X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=31419c8ad24a78cb7661b9923f8c4c523f6bf2c9;hb=793aa31ecc707520037b7380a7b39a9db3ec7d20;hp=d11047e98fdb6880791b63bf49cdd575d1e3b57a;hpb=dd1aed40cf00d837d1643918c380546a1dd2d39a;p=jalview.git

diff --git a/build.xml b/build.xml
index d11047e..31419c8 100755
--- a/build.xml
+++ b/build.xml
@@ -1,20 +1,21 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 <project name="jalviewX" default="usage" basedir=".">
 	<!-- we use jalopy to format our sources -->
@@ -93,7 +94,8 @@
 		<!-- 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+"/>
 
     <!-- Permissions for running Java applets and applications. -->
     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
@@ -114,6 +116,7 @@
 		<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"/> -->
@@ -143,6 +146,7 @@
 				<!-- 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>
@@ -164,6 +168,8 @@
 				<include name="plugin.jar"/>
 			</fileset>
 			<pathelement location="appletlib/${jmolJar}" />
+      <pathelement location="lib/${varnaJar}" />
+
 		</path>
     <!-- default location for outputting javadoc -->
     <property name="javadocDir" value="${packageDir}/javadoc"/>
@@ -294,6 +300,7 @@
 					<!--
 				<association mime-type="application-x/ext-file" extensions="fa"/>
         <association mime-type="application-x/ext-file" extensions="fasta"/>
+        <association mime-type="application-x/ext-file" extensions="mfa"/>
         <association mime-type="application-x/ext-file" extensions="fastq"/>
         <association mime-type="application-x/ext-file" extensions="blc"/>
         <association mime-type="application-x/ext-file" extensions="msf"/>
@@ -451,7 +458,7 @@
 		<mkdir dir="${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">
@@ -667,7 +674,7 @@
     </presetdef>
     <!-- create differently privileged artefacts -->
     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
-    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}"/>
+    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
@@ -688,6 +695,7 @@
     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 
       <fileset dir="${packageDir}/examples">
+        <exclude name="u_*.jar"/>
         <include name="${jalviewLiteJar}" />
         <include name="${jmolJar}" />
         <include name="to_${jalviewLiteJar}" />
@@ -698,12 +706,13 @@
         <include name="ap_${jmolJar}" />
       </fileset>
     </signjar>
-	</target>
-	<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
-	 <javadoc destdir="${javadocDir}">
-	 	<packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
-	 	</packageset>
-	 	</javadoc>
-	</target>
-	
+    <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+    <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+  </target>
+  <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+    <javadoc destdir="${javadocDir}">
+      <packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+      </packageset>
+    </javadoc>
+  </target>
 </project>