X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=0869a7f1a9a397f49e2bae31df8190b7f168011d;hb=df7cccecdefdc618ba9a22760855db1c5bc50329;hp=990cbe6bbb6f35ca55818216286115e78d916bd4;hpb=23c2823b66abf031af741f12f718e4e72b9bb8f5;p=jalview.git

diff --git a/build.xml b/build.xml
index 990cbe6..0869a7f 100755
--- a/build.xml
+++ b/build.xml
@@ -1,20 +1,21 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
 -->
 <project name="jalviewX" default="usage" basedir=".">
   <!-- we use jalopy to format our sources -->
@@ -91,9 +92,9 @@
     <!-- Url path for WebStart in JNLP file -->
     <property name="WebStartLocation" value="http://www.jalview.org/webstart" />
     <!-- Webstart Image - looked for in resources/images -->
-    <property name="WebStartImage" value="JalviewLogo_big.png" />
+    <property name="WebStartImage" value="JalviewLogo_big.png"/>
     <!-- J2SE version needed for webstart launch -->
-    <property name="j2sev" value="1.6+" />
+    <property name="j2sev" value="1.6+"/>
 
     <!-- Permissions for running Java applets and applications. -->
     <!-- Defaults are those suitable for deploying jalview webstart www.jalview.org -->
@@ -137,7 +138,7 @@
         <include name="**/*.jar" />
       </fileset>
       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar" />
+        <include name="plugin.jar"/>
       </fileset>
       <fileset dir="appletlib">
         <!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
@@ -154,7 +155,7 @@
     <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
 		-->
     <!-- jre for 1.4 version -->
-    <property name="applet.jre.tools" value="${java.home}/lib/rt.jar" />
+    <property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
 
     <!-- the classpath for building the 1.1 applet -->
     <path id="jalviewlite.deps">
@@ -162,12 +163,12 @@
         <include name="lib/classes.zip" />
       </fileset>
       <fileset dir="${java.home}/lib">
-        <include name="plugin.jar" />
+        <include name="plugin.jar"/>
       </fileset>
       <pathelement location="appletlib/${jmolJar}" />
     </path>
     <!-- default location for outputting javadoc -->
-    <property name="javadocDir" value="${packageDir}/javadoc" />
+    <property name="javadocDir" value="${packageDir}/javadoc"/>
   </target>
 
 
@@ -188,7 +189,7 @@
 
   <target name="clean" depends="init">
     <!-- not efficient yet. -->
-    <delete dir="${outputDir}" includes="*,**/*" />
+    <delete dir="${outputDir}" includes="*,**/*"/>
   </target>
 
   <target name="distclean" depends="init, clean">
@@ -238,10 +239,9 @@
   </target>
 
   <target name="makefulldist" depends="makedist">
-
     <copy todir="${packageDir}">
       <fileset dir="${resourceDir}/images">
-        <include name="${WebStartImage}" />
+        <include name="${WebStartImage}"/>
       </fileset>
     </copy>
 
@@ -249,43 +249,43 @@
 
     <!-- create a dummy jar which will eventually contain the jnlp template -->
     <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
-          <fileset dir="${packageDir}">
-            <include name="jalview.jar"/>
-          </fileset>
+      <fileset dir="${packageDir}">
+        <include name="jalview.jar" />
+      </fileset>
+    </jar>
+
+    <mkdir dir="${packageDir}/JNLP-INF"/>
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
+      <param name="inih" value="*" />
+      <param name="maxh" value="*"/>
+    </antcall>
+
+    <jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
+      <fileset dir="${packageDir}">
+        <include name="JNLP-INF"/>
+      </fileset>
     </jar>
-  	
-  	<mkdir dir="${packageDir}/JNLP-INF"/>
+
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
+      <param name="inih" value="10M" />
+      <param name="maxh" value="256M"/>
+    </antcall>
+
     <antcall target="writejnlpf">
-       <param name="jnlpFile" value="${packageDir}/JNLP-INF/APPLICATION-TEMPLATE.JNLP"/>
-       <param name="inih" value="*" />
-       <param name="maxh" value="*"/>
+      <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
+      <param name="inih" value="128M" />
+      <param name="maxh" value="512M"/>
     </antcall>
-          	
-  	<jar destfile="${packageDir}/jalview_jnlp_vm.jar" index="true">
-  	      <fileset dir="${packageDir}">
-  	      	<include name="JNLP-INF"/>
-  	      </fileset>
-  	</jar>
-    
-  	<antcall target="writejnlpf">
-  		<param name="jnlpFile" value="${packageDir}/jalview.jnlp"/>
-  		<param name="inih" value="10M" />
-  	  <param name="maxh" value="256M"/>
-  	</antcall>
-  	
-  	<antcall target="writejnlpf">
-  	  <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp"/>
-  	  <param name="inih" value="128M" />
-  		<param name="maxh" value="512M"/>
-  	</antcall>
-  	    
-  	<antcall target="writejnlpf">
-  	  <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
-  	  <param name="inih" value="256M" />
-  	  <param name="maxh" value="1024M"/>
-  	</antcall>
-  	
-  	<!-- finally, need to postprocess to add in associations at end of 'information' element 
+
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp"/>
+      <param name="inih" value="256M" />
+      <param name="maxh" value="1024M"/>
+    </antcall>
+
+    <!-- finally, need to postprocess to add in associations at end of 'information' element 
 			
 			<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
 		
@@ -293,9 +293,10 @@
 			
 			
 			-->
-    <!--
+					<!--
 				<association mime-type="application-x/ext-file" extensions="fa"/>
         <association mime-type="application-x/ext-file" extensions="fasta"/>
+        <association mime-type="application-x/ext-file" extensions="mfa"/>
         <association mime-type="application-x/ext-file" extensions="fastq"/>
         <association mime-type="application-x/ext-file" extensions="blc"/>
         <association mime-type="application-x/ext-file" extensions="msf"/>
@@ -308,9 +309,9 @@
     <!-- and sign the jars -->
     <!-- the default keystore details might need to be edited here -->
     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
-        <fileset dir="${packageDir}">
-          <include name="*.jar" />
-        </fileset>
+      <fileset dir="${packageDir}">
+        <include name="*.jar" />
+      </fileset>
     </signjar>
   </target>
 
@@ -327,38 +328,55 @@
       </echo>
   </target>
   <target name="writejnlpf">
-  	<presetdef name="jnlpf">
-  	    <jnlp codebase="${WebStartLocation}">
-  	      <information>
-  	        <title>Jalview</title>
-  	        <vendor>The Barton Group</vendor>
-  	        <homepage href="http://www.jalview.org" />
-  	        <description>Jalview Multiple Alignment Editor</description>
-  	        <description kind="short">Jalview</description>
-  	        <icon href="${WebStartImage}" />
-  	        <offline_allowed />
-  	      </information>
-  	      <resources>
-  	        <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
-  	        <fileset dir="${packageDir}">
-  	          <include name="jalview.jar" />
-  	        </fileset>
-  	        <fileset dir="${packageDir}">
-  	          <include name="*.jar" />
-  	          <include name="*_*.jar" />
-  	          <exclude name="jalview.jar" />
-  	        </fileset>
-  	        <property name="jalview.version" value="${JALVIEW_VERSION}" />
-  	      </resources>
-  	      <application_desc main_class="jalview.bin.Jalview">
-  	      </application_desc>
-  	      <security>
-  	        <all_permissions />
-  	      </security>
-  	    </jnlp>
-  	    </presetdef>
-
-  	    <jnlpf toFile="${jnlpFile}"/>
+    <presetdef name="jnlpf">
+      <jnlp codebase="${WebStartLocation}">
+        <information>
+          <title>Jalview</title>
+          <vendor>The Barton Group</vendor>
+          <homepage href="http://www.jalview.org" />
+          <description>Jalview Multiple Alignment Editor</description>
+          <description kind="short">Jalview</description>
+          <icon href="${WebStartImage}" />
+          <offline_allowed />
+        </information>
+        <resources>
+          <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+          <fileset dir="${packageDir}">
+            <include name="jalview.jar" />
+          </fileset>
+          <fileset dir="${packageDir}">
+            <include name="*.jar" />
+            <include name="*_*.jar" />
+            <exclude name="jalview.jar" />
+          </fileset>
+          <property name="jalview.version" value="${JALVIEW_VERSION}" />
+        </resources>
+        <application_desc main_class="jalview.bin.Jalview">
+        </application_desc>
+        <security>
+          <all_permissions />
+        </security>
+      </jnlp>
+    </presetdef>
+
+    <jnlpf toFile="${jnlpFile}"/>
+    <replace file="${jnlpFile}">
+      <replacetoken><![CDATA[</information>]]></replacetoken>
+      <replacevalue><![CDATA[
+        <association mime-type="application-x/ext-file" extensions="fa" />
+        <association mime-type="application-x/ext-file" extensions="fasta" />
+        <association mime-type="application-x/ext-file" extensions="mfa" />
+        <association mime-type="application-x/ext-file" extensions="fastq" />
+        <association mime-type="application-x/ext-file" extensions="blc" />
+        <association mime-type="application-x/ext-file" extensions="msf" />
+        <association mime-type="application-x/ext-file" extensions="pfam" />
+        <association mime-type="application-x/ext-file" extensions="aln"/>
+        <association mime-type="application-x/ext-file" extensions="pir"/>
+        <association mime-type="application-x/ext-file" extensions="amsa"/>
+        <association mime-type="application-x/ext-file" extensions="stk"/>
+        <association mime-type="application-x/ext-file" extensions="jvp"/>
+      </information>]]></replacevalue>
+    </replace>
   </target>
   <target name="buildextclients" depends="init">
     <input message="Building external client source from WSDLs - Do you really want to do this ? (Yy/Nn)" validargs="Y,y,n,N" defaultvalue="N" addproperty="doextbuild.response" />
@@ -405,7 +423,7 @@
     <!-- clean dir if it already existed -->
     <delete>
       <fileset dir="${packageDir}">
-        <include name="*.jar" />
+        <include name="*.jar"/>
       </fileset>
     </delete>
     <jar destfile="${packageDir}/${outputJar}" index="true">
@@ -447,16 +465,23 @@
 
 
   <!-- Compile, package and obfuscate Jalview Applet -->
-  <target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation" />
+  <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}" classpathref="jalviewlite.deps" 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">
     <copy file="${resourceDir}/images/idwidth.gif" toFile="${outputDir}/images/idwidth.gif" />
     <copy file="${resourceDir}/images/link.gif" toFile="${outputDir}/images/link.gif" />
+    <copy todir="${outputDir}/lang">
+      <fileset dir="${resourceDir}/lang">
+        <include name="**.*"/>
+      </fileset>
+    </copy>
     <jar destfile="in.jar" index="true">
       <manifest>
         <attribute name="Main-Class" value="jalview.bin.JalviewLite" />
@@ -470,6 +495,7 @@
         <include name=".build_properties" />
         <include name="images/idwidth.gif" />
         <include name="images/link.gif" />
+        <include name="lang/**" />
       </fileset>
     </jar>
   </target>
@@ -491,7 +517,7 @@
       <injar file="in.jar" />
       <outjar file="${jalviewLiteJar}" />
       <libraryjar refid="obfuscateDeps.path" />
-      <dontwarn />
+      <dontwarn/>
       <keep access="public" type="class" name="jalview.bin.JalviewLite">
         <field access="public" />
         <method access="public" />
@@ -545,10 +571,10 @@
         <include name="jalview-jalopy.xml" />
         <include name="JalviewApplet.jpx" />
         <include name="JalviewX.jpx" />
-        <include name="nbbuild.xml" />
-        <include name="nbproject/genfiles.properties" />
-        <include name="nbproject/project.properties" />
-        <include name="nbproject/project.xml" />
+        <include name="nbbuild.xml"/>
+        <include name="nbproject/genfiles.properties"/>
+        <include name="nbproject/project.properties"/>
+        <include name="nbproject/project.xml"/>
         <include name="${sourceDir}/*.java" />
         <include name="${sourceDir}/**/*.java" />
         <include name="${sourceDir}/**/*.cdr" />
@@ -573,18 +599,32 @@
   <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/*" />
+        <include name="**/*"/>
+        <include name="javascript/*"/>
+        <include name="jmol/*"/>
       </fileset>
       <fileset dir=".">
         <include name="${jalviewLiteJar}" />
       </fileset>
       <fileset dir="appletlib">
-        <include name="**/*" />
+        <include name="**/*"/>
       </fileset>
     </copy>
-
+    <jar update="true" index="true" jarfile="${packageDir}/examples/${jalviewLiteJar}"/>
+    <jar update="true" index="true" jarfile="${packageDir}/examples/${jmolJar}">
+      <manifest>
+        <attribute name="Application-Name" value="Jmol (bundled with JalviewLite)"/>
+        <!--          <attribute name="Permissions" value="sandbox" /> -->
+        <!--<attribute name="Trusted-Lib" value="true" /> -->
+        <attribute name="Codebase" value="${applet.codebase}"/>
+        <attribute name="Caller-Allowable-Codebase" value="${applet.caller-codebase}"/>
+      </manifest>
+    </jar>
+    <signjar sigalg="SHA1WithRSA" storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
+      <fileset dir="${packageDir}/examples">
+        <include name="*.jar" />
+      </fileset>
+    </signjar>
     <presetdef name="ap_applet.jar">
       <!-- build a signed applet with 'all-permissions' - 
 			  Needs 'param name="permissions' value="all-permissions"' in applet tag
@@ -650,7 +690,7 @@
     </presetdef>
     <!-- create differently privileged artefacts -->
     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/u_${jalviewLiteJar}" />
-    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}"/>
+    <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true"/>
     <copy file="${packageDir}/examples/${jalviewLiteJar}" tofile="${packageDir}/examples/ap_${jalviewLiteJar}" />
     <copy file="${packageDir}/examples/${jmolJar}" tofile="${packageDir}/examples/ap_${jmolJar}"/>
     <ap_applet.jar jarfile="${packageDir}/examples/ap_${jalviewLiteJar}" />
@@ -671,6 +711,7 @@
     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
 
       <fileset dir="${packageDir}/examples">
+        <exclude name="u_*.jar"/>
         <include name="${jalviewLiteJar}" />
         <include name="${jmolJar}" />
         <include name="to_${jalviewLiteJar}" />
@@ -681,6 +722,8 @@
         <include name="ap_${jmolJar}" />
       </fileset>
     </signjar>
+    <!-- bizarre bug causes JmolApplet to always get signed, even if excluded from above. so copy explicitly -->
+    <copy file="appletlib/${jmolJar}" tofile="${packageDir}/examples/u_${jmolJar}" overwrite="true" />
   </target>
   <target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
     <javadoc destdir="${javadocDir}">
@@ -688,5 +731,4 @@
       </packageset>
     </javadoc>
   </target>
-
 </project>