JAL-3206 avoid divide by zero when threshold is graphMin / graphMax

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index 957684b..9cd966c 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -43,6 +43,7 @@
     <echo message="See docs/building.html and the comments in build file for other targets." />
     <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" />
   </target>
 
 
@@ -476,8 +477,7 @@
     <!-- add the add-modules j2se attribute for java 9 -->
     <replace file="${jnlpFile}" value="j2se version=&quot;1.8+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
           <replacetoken>j2se version="1.8+"</replacetoken>
-           
-        </replace>
+    </replace>
   </target>
 
   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
@@ -699,30 +699,50 @@
   <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="${sourceDir}/jalview/xml/binding/jalview">
+      <include name="*.java" />
+    </fileset>
+  </delete>
+  <exec executable="xjc">
+    <arg value="${schemaDir}/jalview.xsd"/>
+    <arg value="-d"/>
+    <arg value="${sourceDir}"/>
+    <arg value="-p"/>
+    <arg value="jalview.xml.binding.jalview"/>
+  </exec>
   <delete>
-    <fileset dir="${sourceDir}/jalview/schemabinding/version2">
+    <fileset dir="${sourceDir}/jalview/xml/binding/embl">
       <include name="*.java" />
-      <include name="descriptors/*.java" />
     </fileset>
   </delete>
-  <castor-srcgen file="${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}/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 -->