X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=e9e6f6f3e70ab8e200d88e94ad0705516ac0dd52;hb=refs%2Fheads%2Fbugs%2FJAL-2780_JAL-2781_pdbnegativenums;hp=d8f12e094007f01b33086034ee34a430b54ee1d0;hpb=bfe4fa22a61ee595f0d6595a3ee625c966000c6d;p=jalview.git

diff --git a/build.xml b/build.xml
index d8f12e0..e9e6f6f 100755
--- a/build.xml
+++ b/build.xml
@@ -17,7 +17,9 @@
  * 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=".">
+<project name="jalviewX" default="usage" basedir="."
+ xmlns:if="ant:if"
+    xmlns:unless="ant:unless">
   <target name="help" depends="usage" />
   <target name="usage" depends="init">
     <echo message="~~~Jalview Ant build.xml Usage~~~~" />
@@ -96,6 +98,10 @@
 
     <!-- default TestNG groups to run -->
     <property name="testng-groups" value="Functional" />
+    <!-- Java 9 JVM args -->
+    <condition property="java9">
+      <equals arg1="${ant.java.version}" arg2="9"/>
+    </condition>
 
     <!-- Don't change anything below here unless you know what you are doing! -->
     <!-- Url path for WebStart in JNLP file -->
@@ -128,7 +134,7 @@
     <property name="packageDir" value="dist" />
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
-    <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
+    <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
     <property name="varnaJar" value="VARNAv3-93.jar" />
     <property name="jsoup" value="jsoup-1.8.1.jar" />
     <property name="jsonSimple" value="json_simple-1.1.jar" />
@@ -298,6 +304,8 @@
         <pathelement location="${testOutputDir}" />
         <path refid="test.classpath" />
       </classpath>
+      <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
+      <jvmarg value="--illegal-access=warn" if:set="java9"/>
       <classfileset dir="${testOutputDir}" includes="**/*.class" />
     </testng>
   </target>
@@ -425,19 +433,20 @@
           <offline_allowed />
         </information>
         <resources>
-          <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+          <j2se version="1.7+" />
           <jar main="true" href="jalview.jar"/>
           <fileset dir="${packageDir}">
             <exclude name="jalview.jar" />
             <include name="*.jar" />
             <include name="*_*.jar" />
-            <exclude name="*jnilib.jar" />
+            <exclude name="*quaqua*.jar" />
           </fileset>
           <property name="jalview.version" value="${JALVIEW_VERSION}" />
         </resources>
         <resources os="Mac OS X">
           <fileset dir="${packageDir}">
-            <include name="*quaqua*.jnilib.jar" />
+          	 <include name="quaqua-filechooser-only-8.0.jar"/>
+            <include name="*quaqua64*.jnilib.jar" />
           </fileset>
         </resources>
 
@@ -450,7 +459,11 @@
     </presetdef>
 
     <jnlpf toFile="${jnlpFile}" />
-
+    <!-- add the add-modules j2se attribute for java 9 -->
+    <replace file="${jnlpFile}" value="j2se version=&quot;1.7+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
+          <replacetoken>j2se version="1.7+"</replacetoken>
+           
+        </replace>
   </target>
 
   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
@@ -697,8 +710,13 @@
 </target>
 <target name="sourcedist" description="create jalview source distribution" depends="init">
   <delete file="${source.dist.name}" />
-  <tar destfile="${source.dist.name}" compression="gzip">
-    <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+  <!-- temporary copy of source to update timestamps -->
+  <copy todir="_sourcedist">
+    <fileset dir=".">
+      <exclude name=".*" />
+      <exclude name="**/.*" />
+      <exclude name="*.class" />
+      <exclude name="**/*.class" />
       <include name="LICENSE" />
       <include name="README" />
       <include name="build.xml" />
@@ -723,14 +741,41 @@
       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
       <exclude name="utils/InstallAnywhere/**Build*/**" />
       <exclude name="utils/InstallAnywhere/**Build*/**" />
+      <exclude name="utils/InstallAnywhere/.build*.*/**" />
       <exclude name="utils/InstallAnywhere/**locale*" />
       <exclude name="utils/InstallAnywhere/**locale*/**" />
+      <exclude name="utils/InstallAnywhere/**locale*/**" />
       <include name="${schemaDir}/**/*" />
       <include name="utils/**/*" />
       <include name="${docDir}/**/*" />
       <include name="examples/**/*" />
+    </fileset>
+  </copy>
+
+  <tstamp prefix="build">
+    <format property="year" pattern="yyyy" />
+  </tstamp>
+  <!-- each replacetoken CDATA body must be on one line - 
+       otherwise the pattern doesn't match -->
+  <replace value="${JALVIEW_VERSION}">
+    <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+  <replace dir="_sourcedist" value="${build.year}">
+    <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+
+  <tar destfile="${source.dist.name}" compression="gzip">
+    <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
     </tarfileset>
   </tar>
+
+  <delete dir="_sourcedist" />
 </target>
 <target name="prepubapplet_1" depends="makeApplet">
   <copy todir="${packageDir}/examples">