X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=7d63c5689060e6c5625bf92611bf59a20f2852e0;hb=803236e8e3ce17adf10d0a59617c9e42463535cf;hp=5b1066f63b20f1a090c8593eeeacb056c7cd092c;hpb=5aad8085fbd06d2e0f6a97d71e8ed58d0e02e6db;p=jalview.git

diff --git a/build.xml b/build.xml
index 5b1066f..7d63c56 100755
--- a/build.xml
+++ b/build.xml
@@ -151,6 +151,8 @@
 			</fileset>
 			<pathelement location="appletlib/${jmolJar}" />
 		</path>
+    <!-- default location for outputting javadoc -->
+    <property name="javadocDir" value="${packageDir}/javadoc"/>
 	</target>
 
 
@@ -171,7 +173,7 @@
 
 	<target name="clean" depends="init">
 		<!-- not efficient yet. -->
-		<delete dir="${outputDir}" />
+		<delete dir="${outputDir}" includes="*,**/*"/>
 	</target>
 
 	<target name="distclean" depends="init, clean">
@@ -571,6 +573,8 @@
 	  <copy todir="${packageDir}/examples">
 	  <fileset dir="examples">
 	  	<include name="**/*"/>
+	  	<include name="javascript/*"/>
+      <include name="jmol/*"/>
 	  </fileset>
 	  	<fileset dir=".">
 	  	<include name="jalviewApplet.jar"/>
@@ -581,4 +585,11 @@
 	  </copy>
 	  		
 	</target>
+	<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+	 <javadoc destdir="${javadocDir}">
+	 	<packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+	 	</packageset>
+	 	</javadoc>
+	</target>
+	
 </project>