JAL-715 - notify user of parsing problems for results from a service's URL

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index 60c442f..7d63c56 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -122,6 +122,9 @@
                                <include name="*.jar" />
                                <include name="**/*.jar" />
                        </fileset>
+                       <fileset dir="${java.home}/lib">
+                               <include name="plugin.jar"/>
+                       </fileset>
                        <fileset dir="appletlib">
                                <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
                                -->
@@ -131,18 +134,25 @@
                </path>
                <property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
                <!-- The Location of the java 1.1.8 jdk -->
-               <property name="java118.home" value="C:\Sun\jdk1.1.8" />
-               <property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-               <!-- jre for 1.4 version
-               <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+               <!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
                -->
+               <property name="java118.home" value="${java.home}" />
+                   <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
+               --><!-- jre for 1.4 version -->
+               <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+               
                <!-- the classpath for building the 1.1 applet -->
                <path id="jalviewlite.deps">
                        <fileset dir="${java118.home}">
                                <include name="lib/classes.zip" />
                        </fileset>
+                       <fileset dir="${java.home}/lib">
+                               <include name="plugin.jar"/>
+                       </fileset>
                        <pathelement location="appletlib/${jmolJar}" />
                </path>
+    <!-- default location for outputting javadoc -->
+    <property name="javadocDir" value="${packageDir}/javadoc"/>
        </target>
 
 
@@ -163,7 +173,7 @@
 
        <target name="clean" depends="init">
                <!-- not efficient yet. -->
-               <delete dir="${outputDir}" />
+               <delete dir="${outputDir}" includes="*,**/*"/>
        </target>
 
        <target name="distclean" depends="init, clean">
@@ -442,11 +452,13 @@
 
 
        <!-- Compile, package and obfuscate Jalview Applet -->
-       <target name="makeApplet" depends="obfuscate" />
+       <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 
        <target name="compileApplet" depends="init,clean">
                <mkdir dir="${outputDir}" />
-               <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpath="appletlib/${jmolJar}" includes="jalview/appletgui/**" excludes="ext/**,MCview/**,org/**,vamsas/**" />
+               <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
+                       classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
+                       excludes="ext/**,MCview/**,org/**,vamsas/**" />
        </target>
 
        <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -466,7 +478,7 @@
                        </fileset>
                </jar>
        </target>
-       <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
+       <target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
        </target>
        <target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
                <copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
@@ -532,6 +544,10 @@
                                <include name="jalview-jalopy.xml" />
                                <include name="JalviewApplet.jpx" />
                                <include name="JalviewX.jpx" />
+                               <include name="nbbuild.xml"/>
+                               <include name="nbproject/genfiles.properties"/>
+        <include name="nbproject/project.properties"/>
+        <include name="nbproject/project.xml"/>
                                <include name="${sourceDir}/*.java" />
                                <include name="${sourceDir}/**/*.java" />
                                <include name="${sourceDir}/**/*.cdr" />
@@ -549,7 +565,31 @@
                                <include name="${schemaDir}/**/*" />
                                <include name="utils/**/*" />
                                <include name="${docDir}/**/*" />
+                               <include name="examples/**/*" />
                        </tarfileset>
                </tar>
        </target>
+       <target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+         <copy todir="${packageDir}/examples">
+         <fileset dir="examples">
+               <include name="**/*"/>
+               <include name="javascript/*"/>
+      <include name="jmol/*"/>
+         </fileset>
+               <fileset dir=".">
+               <include name="jalviewApplet.jar"/>
+                       </fileset>
+               <fileset dir="appletlib">
+                     <include name="**/*"/>
+                       </fileset>
+         </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>