X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build-j11.xml;h=9f2761bf7881b704b7c78ec2b9461421bd4c0966;hb=6dcb8028ff88bbad2b032435b8e49ae1caeca3b6;hp=35d3926dc7e54e8ce4204288bd03a2ceee107bfb;hpb=4f6d92b81a8bedf3d74c81e02e0dbf6600829a60;p=jalview.git

diff --git a/build-j11.xml b/build-j11.xml
index 35d3926..9f2761b 100755
--- a/build-j11.xml
+++ b/build-j11.xml
@@ -44,6 +44,7 @@
     <echo message="note: compile and makeApplet optionally compile/obfuscate applet against a different Java version by specifying -Djava118.home=PathtoJDK/lib which is the lib directory in the JDK install that contains rt.jar " />
     <echo message="Useful -D flags: -Ddonotobfuscate will prevent applet obfuscation" />
     <echo message="Useful -D flags: -Dclover.jar to specify path to openclover for testng coverage report" />
+    <echo message="Useful -D flags: -Ddeprecation=true to add -Xlint:deprecation to the java compiler" />
   </target>
 
 
@@ -326,7 +327,11 @@
   <taskdef resource="testngtasks" classpath="utils/testnglibs/testng.jar" />
 
   <target name="testng" depends="buildTests">
-    <loadfile property="j11modules" srcFile="modules"/>
+    <loadfile property="j11modules" srcFile="modules">
+      <filterchain>
+        <striplinebreaks/>
+      </filterchain>
+    </loadfile>
     <echo message="j11libDir is '${j11libDir}'" />
     <echo message="j11modules is '${j11modules}'" />
     <testng outputDir="${reportDir}" haltOnFailure="false" groups="${testng-groups}" mode="testng"
@@ -336,7 +341,10 @@
         <pathelement location="${clover.jar}" if:set="clover.jar"/>
         <path refid="test.classpath" />
       </classpath>
-      <jvmarg value="--module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
+      <!--
+      <jvmarg value="DASH_DASH_module-path=${j11libDir}:${java.home}/jmods" if:set="java11"/>
+      -->
+      <jvmarg value="--module-path=${j11libDir}" if:set="java11"/>
       <jvmarg value="--add-modules=${j11modules}" if:set="java11"/>
       <jvmarg value="--add-modules=java.se.ee" if:set="java9"/>
       <jvmarg value="--illegal-access=warn" if:set="java9"/>
@@ -751,6 +759,50 @@
   <delete file="in.jar" />
 </target>
 
+<target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
+  <delete>
+    <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
+      <include name="*.java" />
+    </fileset>
+  </delete>
+  <exec executable="xjc">
+    <arg value="${schemaDir}/jalview.xsd"/>
+    <arg value="-d"/>
+    <arg value="${sourceDir}"/>
+    <arg value="-p"/>
+    <arg value="jalview.xml.binding.jalview"/>
+  </exec>
+  <delete>
+    <fileset dir="${sourceDir}/jalview/xml/binding/embl">
+      <include name="*.java" />
+    </fileset>
+  </delete>
+
+  <exec executable="xjc">
+    <arg value="${schemaDir}/embl.xsd"/>
+    <arg value="-d"/>
+    <arg value="${sourceDir}"/>
+    <arg value="-b"/>
+    <arg value="${schemaDir}/embl_bindings.xml"/>
+    <arg value="-p"/>
+    <arg value="jalview.xml.binding.embl"/>
+  </exec>
+
+  <delete>
+    <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
+      <include name="*.java" />
+    </fileset>
+  </delete>
+
+  <exec executable="xjc">
+    <arg value="${schemaDir}/uniprot.xsd"/>
+    <arg value="-d"/>
+    <arg value="${sourceDir}"/>
+    <arg value="-p"/>
+    <arg value="jalview.xml.binding.uniprot"/>
+  </exec>
+</target>
+
 <target name="sourcedist" description="create jalview source distribution" depends="init">
   <delete file="${source.dist.name}" />
   <!-- temporary copy of source to update timestamps -->
@@ -982,8 +1034,9 @@
 </target>
 
 <target name="signApplet" description="internal target to sign applet" depends="-signappletnotsa,-signapplettsa" />
+<target name="pubapplet" description="Dummy target to keep legacy Jalview build system happy. We don't actually publish the applet anymore."/>
 
-<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
+<target name="_pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet, signApplet">
 
   <!-- 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" />