X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=7feacfb77b17fec1957f58172d1f38c7e1ada43f;hb=2f0ce1f46c5bb22e1db18c27e68b09516958c84d;hp=db7e8b5d02f2721c56550f8ae04acd9f64186755;hpb=8da0312bce8ea058c921bc613fef9a66f3c62a07;p=jalview.git

diff --git a/build.xml b/build.xml
index db7e8b5..7feacfb 100755
--- a/build.xml
+++ b/build.xml
@@ -27,7 +27,9 @@
     <echo message="build - compiles all necessary files for Application" />
     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
-    <echo message="              this needs a keystore and key. Add -Dtimestamp to timestamp signed jars"/>
+    <echo message="              this needs a keystore and key."/>
+    <echo message="              Add -Dtimestamp to timestamp signed jars"/>
+    <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
     <echo message="              See docs/building.html for more information." />
     <echo message="compileApplet - compiles all necessary files for Applet" />
     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
@@ -88,6 +90,9 @@
     <!-- locally valid proxy for signing with external time server -->
     <property name="proxyPort" value="80"/>
     <property name="proxyHost" value="sqid"/>
+    <!-- key sign/digest algorithms -->
+    <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
+    <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
 
     <!-- default TestNG groups to run -->
     <property name="testng-groups" value="Functional" />
@@ -188,9 +193,9 @@
       </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 -->
@@ -297,7 +302,7 @@
     </testng>
   </target>
 
-  <target name="buildindices" depends="init, prepare" unless="help.uptodate">
+  <target name="buildindices" depends="init, prepare,linkcheck" unless="help.uptodate">
     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
       <arg line="html" />
     </java>
@@ -374,7 +379,7 @@
   </target>
 
   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
-    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA"
+    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
       <fileset dir="${packageDir}">
         <include name="*.jar" />
@@ -382,7 +387,7 @@
     </signjar>
   </target>
   <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
-    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
+    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
       <fileset dir="${packageDir}">
         <include name="*.jar" />
       </fileset>
@@ -421,13 +426,11 @@
         </information>
         <resources>
           <j2se version="${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 +573,7 @@
 
 <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">
@@ -609,12 +612,17 @@
   <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>
+  <proguard verbose="true" >
     <injar file="in.jar" />
     <outjar file="${jalviewLiteJar}" />
     <libraryjar refid="obfuscateDeps.path" />
@@ -629,6 +637,31 @@
       <method access="public" />
       <constructor access="public" />
     </keep>
+
+    <keep name="jalview.json.binding**">
+      <constructor/>
+      <method name="*"/>
+    </keep>
+
+    <keep access="public" type="class" name="MCview.PDBfile">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+    <keep access="public" type="class" name="jalview.ws.jws1.Annotate3D">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+    <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
+      <field access="public" />
+      <method access="public" />
+      <constructor access="public" />
+    </keep>
+
+
     <!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
@@ -683,6 +716,8 @@
       <include name="${resourceDir}/**/*" />
       <include name="${helpDir}/**/*" />
       <include name="appletlib/${jmolJar}" />
+      <include name="appletlib/${jsonSimple}" />
+      <include name="appletlib/${javaJson}" />
       <exclude name="**/*locales" />
       <exclude name="*locales/**" />
       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
@@ -723,23 +758,7 @@
       <attribute name="Caller-Allowable-Codebase" value="${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
@@ -841,7 +860,7 @@
   <!-- 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">
+<target name="-signapplet" depends="prepubapplet_1">
   <fileset id="signappletjarset" dir="${packageDir}/examples">
     <exclude name="u_*.jar" />
     <include name="${jalviewLiteJar}" />
@@ -880,6 +899,8 @@
 
   <!-- 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>
@@ -905,4 +926,12 @@
     </packageset>
   </javadoc>
 </target>
+<target name="linkcheck">
+  <!-- finally, publish the help files -->
+  <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
+  <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
+    <arg file="${helpDir}"/>
+    <arg value="-nointernet"/>
+  </java>
+</target>
 </project>