JAL-2663 flag and filter to exclude non-standard amino acids from submission

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index 1d4878b..c965bc9 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" />
@@ -426,6 +426,7 @@
         </information>
         <resources>
           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+          <j2se version="9+" initial_heap_size="${inih}" max_heap_size="${maxh}" java-vm-args="--add-modules java.rmi,java.xml,java.xml.bind,java.xml.ws"/>
           <jar main="true" href="jalview.jar"/>
           <fileset dir="${packageDir}">
             <exclude name="jalview.jar" />
@@ -700,6 +701,10 @@
   <!-- 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 +729,10 @@
       <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}/**/*" />