X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=57cd9d2c55c7731e20704ef1e0466642130ce6d7;hb=de6f16e01ddb7846dc67f8f7a71ed6862d7aa986;hp=9f5682009339d251a25c90883fe701235b4b26b7;hpb=16359e92bebc20edafc4958b7b580c8ceedd4d37;p=jalview.git

diff --git a/build.xml b/build.xml
index 9f56820..57cd9d2 100755
--- a/build.xml
+++ b/build.xml
@@ -188,9 +188,9 @@
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
       <pathelement location="lib/${varnaJar}" />
-      <pathelement location="lib/${jsoup}" />
-      <pathelement location="lib/${jsonSimple}" />
-      <pathelement location="lib/${javaJson}" />
+      <pathelement location="appletlib/${jsoup}" />
+      <pathelement location="appletlib/${jsonSimple}" />
+      <pathelement location="appletlib/${javaJson}" />
 
     </path>
     <!-- default location for outputting javadoc -->
@@ -421,13 +421,11 @@
         </information>
         <resources>
           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+          <jar main="true" href="jalview.jar"/>
           <fileset dir="${packageDir}">
-            <include name="jalview.jar" />
-          </fileset>
-          <fileset dir="${packageDir}">
+            <exclude name="jalview.jar" />
             <include name="*.jar" />
             <include name="*_*.jar" />
-            <exclude name="jalview.jar" />
             <exclude name="*jnilib.jar" />
           </fileset>
           <property name="jalview.version" value="${JALVIEW_VERSION}" />
@@ -570,7 +568,7 @@
 
 <target name="compileApplet" depends="init,clean">
   <mkdir dir="${outputDir}" />
-  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**" />
+  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -609,15 +607,20 @@
   <path id="obfuscateDeps.path">
     <pathelement location="${applet.jre.tools}" />
     <pathelement location="appletlib/${jmolJar}" />
+    <pathelement location="lib/${varnaJar}" />
+    <pathelement location="appletlib/${jsoup}" />
     <pathelement location="appletlib/${jsonSimple}" />
     <pathelement location="appletlib/${javaJson}" />
+ 	<fileset dir="${java.home}/lib">
+        <include name="plugin.jar" />
+    </fileset>
   </path>
   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 
-  <proguard>
-    <injar file="in.jar" />
-    <outjar file="${jalviewLiteJar}" />
-    <libraryjar refid="obfuscateDeps.path" />
+  <proguard verbose="true" >
+    <injar file="in.jar" />    
+    <outjar file="${jalviewLiteJar}" />    
+    <libraryjar refid="obfuscateDeps.path" />    
     <dontwarn />
     <keep access="public" type="class" name="jalview.bin.JalviewLite">
       <field access="public" />
@@ -629,6 +632,31 @@
       <method access="public" />
       <constructor access="public" />
     </keep>
+
+    <keep name="jalview.json.binding**">
+      <constructor/>
+      <method name="*"/>
+    </keep>
+   
+    <keep access="public" type="class" name="MCview.PDBfile">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+    <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+    
+    <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+    
+    
     <!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
@@ -683,6 +711,8 @@
       <include name="${resourceDir}/**/*" />
       <include name="${helpDir}/**/*" />
       <include name="appletlib/${jmolJar}" />
+      <include name="appletlib/${jsonSimple}" />
+      <include name="appletlib/${javaJson}" />
       <exclude name="**/*locales" />
       <exclude name="*locales/**" />
       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
@@ -723,23 +753,7 @@
       <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}" />
     </manifest>
   </jar>
-</target>
-<target name="-signexdirsnotsa" depends="prepubapplet_1" unless="timestamp">
-  <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
-    <fileset dir="${packageDir}/examples">
-      <include name="*.jar" />
-    </fileset>
-  </signjar>
-</target>
-<target name="-signexdirstsa" depends="prepubapplet_1" if="timestamp">
-  <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
-    <fileset dir="${packageDir}/examples">
-      <include name="*.jar" />
-    </fileset>
-  </signjar>
-</target>
 
-<target name="prepubapplet_2" depends="-signexdirsnotsa,-signexdirstsa">
   <presetdef name="ap_applet.jar">
     <!-- build a signed applet with 'all-permissions' - 
 			  Needs 'param name="permissions' value="all-permissions"' in applet tag
@@ -841,8 +855,8 @@
   <!-- todo - write examples/downloads for alternate versions of the applet 
     probably don't need to do this now since we don't have alternate versions anymore !-->
 </target>
-<target name="-signapplet" depends="prepubapplet_2">
-  <fileset name="signappletjarset" dir="${packageDir}/examples">
+<target name="-signapplet" depends="prepubapplet_1">
+  <fileset id="signappletjarset" dir="${packageDir}/examples">
     <exclude name="u_*.jar" />
     <include name="${jalviewLiteJar}" />
     <include name="${jmolJar}" />
@@ -880,6 +894,8 @@
 
   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+  <copy file="appletlib/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true" />
+  <copy file="appletlib/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true" />
   <!-- finally, replace any launchApp servlet tags with a version specification -->
   <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
     <replacetoken>