JAL-2679 update query id to actual case of retrieved gene

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index 7235950..4931cfb 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -128,7 +128,7 @@
     <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" />
@@ -425,7 +425,7 @@
           <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" />
@@ -450,7 +450,11 @@
     </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">
@@ -700,6 +704,10 @@
   <!-- 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" />
@@ -724,8 +732,10 @@
       <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}/**/*" />
@@ -736,18 +746,16 @@
   <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>
+    <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
     <fileset dir="_sourcedist">
       <include name="**/*" />
     </fileset>
   </replace>
   <replace dir="_sourcedist" value="${build.year}">
-    <replacetoken>
-      <![CDATA[$$Year-Rel$$]]>
-    </replacetoken>
+    <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
     <fileset dir="_sourcedist">
       <include name="**/*" />
     </fileset>