From f7a218c00134933e239f6a74b1dccffddb2219e0 Mon Sep 17 00:00:00 2001
From: Jim Procter <jprocter@compbio.dundee.ac.uk>
Date: Sun, 9 Jun 2013 19:33:54 +0100
Subject: [PATCH] JAL-674 - update applet build dependency on VARNA

---
 build.xml                    |    6 ++++--
 nbproject/project.properties |    2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/build.xml b/build.xml
index 47a0188..8e4d44d 100755
--- a/build.xml
+++ b/build.xml
@@ -105,7 +105,7 @@
 		<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-dev.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"/> -->
@@ -157,6 +157,8 @@
 				<include name="plugin.jar"/>
 			</fileset>
 			<pathelement location="appletlib/${jmolJar}" />
+      <pathelement location="lib/${varnaJar}" />
+
 		</path>
     <!-- default location for outputting javadoc -->
     <property name="javadocDir" value="${packageDir}/javadoc"/>
@@ -457,7 +459,7 @@
 		<mkdir dir="${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">
diff --git a/nbproject/project.properties b/nbproject/project.properties
index 8bee743..b505d62 100644
--- a/nbproject/project.properties
+++ b/nbproject/project.properties
@@ -71,7 +71,7 @@ file.reference.wsdl4j.jar=lib/wsdl4j.jar
 file.reference.xercesImpl.jar=lib/xercesImpl.jar
 file.reference.xml-apis.jar=lib/xml-apis.jar
 file.reference.miglayout-4.0-swing.jar=lib/miglayout-4.0-swing.jar
-file.reference.varna-3.9-dev.jar=lib/VARNAv3.9-dev.jar
+file.reference.varna-3.9-dev.jar=lib/VARNAv3.9.jar
 includes=**
 jar.compress=false
 javac.classpath=\
-- 
1.7.10.2