X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=dd903732398f10c1fbff251f4a01309f2cab8e9c;hb=a414d1d72a2dd50a6e00ce02a2cca533f0d4a12a;hp=f6fb5d7150ec6e3b7aa3d1cf1db6630f370e5efc;hpb=fab0afc9e1e7a5ca460f0cbd48545536f989a435;p=jalview.git

diff --git a/build.xml b/build.xml
index f6fb5d7..dd90373 100755
--- a/build.xml
+++ b/build.xml
@@ -148,6 +148,7 @@
     <property name="reportDir" value="test-reports" />
     <property name="testDir" value="test" />
     <property name="testOutputDir" value="tests" />
+  	<property name="cloverOutputDir" value="clover" if:set="clover.jar" />
     <!-- switch to indicate if we should obfuscate jalviewLite -->
     <!-- <property name="donotobfuscate" value="true"/> -->
     <!-- switch to exclude associations from generated jnlp files -->
@@ -272,6 +273,7 @@
         <include name="**/*.*" />
       </fileset>
     </copy>
+  	<mkdir dir="${cloverOutputDir}" if:set="clover.jar"/>
   </target>
 
   <target name="build" depends="prepare">
@@ -701,30 +703,50 @@
   <delete file="in.jar" />
 </target>
 
-<target name="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
-  <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
+<target name="jaxb-bindings" depends="init" description="Generates JAXB bindings for supported Jalview XML models (needs xjc on the path)">
   <delete>
-    <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+    <fileset dir="${sourceDir}/jalview/xml/binding/jalview">
       <include name="*.java" />
-      <include name="descriptors/*.java" />
     </fileset>
   </delete>
-  <castor-srcgen file="${schemaDir}/vamsas.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <castor-srcgen file="${schemaDir}/JalviewWsParamSet.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <castor-srcgen file="${schemaDir}/jalview.xsd" todir="${sourceDir}" package="jalview.schemabinding.version2" warnings="false" nodesc="false" verbose="true" properties="${schemaDir}/jalview.properties" />
-  <!-- 
-		now build the jalview.binding package with the old schema set
-		-->
+  <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="${sourceDir}/jalview/binding/">
-      <include name="**" />
+    <fileset dir="${sourceDir}/jalview/xml/binding/uniprot">
+      <include name="*.java" />
     </fileset>
   </delete>
-  <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-  <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
-  <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd" todir="${sourceDir}" package="jalview.binding" warnings="false" nodesc="true" verbose="true" properties="${schemaDir}/jalview.nodesc.properties" />
+
+  <exec executable="xjc">
+    <arg value="${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 -->
@@ -1014,8 +1036,7 @@
 
 </target>
 
-<target name="build-site" depends="init,prepare,compile-site,unzip-to-site">
-  <!-- closure compile -->
+<target name="build-site" depends="init,prepare,compile-site,unzip-to-site,make-j2s-cores">
   <!-- tarball -->
   <tar compression="gzip" destfile="site.tar.gz">
     <tarfileset dir="site" />
@@ -1118,4 +1139,8 @@
     </fileset>
   </unzip>
 </target>
+
+  <target name="make-j2s-cores" depends="">
+    <ant antfile="buildcore.xml" target="build-all-cores"/>
+  </target>
 </project>