This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository mauve.
commit 9687c28cdfdaad196ef049537cef2d5bd0979d62 Author: Andreas Tille <[email protected]> Date: Thu Apr 30 13:04:50 2015 +0200 Imported Upstream version 2.4.0+4734 --- debian/bin/mauve | 7 - debian/changelog | 5 - debian/compat | 1 - debian/control | 49 ---- debian/copyright | 21 -- debian/get-orig-source | 38 --- debian/install | 3 - debian/mauve.manifest | 2 - debian/patches/build_xml.patch | 284 --------------------- debian/patches/debian_classes.patch | 77 ------ debian/patches/series | 3 - .../use_JConsole_of_zeus-jscl_properly.patch | 68 ----- debian/rules | 38 --- debian/source/format | 1 - debian/upstream/metadata | 12 - debian/watch | 1 - ext/goose.jar | Bin 89124 -> 0 bytes 17 files changed, 610 deletions(-) diff --git a/debian/bin/mauve b/debian/bin/mauve deleted file mode 100755 index f23bdeb..0000000 --- a/debian/bin/mauve +++ /dev/null @@ -1,7 +0,0 @@ -#! /bin/sh -set -e - -# Include the wrappers utility script -. /usr/lib/java-wrappers/java-wrappers.sh - -run_java -Xms128M -Xmx1G -jar /usr/share/java/Mauve.jar "$@" diff --git a/debian/changelog b/debian/changelog deleted file mode 100644 index e1eea8e..0000000 --- a/debian/changelog +++ /dev/null @@ -1,5 +0,0 @@ -mauve (2.4.0+4734-1) UNRELEASED; urgency=medium - - * Initial release (Closes: #??????) - - -- Andreas Tille <[email protected]> Fri, 17 Apr 2015 15:38:22 +0200 diff --git a/debian/compat b/debian/compat deleted file mode 100644 index ec63514..0000000 --- a/debian/compat +++ /dev/null @@ -1 +0,0 @@ -9 diff --git a/debian/control b/debian/control deleted file mode 100644 index fecfa8f..0000000 --- a/debian/control +++ /dev/null @@ -1,49 +0,0 @@ -Source: mauve -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Andreas Tille <[email protected]> -Section: science -Priority: optional -Build-Depends: debhelper (>= 9), - javahelper, - default-jdk, - ant, - ant-contrib, - junit, - libbiojava-java, - libcommons-cli-java, - libdbus-java, - libzeus-jscl-java, - icedtea-netx-common, - libunixsocket-java -Standards-Version: 3.9.6 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mauve.git -Vcs-Git: git://anonscm.debian.org/debian-med/mauve.git -Homepage: http://darlinglab.org/mauve/ - -Package: mauve -Architecture: any -Depends: ${java:Depends}, - ${misc:Depends} -Recommends: ${java:Recommends}, - libpostgresql-jdbc-java -Description: multiple genome alignment - Mauve is a system for efficiently constructing multiple genome alignments - in the presence of large-scale evolutionary events such as rearrangement - and inversion. Multiple genome alignment provides a basis for research - into comparative genomics and the study of evolutionary dynamics. Aligning - whole genomes is a fundamentally different problem than aligning short - sequences. - . - Mauve has been developed with the idea that a multiple genome aligner - should require only modest computational resources. It employs algorithmic - techniques that scale well in the amount of sequence being aligned. For - example, a pair of Y. pestis genomes can be aligned in under a minute, - while a group of 9 divergent Enterobacterial genomes can be aligned in - a few hours. - . - Mauve computes and interactively visualizes genome sequence comparisons. - Using FastA or GenBank sequence data, Mauve constructs multiple genome - alignments that identify large-scale rearrangement, gene gain, gene loss, - indels, and nucleotide substutition. - . - Mauve is developed at the University of Wisconsin. diff --git a/debian/copyright b/debian/copyright deleted file mode 100644 index 516ac9b..0000000 --- a/debian/copyright +++ /dev/null @@ -1,21 +0,0 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Upstream-Name: libMems -Upstream-Contact: Aaron Darling <[email protected]> -Source: http://sourceforge.net/p/mauve/code/HEAD/tree/libMems/trunk/ - -Files: * -Copyright: 2003 - 2014 Aaron Darling -- [email protected] -License: GPL-2+ - -Files: debian/* -Copyright: 2015 Andreas Tille <[email protected]> -License: GPL-2+ - -License: GPL-2+ - This package is free software; you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation; either version 2 of the License, or - (at your option) any later version. - . - On Debian systems, the complete text of the licenses can be found in: - GPL-2 - `/usr/share/common-licenses/GPL-2' diff --git a/debian/get-orig-source b/debian/get-orig-source deleted file mode 100755 index e0b7a45..0000000 --- a/debian/get-orig-source +++ /dev/null @@ -1,38 +0,0 @@ -#!/bin/sh -# get source for mauve from SVN because there is no source tarball distribution - -set -e -NAME=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'` - -if ! echo $@ | grep -q upstream-version ; then - VERSION=`dpkg-parsechangelog | awk '/^Version:/ { print $2 }' | sed 's/\([0-9\.]\+\)-[0-9]\+$/\1/'` -else - VERSION=`echo $@ | sed "s?^.*--upstream-version \([0-9.]\+\) .*${NAME}.*?\1?"` - if echo "$VERSION" | grep -q "upstream-version" ; then - echo "Unable to parse version number" - exit - fi -fi - -SVNURI="svn://svn.code.sf.net/p/mauve/code/mauve/trunk" -revision=`LANG=C svn info ${SVNURI} | grep "^Last Changed Rev:" | sed 's/Last Changed Rev: *//'` -VERSION=`echo ${VERSION}| sed "s/+[0-9]\+$//"`+${revision} - -TARDIR=${NAME}-${VERSION} - -mkdir -p ../tarballs -cd ../tarballs -# svn export conserves time stamps of the files, checkout does not -LC_ALL=C svn export ${SVNURI} ${TARDIR} >/dev/null 2>/dev/null - -cd ${TARDIR} -rm -rf osx win32 win64 -rm -rf linux-x64/mauveAligner linux-x86/mauveAligner linux-x64/progressiveMauve linux-x86/progressiveMauve -for libjava in ant bytecode commons-cli core dbus gui jebl jnlp postgres unix zeus-jscl ; do - find . -name "*${libjava}*.jar" -delete -done -rm -rf build_support -cd .. - -tar --owner=root --group=root --mode=a+rX -caf "$NAME"_"$VERSION".orig.tar.xz "${TARDIR}" -rm -rf "${NAME}"-"$VERSION" diff --git a/debian/install b/debian/install deleted file mode 100644 index d47d025..0000000 --- a/debian/install +++ /dev/null @@ -1,3 +0,0 @@ -debian/bin usr -Mauve.jar usr/share/java -ext usr/share/Mauve \ No newline at end of file diff --git a/debian/mauve.manifest b/debian/mauve.manifest deleted file mode 100644 index 1c12b40..0000000 --- a/debian/mauve.manifest +++ /dev/null @@ -1,2 +0,0 @@ -usr/share/java/Mauve.jar: - Class-Path: /usr/share/java/biojava.jar /usr/share/java/commons-cli.jar /usr/share/icedtea-web/netx.jar /usr/share/java/zeus-jscl.jar /usr/share/java/dbus.jar /usr/share/java/unix.jar /usr/share/Mauve/ext/goose.jar diff --git a/debian/patches/build_xml.patch b/debian/patches/build_xml.patch deleted file mode 100644 index c3c83b8..0000000 --- a/debian/patches/build_xml.patch +++ /dev/null @@ -1,284 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Updated: Fri, 17 Apr 2015 15:38:22 +0200 -Description: Drop OSX specific things from build.xml, - Prevent build from calling home at build time - ---- a/build.xml -+++ b/build.xml -@@ -19,7 +19,6 @@ - --> - <!-- deployment locations for standalone releases --> - <property name="deploy.address" value="[email protected]" /> -- <property name="deploy.bareaddress" value="darlinglab.org" /> - <property name="deploy.username" value="darlini8" /> - <property name="deploy.win32.keyfile" value="C:\Documents and Settings\koadman\plonk.ppk" /> - <property name="deploy.serverdir" value="/home3/darlini8/www/mauve/downloads" /> -@@ -44,14 +43,6 @@ - <!-- get any environment variables --> - <property environment="env" /> - -- <!-- osxant.jar creates Mac OS X disk images --> -- <taskdef name="dmg" classname="com.amberarcher.ant.osx.DmgTask"> -- <classpath> -- <pathelement path="${support}/osxant.jar"/> -- </classpath> -- </taskdef> -- <!-- maverick-ant.jar supports secure FTP for deployment --> -- <taskdef name="ssh" classname="com.sshtools.ant.Ssh" classpath="${support}/maverick-ant.jar"/> - <taskdef resource="net/sf/antcontrib/antcontrib.properties"> - <classpath> - <pathelement path="${support}/ant-contrib-1.0b3.jar"/> -@@ -189,7 +180,7 @@ - <copy todir="C:\htdocs" file="./jws/mauve.jnlp" /> - </target> - -- <target name="dist" depends="jar,getChangeLog" description="generate the distribution" > -+ <target name="dist" depends="jar" description="generate the distribution" > - <!-- Create the distribution directory --> - <mkdir dir="${dist}" /> - -@@ -221,146 +212,6 @@ - </tar> - </target> - -- <taskdef name="bundleapp" -- classname="com.oracle.appbundler.AppBundlerTask" -- classpath="build_support/appbundler-1.0.jar" /> -- --<!-- Create a DMG - This only works on MacOSX (requires hdiutil) --> --<target name="dmg" depends="macdist" description="Create a DMG package for MacOSX (only works on MacOSX)"> -- -- <!-- Set this property value to your application name --> -- <property name="app.name" value="Mauve-${release.version}"/> -- -- <!-- Set this property value to a directory where you can -- mount temporarily your images, for example /tmp --> -- <property name="mountdir" value="/tmp"/> -- -- <!-- Delete previously created DMG --> -- <delete file="${dist}/${app.name}.dmg" quiet="yes" failonerror="false"/> -- -- <!-- Create a temporary Disk Image --> -- <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true"> -- <arg value="create"/> -- <arg value="-srcfolder"/> -- <arg value="staging"/> -- <arg value="-volname"/> -- <arg value="${app.name}"/> -- <arg value="-ov"/> -- <arg value="${dist}/${app.name}-tmp.dmg"/> -- <arg value="-format"/> -- <arg value="UDRW"/> -- </exec> -- -- <!-- Attach the temporary image --> -- <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true"> -- <arg value="attach"/> -- <arg value="${dist}/${app.name}-tmp.dmg"/> -- <arg value="-mountroot"/> -- <arg value="${mountdir}/"/> -- </exec> -- -- <!-- Copy the background, the volume icon and DS_Store files --> -- <mkdir dir="${mountdir}/${app.name}/.background"/> -- <copy file="osx/background.png" tofile="${mountdir}/${app.name}/.background/background.png" overwrite="true"/> -- <copy file="osx/mauve.icns" tofile="${mountdir}/${app.name}/.VolumeIcon.icns" overwrite="true"/> -- <copy file="osx/DS_Store" tofile="${mountdir}/${app.name}/.DS_Store" overwrite="true"/> -- -- -- <!-- Indicate that we want a custom icon --> -- <exec executable="SetFile" os="Mac OS X"> -- <arg value="-a"/> -- <arg value="C"/> -- <arg value="${mountdir}/${app.name}"/> -- </exec> -- -- <!-- Add a symbolic link to the Applications directory --> -- <symlink link="${mountdir}/${app.name}" resource="/Applications"/> -- -- -- -- <!-- Detach the temporary image --> -- <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true"> -- <arg value="detach"/> -- <arg value="${mountdir}/${app.name}"/> -- </exec> -- -- <!-- Compress it to a new image --> -- <exec executable="/usr/bin/hdiutil" os="Mac OS X" failonerror="true"> -- <arg value="convert"/> -- <arg value="${dist}/${app.name}-tmp.dmg"/> -- <arg value="-format"/> -- <arg value="UDZO"/> -- <arg value="-o"/> -- <arg value="${dist}/${app.name}.dmg"/> -- </exec> -- -- <!-- Delete the temporary image --> -- <delete file="${dist}/${app.name}-tmp.dmg" quiet="yes" failonerror="false"/> --</target> -- -- -- <!-- Create an OS X application and disk image --> -- <target name="macdist" depends="jar,getChangeLog" description="Generate a Mac OS X disk image" > -- <!-- Create the distribution directory --> -- <mkdir dir="${dist}" /> -- <delete dir="${dist}/Mauve.app"/> -- -- <!-- get the java home --> -- <exec executable="/usr/libexec/java_home" os="Mac OS X" failonerror="true" outputproperty="osx.java.home"/> -- <bundleapp outputdirectory="${dist}" -- name="Mauve" -- displayname="Mauve ${release.version}" -- identifier="components.Mauve" -- icon="osx/mauve.icns" -- shortversion="${release.version}" -- copyright="(c) 2003-2015 http://darlinglab.org/mauve"; -- mainclassname="org.gel.mauve.gui.Mauve"> -- <classpath file="Mauve.jar" /> -- <classpath file="ext/*.jar" /> -- <librarypath file="osx/progressiveMauve" /> -- <librarypath file="osx/mauveAligner" /> -- <runtime dir="${osx.java.home}" /> -- <option value="-Dapple.laf.useScreenMenuBar=false"/> -- <option value="-Xmx500m"/> -- </bundleapp> -- -- <!-- Create a staging directory for the Disk Image filesystem --> -- <mkdir dir="staging"/> -- <exec executable="ditto" failonerror="true"> -- <arg value="-v"/> -- <arg value="${dist}/Mauve.app"/> -- <arg value="staging/Mauve.app"/> -- </exec> -- <copy todir="staging"> -- <fileset dir="${basedir}"> -- <include name="ChangeLog.html"/> -- </fileset> -- </copy> -- -- <!-- copy text files to the staging directory, adding .txt -- to their filename --> -- <copy todir="staging"> -- <fileset dir="${basedir}"> -- <include name="COPYING"/> -- </fileset> -- <mapper type="glob" from="*" to="*.txt"/> -- </copy> -- <chmod file="staging/Mauve.app/Contents/MacOS/JavaAppLauncher" perm="755"/> -- <chmod file="staging/Mauve.app/Contents/MacOS/mauveAligner" perm="755"/> -- <chmod file="staging/Mauve.app/Contents/MacOS/progressiveMauve" perm="755"/> -- --<!-- sign the app --> --<exec executable="/usr/bin/codesign" os="Mac OS X" failonerror="true"> -- <arg value="-s"/> -- <arg value="Developer ID Application: Aaron Darling"/> -- <arg value="--deep"/> -- <arg value="staging/Mauve.app"/> --</exec> --<!----> -- --<!-- <dmg destfile="${dist}/Mauve-${release.version}.dmg" name="Mauve ${release.version}" srcdir="staging" compressed="true"/> --> -- </target> -- - <target name="srcdist" depends="init" description="package a source distribution"> - <tar destfile="${dist}/mauve_source_${datestamp}.tar.gz" compression="gzip"> - <!-- Copy support files into the dist directory--> -@@ -384,27 +235,6 @@ - </tar> - </target> - -- <target name="getChangeLog" > -- <get src="http://darlinglab.org/mauve/user-guide/versions.html"; dest="ChangeLog.html" usetimestamp="true"/> -- <copy file="ChangeLog.html" tofile="ChangeLog"/> -- </target> -- -- <target name="nsicompile" depends="jar,getChangeLog" description="make windows installer" > -- -- <!-- create output directory --> -- <mkdir dir="${dist}" /> -- -- <!-- Make timestamp and timestampdash for installer making --> -- <property environment="env" /> -- <echo message="Program files: ${env.ProgramFiles}"/> -- <exec executable="C:\Program Files (x86)\NSIS\makensis.exe" dir="."> -- <arg line="/V2 /NOCD win32\mauve.nsi" /> -- <env key="release_version" value="${release.version}" /> -- <env key="datestamp" value="${datestamp}" /> -- </exec> -- </target> -- -- - <target name="run" depends="jar" description="run Mauve"> - <java jar="Mauve.jar" fork="true" /> - </target> -@@ -439,68 +269,8 @@ - </filterset> - </copy> - -- <!-- copy unmodified files to the server --> -- <ssh host="${deploy.bareaddress}" -- username="${deploy.username}" -- version="2" -- keyfile="${deploy.win32.keyfile}"> -- <sftp action="put" remotedir="${deploy.asapdir}" verbose="true" newer="true"> -- <fileset dir="."> -- <include name="Mauve.jar" /> -- <include name="mauveApplet.jar" /> -- </fileset> -- <fileset dir="./ext"> -- <include name="*.jar"/> -- </fileset> -- <fileset dir="./src/images"> -- <include name="mauve_icon.gif" /> -- <include name="mauve_logo.png" /> -- </fileset> -- <fileset dir="${dist}"> -- <include name="mauve.jnlp"/> -- </fileset> -- </sftp> -- <!-- set the permissions so others in the group can modify them --> -- <exec cmd="chgrp annotation ${deploy.asapdir}/*"/> -- <exec cmd="chmod 664 ${deploy.asapdir}/*"/> -- <!-- jar files should have the execute bit set --> -- <exec cmd="chmod 775 ${deploy.asapdir}/*.jar"/> -- </ssh> -- </target> -- -- <!-- assumes that an ssh key has been registered with the web server --> -- <target name="deployWin32" depends="nsicompile"> -- <echo file="${dist}\latest" message="${datestamp}"/> -- <echo file="${dist}\latest.windows" message="${datestamp}"/> -- <ssh host="${deploy.bareaddress}" -- username="${deploy.username}" -- version="2" -- keyfile="${deploy.win32.keyfile}"> -- -- <sftp action="put" remotedir="${deploy.serverdir}" verbose="true"> -- <fileset dir="${dist}"> -- <include name="mauve_installer_${release.version}.exe"/> -- <include name="${dist}\latest"/> -- <include name="${dist}\latest.windows"/> -- </fileset> -- </sftp> -- <exec cmd="cp ${deploy.serverdir}/mauve_installer_${release.version}.exe ${deploy.serverdir}/mauve_installer_${datestamp}.exe"/> -- </ssh> - </target> -- -- <!-- assumes that passwordless ssh authentication has been configured to the web server --> -- <target name="deployMacOSX" depends="dmg"> -- <exec executable="scp"> -- <arg value="${dist}/Mauve-${release.version}.dmg" /> -- <arg value="${deploy.address}:${deploy.serverdir}" /> -- </exec> -- <echo file="${dist}/latest.mac" message="${datestamp}"/> -- <exec executable="scp"> -- <arg value="${dist}/latest.mac" /> -- <arg value="${deploy.address}:${deploy.serverdir}" /> -- </exec> -- </target> -- -+ - <!-- assumes that passwordless ssh authentication has been configured to the web server --> - <target name="deployLinux" depends="dist"> - <exec executable="scp"> diff --git a/debian/patches/debian_classes.patch b/debian/patches/debian_classes.patch deleted file mode 100644 index 46153cd..0000000 --- a/debian/patches/debian_classes.patch +++ /dev/null @@ -1,77 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Updated: Fri, 17 Apr 2015 15:38:22 +0200 -Description: Use Debian packaged classes - ---- a/build.xml -+++ b/build.xml -@@ -30,7 +30,8 @@ - <property name="build" location="bin"/> - <property name="dist" location="dist"/> - <property name="ext" location="ext"/> -- <property name="support" location="build_support"/> -+ <property name="deblib" location="/usr/share/java" /> -+ <property name="support" location="/usr/share/java"/> - - <!-- Make datestamp for update checks --> - <tstamp> -@@ -45,7 +46,7 @@ - - <taskdef resource="net/sf/antcontrib/antcontrib.properties"> - <classpath> -- <pathelement path="${support}/ant-contrib-1.0b3.jar"/> -+ <pathelement path="${support}/ant-contrib.jar"/> - </classpath> - </taskdef> - -@@ -77,17 +78,14 @@ - <!-- Build all java source files --> - <javac - classpath=" -- ${ext}/core-1.9.2-SNAPSHOT.jar; -- ${ext}/bytecode-1.9.2-SNAPSHOT.jar; -- ${ext}/gui-1.9.2-SNAPSHOT.jar; -- ${ext}/commons-cli-1.2.jar; -+ ${deblib}/biojava.jar; -+ ${deblib}/commons-cli.jar; - ${support}/junit.jar; -- ${ext}/zeus-jscl.jar; -+ ${deblib}/zeus-jscl.jar; - ${ext}/goose.jar; -- ${ext}/ant-1.7.1.jar; -- ${ext}/dbus-2.6.jar; -- ${ext}/jebl-0.4.jar; -- ${ext}/unix-0.5.jar" -+ ${deblib}/ant.jar; -+ ${deblib}/dbus.jar; -+ ${deblib}/unix.jar" - srcdir="${src}" - destdir="${build}" - target="1.6" ---- a/.classpath -+++ b/.classpath -@@ -3,18 +3,14 @@ - <classpathentry kind="src" path="src"/> - <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER"/> - <classpathentry kind="var" path="JUNIT_HOME/junit.jar" sourcepath="ECLIPSE_HOME/plugins/org.eclipse.jdt.source_3.0.0/src/org.junit_3.8.1/junitsrc.zip"/> -- <classpathentry kind="lib" path="ext/commons-cli-1.2.jar"/> -- <classpathentry kind="lib" path="ext/ant-1.7.1.jar"/> -- <classpathentry kind="lib" path="ext/jebl-0.4.jar" sourcepath="/jebl/src"/> -+ <classpathentry kind="lib" path="/usr/share/java/commons-cli.jar"/> -+ <classpathentry kind="lib" path="/usr/share/java/ant.jar"/> - <classpathentry kind="src" path="test"/> -- <classpathentry kind="lib" path="ext/zeus-jscl.jar"/> -- <classpathentry kind="lib" path="ext/dbus-2.6.jar"/> -- <classpathentry kind="lib" path="ext/unix-0.5.jar"/> -- <classpathentry kind="lib" path="ext/jsc.jar"/> -+ <classpathentry kind="lib" path="/usr/share/java/zeus-jscl.jar"/> -+ <classpathentry kind="lib" path="/usr/share/java/dbus.jar"/> -+ <classpathentry kind="lib" path="/usr/share/java/unix.jar"/> - <classpathentry kind="lib" path="ext/goose.jar"/> -- <classpathentry kind="lib" path="ext/jnlp.jar"/> -- <classpathentry kind="lib" path="ext/bytecode-1.9.2-SNAPSHOT.jar"/> -- <classpathentry kind="lib" path="ext/core-1.9.2-SNAPSHOT.jar"/> -- <classpathentry kind="lib" path="ext/gui-1.9.2-SNAPSHOT.jar"/> -+ <classpathentry kind="lib" path="/usr/share/icedtea-web/netx.jar"/> -+ <classpathentry kind="lib" path="/usr/share/java/biojava.jar"/> - <classpathentry kind="output" path="bin"/> - </classpath> diff --git a/debian/patches/series b/debian/patches/series deleted file mode 100644 index 3eef136..0000000 --- a/debian/patches/series +++ /dev/null @@ -1,3 +0,0 @@ -build_xml.patch -debian_classes.patch -use_JConsole_of_zeus-jscl_properly.patch diff --git a/debian/patches/use_JConsole_of_zeus-jscl_properly.patch b/debian/patches/use_JConsole_of_zeus-jscl_properly.patch deleted file mode 100644 index b0151eb..0000000 --- a/debian/patches/use_JConsole_of_zeus-jscl_properly.patch +++ /dev/null @@ -1,68 +0,0 @@ -From: Markus Koschany <[email protected]> -Date: Sun, 26 Apr 2015 15:22:19 +0200 -Subject: Adapt to latest libzeus-jscl-java version - For a detailed explanation see the debian-java mailing list archive - https://lists.debian.org/debian-java/2015/04/msg00106.html - ---- a/src/org/gel/mauve/MyConsole.java -+++ b/src/org/gel/mauve/MyConsole.java -@@ -10,18 +10,20 @@ import java.io.PrintStream; - public class MyConsole { - private static boolean useSwing = false; - -- private static JConsole console; -+ private static JConsole console = new JConsole(); - - public static void setUseSwing (boolean b) { - if (b && !useSwing) { -- console = JConsole.getConsole (); - console.setTitle ("Mauve Console"); - console.setSize (400, 400); - Dimension dim = Toolkit.getDefaultToolkit().getScreenSize(); - console.setLocation(dim.width-400, 0); -- console.startConsole (); -+ JConsole.getConsole().startConsole (); -+ if (!console.isVisible()) { -+ console.setVisible(true); -+ } - } else if (!b && useSwing) { -- console.stopConsole (); -+ JConsole.getConsole().stopConsole (); - console = null; - } - -@@ -30,13 +32,13 @@ public class MyConsole { - - public static void showConsole () { - if (useSwing) { -- console.showConsole (); -+ JConsole.getConsole().showConsole (); - } - } - - public static PrintStream err () { - if (useSwing) { -- console.showConsole (); -+ JConsole.getConsole().showConsole (); - } - return System.err; - } -@@ -44,4 +46,4 @@ public class MyConsole { - public static PrintStream out () { - return System.out; - } --} -\ No newline at end of file -+} ---- a/src/org/gel/mauve/gui/MauveFrame.java -+++ b/src/org/gel/mauve/gui/MauveFrame.java -@@ -497,8 +497,7 @@ public class MauveFrame extends JFrame implements ActionListener, ModelProgressL - } - if (source == jMenuHelpConsole || ae.getActionCommand().equals("Console")) - { -- JConsole console = JConsole.getConsole(); -- console.showConsole(); -+ JConsole.getConsole().showConsole(); - } - if (source == jMenuHelpClearCache || ae.getActionCommand().equals("ClearCache")) - { diff --git a/debian/rules b/debian/rules deleted file mode 100755 index 68fadd2..0000000 --- a/debian/rules +++ /dev/null @@ -1,38 +0,0 @@ -#!/usr/bin/make -f -# -*- makefile -*- -# debian/rules file for mauve -# Andreas Tille <[email protected]> -# GPL - -#export DH_VERBOSE=1 - -PACKAGE := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p') - -JAVA_HOME := /usr/lib/jvm/default-java - -DEBJAR := /usr/share/java -CLASS_PATH := $(DEBJAR)/biojava.jar:$(DEBJAR)/commons-cli.jar:$(DEBJAR)/dbus.jar:$(DEBJAR)/jebl.jar:$(DEBJAR)/zeus-jscl.jar -## :$(DEBJAR)/postgresql-jdbc4.jar - -# to run the test suite -JAVA := $(JAVA_HOME)/bin/java -ANT_HOME := /usr/share/ant -ANT_BIN := $(ANT_HOME)/bin/ant -ANT_ARGS := -Dcompile.debug=true -Dcompile.optimize=true - -%: - dh $@ --with javahelper - -override_dh_auto_clean: - echo "Manual cleaning needed since build.xml has no clean target" - find . -name "*.class" -delete - rm -rf bin dist - rm -rf build.number src/version.properties - rm -rf Mauve.jar ChangeLog* - -override_dh_auto_build: - # CLASSPATH=$(CLASS_PATH) - ant dist - -get-orig-source: - . debian/get-orig-source diff --git a/debian/source/format b/debian/source/format deleted file mode 100644 index 163aaf8..0000000 --- a/debian/source/format +++ /dev/null @@ -1 +0,0 @@ -3.0 (quilt) diff --git a/debian/upstream/metadata b/debian/upstream/metadata deleted file mode 100644 index b38c69e..0000000 --- a/debian/upstream/metadata +++ /dev/null @@ -1,12 +0,0 @@ -Reference: - Author: "Mauve: multiple alignment of conserved genomic sequence with rearrangements" - Title: Aaron C. E. Darling and Bob Mau and Frederick R. Blattner and Nicole T. Perna - Journal: Genome research - Year: 2004 - Volume: 14 - Number: 7 - Pages: 1394-1403 - DOI: 10.1101/gr.2289704 - PMID: 15231754 - URL: http://genome.cshlp.org/content/14/7/1394.short - eprint: http://genome.cshlp.org/content/14/7/1394.full.pdf+html diff --git a/debian/watch b/debian/watch deleted file mode 100644 index cf22602..0000000 --- a/debian/watch +++ /dev/null @@ -1 +0,0 @@ -# There is no tarball download location, libMuscle is only available in SVN diff --git a/ext/goose.jar b/ext/goose.jar deleted file mode 100644 index a10b37c..0000000 Binary files a/ext/goose.jar and /dev/null differ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mauve.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
