X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=681804dbaf28d07d6ba2c81572745f510e77eff0;hb=refs%2Fheads%2FRelease_2_8_2_Branch_i18n;hp=1ac7afcfb2a55ad85b41cbfd986a3446d05b032e;hpb=2101b85469284f109fc44c4fda1752d3e02b7798;p=jalview.git

diff --git a/build.xml b/build.xml
index 1ac7afc..681804d 100755
--- a/build.xml
+++ b/build.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -18,15 +18,6 @@
  * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 <project name="jalviewX" default="usage" basedir=".">
-  <!-- we use jalopy to format our sources -->
-  <taskdef name="jalopy" classname="de.hunsicker.jalopy.plugin.ant.AntPlugin">
-    <classpath>
-      <fileset dir="utils/jalopy/lib">
-        <include name="*.jar" />
-      </fileset>
-    </classpath>
-  </taskdef>
-
   <target name="help" depends="usage" />
   <target name="usage">
     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
@@ -86,15 +77,14 @@
     <!-- Key Password -->
     <property name="jalview.key.pass" value="alignmentisfun" />
 
-
-
     <!-- Don't change anything below here unless you know what you are doing! -->
     <!-- Url path for WebStart in JNLP file -->
     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
     <!-- Webstart Image - looked for in resources/images -->
     <property name="WebStartImage" value="JalviewLogo_big.png"/>
     <!-- J2SE version needed for webstart launch -->
-    <property name="j2sev" value="1.6+"/>
+    <!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
+    <property name="j2sev" value="1.7+"/>
 
     <!-- Permissions for running Java applets and applications. -->
     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
@@ -116,6 +106,7 @@
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
+    <property name="varnaJar" value="VARNAv3-9.jar" />
     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
     <!-- switch to indicate if we should obfuscate jalviewLite -->
     <!-- <property name="donotobfuscate" value="true"/> -->
@@ -147,15 +138,15 @@
         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
 				-->
         <include name="${jmolJar}" />
+        <include name="${varnaJar}" />
       </fileset>
 
     </path>
     <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
     <!-- The Location of the java 1.1.8 jdk -->
-    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
-		-->
+    <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" /> -->
     <property name="java118.home" value="${java.home}" />
-    <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
+    <!-- <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 		-->
     <!-- jre for 1.4 version -->
     <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
@@ -169,6 +160,7 @@
         <include name="plugin.jar"/>
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
+      <pathelement location="lib/${varnaJar}" />
     </path>
     <!-- default location for outputting javadoc -->
     <property name="javadocDir" value="${packageDir}/javadoc"/>
@@ -364,13 +356,13 @@
     </presetdef>
 
     <jnlpf toFile="${jnlpFile}"/>
-  
+
   </target>
-  
+
   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
     <echo message="Not adding JNLP File Associations"/>
   </target>
-  
+
   <target name="-dojnlpfileassoc" depends="-generatejnlpf" unless="nojnlpfileassocs">
     <replace file="${jnlpFile}">
       <replacetoken>
@@ -390,9 +382,9 @@
         <association mime-type="application-x/ext-file" extensions="stk"/>
         <association mime-type="application-x/ext-file" extensions="jvp"/>
       </information>]]></replacevalue>
-    </replace>
-    <echo message="Added file associations to JNLP file"/>
-    </target>
+  </replace>
+  <echo message="Added file associations to JNLP file"/>
+</target>
 <target name="writejnlpf" depends="-dojnlpfileassoc,-dofakejnlpfileassoc">
 </target>
 
@@ -489,7 +481,7 @@
   <mkdir dir="${outputDir}" />
   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
 			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
-			excludes="ext/**,MCview/**,org/**,vamsas/**" />
+			excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">