JAL-1780 JAL-653 organise imports

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index 3705821..c079df9 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -62,8 +62,12 @@
         <include name="*.jar"/>
       </fileset> -->
       </path>
+       
     <!-- Jalview Version String displayed by application on startup and used to check for updates -->
     <property name="JALVIEW_VERSION" value="DEVELOPMENT" />
+       
+    <property name="INSTALLATION" value="Source" />
+       
     <!-- 2.4 (VAMSAS)" -->
     <!-- Include debugging information in javac true or false -->
     <property name="javac.debug" value="true" />
@@ -107,13 +111,16 @@
     <!-- Jalview Applet JMol Jar Dependency -->
     <property name="jmolJar" value="JmolApplet-12.2.4.jar" />
     <property name="varnaJar" value="VARNAv3-91.jar" />
+    <property name="jsoup" value="jsoup-1.8.1.jar" />
+    <property name="jsonSimple" value="json_simple-1.1.jar" />
+    <property name="javaJson" value="java-json.jar" />
     <property name="jalviewLiteJar" value="jalviewApplet.jar" />
     <!-- switch to indicate if we should obfuscate jalviewLite -->
     <!-- <property name="donotobfuscate" value="true"/> -->
     <!-- switch to exclude associations from generated jnlp files -->
     <!-- <property name="nojnlpfileassocs" value="true"/> -->
 
-    <!-- Jalview Web Service Clients - see the comments in 'buildextexcclients' for details -->
+    <!-- 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" />
@@ -161,6 +168,10 @@
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
       <pathelement location="lib/${varnaJar}" />
+      <pathelement location="lib/${jsoup}" />
+      <pathelement location="lib/${jsonSimple}" />
+      <pathelement location="lib/${javaJson}" />
+      
     </path>
     <!-- default location for outputting javadoc -->
     <property name="javadocDir" value="${packageDir}/javadoc"/>
@@ -175,8 +186,9 @@
     <properties file="${outputDir}/.build_properties">
       <header>
           ---Jalview Build Details---
-        </header>
+        </header>      
       <property name="VERSION" value="${JALVIEW_VERSION}" />
+      <property name="INSTALLATION" value="${INSTALLATION}" />
       <property name="BUILD_DATE" value="${build.date}" />
     </properties>
   </target>
@@ -344,9 +356,16 @@
             <include name="*.jar" />
             <include name="*_*.jar" />
             <exclude name="jalview.jar" />
+               <exclude name="*jnilib.jar"/>
           </fileset>
+       </resources>
+        <resources os="Mac OS X">
           <property name="jalview.version" value="${JALVIEW_VERSION}" />
+               <fileset dir="${packageDir}">
+                       <include name="*quaqua*.jnilib.jar"/>
+               </fileset>
         </resources>
+       
         <application_desc main_class="jalview.bin.Jalview">
         </application_desc>
         <security>
@@ -481,7 +500,7 @@
   <mkdir dir="${outputDir}" />
   <javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
                        classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
-                       excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/io/**,jalview/ext/paradise/**" />
+                       excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -520,6 +539,8 @@
   <path id="obfuscateDeps.path">
     <pathelement location="${applet.jre.tools}" />
     <pathelement location="appletlib/${jmolJar}" />
+    <pathelement location="appletlib/${jsonSimple}" />
+    <pathelement location="appletlib/${javaJson}" />
   </path>
   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 
@@ -621,6 +642,8 @@
     </fileset>
   </copy>
   <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${javaJson}"/>
+  <jar update="true" index="true" jarfile="${packageDir}/examples/${jsonSimple}"/>
   <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
     <manifest>
       <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
@@ -701,21 +724,37 @@
   <!-- create differently privileged artefacts -->
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/u_${javaJson}" overwrite="true"/>
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/u_${jsonSimple}" overwrite="true"/>
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/ap_${javaJson}"/>
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/ap_${jsonSimple}"/>
   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
   <ap_applet.jar jarfile="${packageDir}/examples/ap_${jmolJar}" />
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${javaJson}" />
+  <ap_applet.jar jarfile="${packageDir}/examples/ap_${jsonSimple}" />
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/tl_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/tl_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/tl_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/tl_${jsonSimple}" />
   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jalviewLiteJar}" />
   <tl_applet.jar jarfile="${packageDir}/examples/tl_${jmolJar}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${javaJson}" />
+  <tl_applet.jar jarfile="${packageDir}/examples/tl_${jsonSimple}" />
   <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/to_${jalviewLiteJar}" />
   <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/to_${jmolJar}" />
+  <copy file="${packageDir}/examples/${javaJson}" tofile="${packageDir}/examples/to_${javaJson}" />
+  <copy file="${packageDir}/examples/${jsonSimple}" tofile="${packageDir}/examples/to_${jsonSimple}" />
   <to_applet.jar jarfile="${packageDir}/examples/to_${jalviewLiteJar}" />
   <to_applet.jar jarfile="${packageDir}/examples/to_${jmolJar}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${javaJson}" />
+  <to_applet.jar jarfile="${packageDir}/examples/to_${jsonSimple}" />
   <!-- finally, create manifest for original jars -->
   <applet.jar jarfile="${packageDir}/examples/${jalviewLiteJar}" />
   <applet.jar jarfile="${packageDir}/examples/${jmolJar}" />
+  <applet.jar jarfile="${packageDir}/examples/${javaJson}" />
+  <applet.jar jarfile="${packageDir}/examples/${jsonSimple}" />
 
   <!-- todo - write examples/downloads for alternate versions of the applet -->
   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
@@ -724,16 +763,38 @@
       <exclude name="u_*.jar"/>
       <include name="${jalviewLiteJar}" />
       <include name="${jmolJar}" />
+      <include name="${javaJson}" />
+      <include name="${jsonSimple}" />
       <include name="to_${jalviewLiteJar}" />
       <include name="to_${jmolJar}" />
+      <include name="to_${javaJson}" />
+      <include name="to_${jsonSimple}" />
       <include name="tl_${jalviewLiteJar}" />
       <include name="tl_${jmolJar}" />
+      <include name="tl_${javaJson}" />
+      <include name="tl_${jsonSimple}" />
       <include name="ap_${jalviewLiteJar}" />
       <include name="ap_${jmolJar}" />
+      <include name="ap_${javaJson}" />
+      <include name="ap_${jsonSimple}" />
     </fileset>
   </signjar>
   <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
   <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
+       <!-- finally, replace any launchApp servlet tags with a version specification -->
+       <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}&quot;">
+               <replacetoken><![CDATA[http://www.jalview.org/services/launchApp"]]></replacetoken>
+               <fileset dir="${packageDir}/examples">
+                       <include name="**/*.html"/>
+               </fileset>
+       </replace>
+       <replace value="http://www.jalview.org/services/launchApp?version=${JALVIEW_VERSION}'">
+               <replacetoken><![CDATA[http://www.jalview.org/services/launchApp']]></replacetoken>
+               <fileset dir="${packageDir}/examples">
+                       <include name="**/*.html"/>
+               </fileset>
+       </replace>
+
 </target>
 <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
   <javadoc destdir="${javadocDir}">