC} && \
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# ${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
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# ${MAKE_ARGS}
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#.endif
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post-install:
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.for app in ${APPLIST}
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@ (cd ${${app}_WRKSRC} && \
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@ cd ${${app}_WRKSRC} && \
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${SETENV} ${MAKE_ENV} ${GMAKE} ${MAKE_FLAGS} ${MAKEFILE} \
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${MAKE_ARGS} ${INSTALL_TARGET})
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${MAKE_ARGS} ${INSTALL_TARGET}
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.endfor
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@ ${PERL} -pe 's#%%PREFIX%%#${PREFIX}#' \
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${CONFIG_FILE} > ${PREFIX}/etc/emboss.default.sample && \
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@ -1,7 +1,7 @@
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MD5 (emboss/EMBOSS-2.2.0.tar.gz) = c6d755f98f558f9f98649c1d1cca44a6
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MD5 (emboss/EMNU-1.0.5.tar.gz) = 6ba42bfd8484b313f39ef81e03141f66
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MD5 (emboss/HMMER-2.1.1.tar.gz) = aff42ea8ced9c049f2cc4f84a10efd21
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MD5 (emboss/MEME-2.3.1.tar.gz) = 92302d22ccb94f9e77c1bb2ca35c0f9c
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MD5 (emboss/MSE-0.0.4.tar.gz) = fdfdb7f4d92f67323b14b7030a1135c9
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MD5 (emboss/PHYLIP-3.573c.tar.gz) = 5fa81a3cfb4f502c627a30428d49a084
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MD5 (emboss/TOPO-0.1.tar.gz) = 96fced0b0979157e344fd9b08dc2aa64
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MD5 (emboss/EMBOSS-2.4.1.tar.gz) = f8e8f053362346d45b696ad6d0ec4aad
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MD5 (emboss/EMNU-1.0.5.tar.gz) = 628f28b24762e75a9546b608cc60f179
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MD5 (emboss/HMMER-2.1.1.tar.gz) = 1bce29d9f215076c90d2b95b9ba6942f
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MD5 (emboss/MEME-2.3.1.tar.gz) = 6961f0308b122d170a5e8d27f02edbc3
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MD5 (emboss/MSE-0.0.4.tar.gz) = 067952daa34ce4af71e88d9e87136257
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MD5 (emboss/PHYLIP-3.573c.tar.gz) = 4e69bc86f429d95f99b5e9d3f83036ab
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MD5 (emboss/TOPO-0.1.tar.gz) = 8ca248a5cf0ad230d3959fbcce013942
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11
biology/emboss/files/patch-ajax::ajjava.c
Normal file
11
biology/emboss/files/patch-ajax::ajjava.c
Normal file
@ -0,0 +1,11 @@
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--- ajax/ajjava.c.orig Thu May 2 22:06:08 2002
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+++ ajax/ajjava.c Sun May 26 09:14:20 2002
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@@ -75,7 +75,7 @@
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#endif
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#ifndef __ppc__
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-#include <crypt.h>
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+#include <unistd.h>
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#endif
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@ -188,7 +188,6 @@ bin/polydot
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bin/preg
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bin/prettyplot
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bin/prettyseq
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bin/primer3
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bin/primersearch
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bin/printsextract
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bin/profit
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@ -210,9 +209,6 @@ bin/scope
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bin/seealso
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bin/seqmatchall
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bin/seqret
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bin/seqretall
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bin/seqretallfeat
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bin/seqretset
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bin/seqretsplit
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bin/showalign
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bin/showdb
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@ -320,6 +316,7 @@ share/EMBOSS/acd/emma.acd
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share/EMBOSS/acd/emowse.acd
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share/EMBOSS/acd/entrails.acd
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share/EMBOSS/acd/entret.acd
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share/EMBOSS/acd/eprimer3.acd
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share/EMBOSS/acd/equicktandem.acd
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share/EMBOSS/acd/est2genome.acd
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share/EMBOSS/acd/etandem.acd
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@ -339,6 +336,7 @@ share/EMBOSS/acd/hmoment.acd
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share/EMBOSS/acd/iep.acd
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share/EMBOSS/acd/infoalign.acd
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share/EMBOSS/acd/infoseq.acd
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share/EMBOSS/acd/interface.acd
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share/EMBOSS/acd/isochore.acd
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share/EMBOSS/acd/lindna.acd
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share/EMBOSS/acd/listor.acd
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@ -365,6 +363,7 @@ share/EMBOSS/acd/pasteseq.acd
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share/EMBOSS/acd/patmatdb.acd
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share/EMBOSS/acd/patmatmotifs.acd
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share/EMBOSS/acd/patmattest.acd
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share/EMBOSS/acd/pdbtosp.acd
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share/EMBOSS/acd/pepcoil.acd
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share/EMBOSS/acd/pepinfo.acd
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share/EMBOSS/acd/pepnet.acd
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@ -379,7 +378,6 @@ share/EMBOSS/acd/preg.acd
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share/EMBOSS/acd/prettyplot.acd
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share/EMBOSS/acd/prettyseq.acd
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share/EMBOSS/acd/prima.acd
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share/EMBOSS/acd/primer3.acd
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share/EMBOSS/acd/primers.acd
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share/EMBOSS/acd/primersearch.acd
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share/EMBOSS/acd/printsextract.acd
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@ -397,16 +395,19 @@ share/EMBOSS/acd/restover.acd
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share/EMBOSS/acd/restrict.acd
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share/EMBOSS/acd/revseq.acd
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share/EMBOSS/acd/scopalign.acd
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share/EMBOSS/acd/scopparse.acd
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share/EMBOSS/acd/scope.acd
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share/EMBOSS/acd/seealso.acd
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share/EMBOSS/acd/seqinfo.acd
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share/EMBOSS/acd/seqmatchall.acd
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share/EMBOSS/acd/seqnr.acd
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share/EMBOSS/acd/seqret.acd
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share/EMBOSS/acd/seqretall.acd
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share/EMBOSS/acd/seqretallfeat.acd
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share/EMBOSS/acd/seqretset.acd
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share/EMBOSS/acd/seqretsingle.acd
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share/EMBOSS/acd/seqretsplit.acd
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share/EMBOSS/acd/seqsort.acd
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share/EMBOSS/acd/showalign.acd
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share/EMBOSS/acd/showdb.acd
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share/EMBOSS/acd/showfeat.acd
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@ -429,16 +430,20 @@ share/EMBOSS/acd/tfextract.acd
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share/EMBOSS/acd/tfm.acd
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share/EMBOSS/acd/tfscan.acd
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share/EMBOSS/acd/tmap.acd
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share/EMBOSS/acd/tranalign.acd
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share/EMBOSS/acd/transeq.acd
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share/EMBOSS/acd/treetypedisplay.acd
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share/EMBOSS/acd/trimest.acd
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share/EMBOSS/acd/trimseq.acd
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share/EMBOSS/acd/union.acd
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share/EMBOSS/acd/vectorstrip.acd
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share/EMBOSS/acd/water.acd
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share/EMBOSS/acd/whichdb.acd
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share/EMBOSS/acd/wobble.acd
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share/EMBOSS/acd/wordcount.acd
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share/EMBOSS/acd/wordmatch.acd
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share/EMBOSS/acd/wossname.acd
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share/EMBOSS/acd/yank.acd
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share/EMBOSS/data/CODONS/Eacc.cut
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share/EMBOSS/data/CODONS/Eadenovirus5.cut
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share/EMBOSS/data/CODONS/Eadenovirus7.cut
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@ -721,6 +726,7 @@ share/EMBOSS/data/PROSITE/dummyfile
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share/EMBOSS/data/REBASE/dummyfile
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share/EMBOSS/data/embossre.equ
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share/EMBOSS/emboss.default.template
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share/EMBOSS/jemboss/README
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share/EMBOSS/jemboss/LICENSE
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share/EMBOSS/jemboss/api/allclasses-frame.html
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share/EMBOSS/jemboss/api/deprecated-list.html
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@ -791,79 +797,6 @@ share/EMBOSS/jemboss/api/package-list
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share/EMBOSS/jemboss/api/packages.html
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share/EMBOSS/jemboss/api/serialized-form.html
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share/EMBOSS/jemboss/api/stylesheet.css
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share/EMBOSS/jemboss/embreo/LICENSE
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share/EMBOSS/jemboss/embreo/Modules/EmbossSoap.pm
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share/EMBOSS/jemboss/embreo/Modules/EmbreoFile.pm
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share/EMBOSS/jemboss/embreo/Modules/ParseSoapOptions.pm
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share/EMBOSS/jemboss/embreo/Modules/README
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share/EMBOSS/jemboss/embreo/PROBLEMS
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share/EMBOSS/jemboss/embreo/README
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share/EMBOSS/jemboss/embreo/README.macos
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share/EMBOSS/jemboss/embreo/README.properties
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share/EMBOSS/jemboss/embreo/api-docs/allclasses-frame.html
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share/EMBOSS/jemboss/embreo/api-docs/deprecated-list.html
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share/EMBOSS/jemboss/embreo/api-docs/help-doc.html
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share/EMBOSS/jemboss/embreo/api-docs/index-all.html
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share/EMBOSS/jemboss/embreo/api-docs/index.html
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share/EMBOSS/jemboss/embreo/api-docs/overview-tree.html
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share/EMBOSS/jemboss/embreo/api-docs/package-list
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share/EMBOSS/jemboss/embreo/api-docs/serialized-form.html
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share/EMBOSS/jemboss/embreo/api-docs/stylesheet.css
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoACD.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAnnotate.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAppList.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthException.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthPopup.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoAuthPrompt.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoException.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoFrame.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoGroupList.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoGroupTree.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoHelp.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoHelpView.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoJList.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoListFile.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoMakeFileSafe.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoParams.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPendingResults.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPrivateRequest.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoPublicRequest.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResList.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResListView.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResSave.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResView.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoResult.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoRun.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoServiceDesc.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoShowDB.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoStartup.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoTreeCellRenderer.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/EmbreoUtils.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFile.html
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share/EMBOSS/jemboss/embreo/api-docs/uk/ac/mrc/hgmp/embreo/filemgr/EmbreoFileGet.html
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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
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||||
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
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||||
share/EMBOSS/jemboss/embreo/cgi-bin/soap.cgi
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||||
share/EMBOSS/jemboss/embreo/embreo-full.jar
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||||
share/EMBOSS/jemboss/images/Backward_arrow_button.gif
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||||
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
|
||||
|
||||
Loading…
Reference in New Issue
Block a user