X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=cca7ce7f0c736e8cdf3423d531b3455effb0918e;hb=f3c89a889a044504d43fa586a01b31720d113c69;hp=deb50ed87448122673fcba75ab8d4687c1aaa8df;hpb=f272ca53b594c5ae586811ff5f9ad034b7b82d2f;p=jalview.git

diff --git a/build.xml b/build.xml
index deb50ed..cca7ce7 100755
--- a/build.xml
+++ b/build.xml
@@ -1,20 +1,20 @@
 <?xml version="1.0"?>
 <!--
-   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
-   * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
-   * 
-   * This file is part of Jalview.
-   * 
-   * Jalview 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 3 of the License, or (at your option) any later version.
-   * 
-   * Jalview is distributed in the hope that it will be useful, but 
-   * WITHOUT ANY WARRANTY; without even the implied warranty 
-   * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
-   * PURPOSE.  See the GNU General Public License for more details.
-   * 
-   * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 -->
 <project name="jalviewX" default="usage" basedir=".">
 	<!-- we use jalopy to format our sources -->
@@ -99,7 +99,7 @@
 		<property name="packageDir" value="dist" />
 		<property name="outputJar" value="jalview.jar" />
 		<!-- Jalview Applet JMol Jar Dependency -->
-		<property name="jmolJar" value="JmolApplet-12.1.11_dev.jar" />
+		<property name="jmolJar" value="JmolApplet-12.1.13.jar" />
 		<property name="jalviewLiteJar" value="jalviewApplet.jar" />
 		<!-- switch to indicate if we should obfuscate jalviewLite -->
 		<!--<property name="donotobfuscate" value="true"/> -->
@@ -122,6 +122,9 @@
 				<include name="*.jar" />
 				<include name="**/*.jar" />
 			</fileset>
+			<fileset dir="${java.home}/lib">
+				<include name="plugin.jar"/>
+			</fileset>
 			<fileset dir="appletlib">
 				<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
 				-->
@@ -141,6 +144,9 @@
 			<fileset dir="${java118.home}">
 				<include name="lib/classes.zip" />
 			</fileset>
+			<fileset dir="${java.home}/lib">
+				<include name="plugin.jar"/>
+			</fileset>
 			<pathelement location="appletlib/${jmolJar}" />
 		</path>
 	</target>
@@ -398,9 +404,14 @@
 	</target>
 
 	<target name="makedist" depends="build, buildPropertiesFile, buildindices">
-		<!-- make the package jar -->
+		<!-- make the package jar if not already existing -->
 		<mkdir dir="${packageDir}" />
-
+		<!-- clean dir if it already existed -->
+		<delete>
+			<fileset dir="${packageDir}">
+				<include name="*.jar"/>
+			</fileset>
+		</delete>
 		<jar destfile="${packageDir}/${outputJar}">
 			<manifest>
 				<attribute name="Main-Class" value="jalview.bin.Jalview" />
@@ -441,7 +452,9 @@
 
 	<target name="compileApplet" depends="init,clean">
 		<mkdir dir="${outputDir}" />
-		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpath="appletlib/${jmolJar}" includes="jalview/appletgui/**" excludes="ext/**,MCview/**,org/**,vamsas/**" />
+		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
+			classpathref="jalviewlite.deps" includes="jalview/appletgui/**" 
+			excludes="ext/**,MCview/**,org/**,vamsas/**" />
 	</target>
 
 	<target name="packageApplet" depends="compileApplet, buildPropertiesFile">