removed dross, added a safety check to buildextclients and added references to docs...

diff --git a/build.xml b/build.xml
index 4c5c503..4985f91 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -10,16 +10,19 @@
   </classpath>
 </taskdef>
 
+   <target name="help" depends="usage"/>
    <target name="usage">
      <echo message="~~~Jalview Ant build.xml Usage~~~~"/>
-     <echo message="Targets available:"/>
+     <echo message="Targets include:"/>
      <echo message="usage - default target, displays this message"/>
      <echo message="buildindices - generates JavaHelpSearch from the help files"/>
      <echo message="build - compiles all necessary files for Application"/>
      <echo message="makedist - compiles and places all necessary jar files into directory dist"/>
      <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution"/>
+     <echo message="              this needs a keystore and key. See docs/building.html for more information."/>
      <echo message="compileApplet - compiles all necessary files for Applet"/>
      <echo message="makeApplet - compiles, then packages and obfuscates the Applet"/>
+     <echo message="See docs/building.html and the comments in build file for other targets."/>
    </target>
 
 
@@ -49,9 +52,12 @@
           <include name="*.jar"/>
         </fileset> -->
       </path>
-
+      <!-- Jalview Version String displayed by application on startup and used to check for updates -->
       <property name="JALVIEW_VERSION" value="ANNOTATION_TEST"/>
-      <property name="" value=""/>
+      <!-- Don't change anything below here unless you know what you are doing! -->
+      <!-- Url path for WebStart in JNLP file -->
+      <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
+      <!-- build directory configuration -->
       <property name="libDir" value="lib"/>
       <property name="resourceDir" value="resources"/>
       <property name="helpDir" value="help"/>
@@ -60,16 +66,15 @@
       <property name="outputDir" value="classes" />
       <property name="packageDir" value="dist" />
       <property name="outputJar" value="jalview.jar" />
+      <!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
       <property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
       <property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
       <property name="wsdl.MsaWS" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/MuscleWS?wsdl" />
       <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
-      <property name="wsdl.MsaWS2" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/ClustalWS?wsdl" />
-        <property name="WSInterf" value="MsaWS" />
-      <property name="WebStartLocation" value="http://www.jalview.org/webstart"/>
+      <property name="WSInterf" value="MsaWS" />
       <property name="wsdl.Namespace" value="vamsas" />
       <property name="wsdl.ClientNS" value="ext.vamsas" />
-
+      <!-- the class path for building the application -->
       <path id="build.classpath">
         <fileset dir="utils">
           <include name="*.jar"/>
@@ -79,18 +84,7 @@
           <include name="*.jar"/>
           <include name="**/*.jar"/>
         </fileset>
-<!--        <fileset dir="old_lib_signed">
-<include name="lib_axis.jar"/>
-
-        </fileset>-->
       </path>
-      <!-->    <uptodate property="help.uptodate"
-      targetfile="${helpDir}/helpIndex.xml">
-      <srcfiles
-                 dir="${helpDir}"
-                 includes="**/*.html" />
-               </uptodate>
-      -->
     </target>
 
 
@@ -239,6 +233,18 @@
     </target>
 
     <target name="buildextclients" depends="init">
+      <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)"
+      validargs="Y,y,n,N" defaultvalue="N"
+      addproperty="doextbuild.response"/>
+      <condition property="dontextbuild">
+        <equals arg1="n" arg2="${doextbuild.response}"/>
+      </condition>
+      <condition property="dontextbuild">
+        <equals arg1="N" arg2="${doextbuild.response}"/>
+      </condition>
+      <fail if="dontextbuild">
+        Build External Client Code process aborted by user. Jalview source is unchanged.
+      </fail>
 <!-- Currently, this doesn't happen automatically.
      1. Run WSDL2Java as below, which generates an ext.vamsas +
      vamsas.<datapackages> fileset.
@@ -250,7 +256,6 @@
 
 -->
       <path id="axisbuild">
-        <!--        <path refid="axis.classpath"/> -->
         <path refid="build.classpath"/>
       </path>
       <taskdef resource="axis-tasks.properties" classpathref="axisbuild"/>
@@ -307,10 +312,6 @@
   </target>
 
 
-
-  <target name="package" depends="init, build">
-
-  </target>
   <!-- jalopy code reformatter -->
   <target name="sourcescrub" depends="init,build">
     <jalopy destdir="jsrc" classpathref="run.classpath"