X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=136ca1d260154c41a651994ad2e59285397e6478;hb=6fb502e4a8749d1d98f5442c3b8156ab47996b77;hp=95c855ad9a220964a215b307ae3811ab682e8f02;hpb=7dd17e89f1507a5e445425331c56efca6062e03c;p=jalview.git

diff --git a/build.xml b/build.xml
index 95c855a..136ca1d 100755
--- a/build.xml
+++ b/build.xml
@@ -91,7 +91,8 @@
 		<!-- 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+"/>
 		<!-- build directory configuration -->
 		<property name="libDir" value="lib" />
 		<property name="resourceDir" value="resources" />
@@ -104,6 +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.jar" />
 		<property name="jalviewLiteJar" value="jalviewApplet.jar" />
 		<!-- switch to indicate if we should obfuscate jalviewLite -->
 		<!--<property name="donotobfuscate" value="true"/> -->
@@ -133,6 +135,7 @@
 				<!-- 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>
@@ -154,6 +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"/>
@@ -228,7 +233,7 @@
 
 	<target name="makefulldist" depends="makedist">
 		<!-- the default keystore details might need to be edited here -->
-		<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+		<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 
 			<fileset dir="${packageDir}">
 				<include name="*.jar" />
@@ -412,7 +417,7 @@
 				<include name="*.jar"/>
 			</fileset>
 		</delete>
-		<jar destfile="${packageDir}/${outputJar}">
+		<jar destfile="${packageDir}/${outputJar}" index="true">
 			<manifest>
 				<attribute name="Main-Class" value="jalview.bin.Jalview" />
         <attribute name="Permissions" value="all-permissions" />
@@ -458,19 +463,21 @@
 		<mkdir dir="${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">
 		<copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
 		<copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
-		<jar destfile="in.jar">
+		<copy todir="${outputDir}/lang">
+			<fileset dir="${resourceDir}/lang"><include name="**.*"/></fileset></copy>
+		<jar destfile="in.jar" index="true">
 			<manifest>
 				<attribute name="Main-Class" value="jalview.bin.JalviewLite" />
-			  <!--				<attribute name="Permissions" value="sandbox" /> -->
+			  	<attribute name="Permissions" value="sandbox" /> 
         <!--<attribute name="Trusted-Lib" value="true" /> -->
 				<attribute name="Application-Name" value="JalviewLite Applet"/>
-				<attribute name="Codebase" value="*"/>
+				<attribute name="Codebase" value="www.jalview.org"/>
 			</manifest>
 			<fileset dir="${outputDir}">
 				<include name="com/**" />
@@ -479,6 +486,7 @@
 				<include name=".build_properties" />
 				<include name="images/idwidth.gif" />
 				<include name="images/link.gif" />
+				<include name="lang/**" />
 			</fileset>
 		</jar>
 	</target>
@@ -500,11 +508,17 @@
 			<injar file="in.jar" />
 			<outjar file="${jalviewLiteJar}" />
 			<libraryjar refid="obfuscateDeps.path" />
+			<dontwarn/>
 			<keep access="public" type="class" name="jalview.bin.JalviewLite">
 				<field access="public" />
 				<method access="public" />
 				<constructor access="public" />
 			</keep>
+			<keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+				<field access="public" />
+				<method access="public" />
+				<constructor access="public" />
+			</keep>
 			<!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar