Merge branch 'feature/JAL-3063JAXB' into feature/JAL-3063jaxbNoCastor

diff --cc .ant-targets-build.xml
Simple merge

diff --cc build.xml
index 0415735,bed6d68..9cd966c
--- 1/build.xml
--- 2/build.xml
+++ b/build.xml
@@@ -699,6 -699,74 +699,50 @@@
    <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="castorbinding" depends="init" description="Generate Java bindings to supported Jalview XML models.">
 -  <taskdef name="castor-srcgen" classname="org.castor.anttask.CastorCodeGenTask" classpathref="build.classpath" />
 -  <delete>
 -    <fileset dir="${sourceDir}/jalview/schemabinding/version2">
 -      <include name="*.java" />
 -      <include name="descriptors/*.java" />
 -    </fileset>
 -  </delete>
 -  <castor-srcgen file="${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="${schemaDir}/jalview.properties" />
 -  <!-- 
 -              now build the jalview.binding package with the old schema set
 -              -->
 -  <delete>
 -    <fileset dir="${sourceDir}/jalview/binding/">
 -      <include name="**" />
 -    </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="${schemaDir}/jalview.nodesc.properties" />
 -</target>
  <target name="sourcedist" description="create jalview source distribution" depends="init">
    <delete file="${source.dist.name}" />
    <!-- temporary copy of source to update timestamps -->