X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=4931cfb5ea521224b6c048e284f47e607b1d5be8;hb=refs%2Fheads%2Ffeature%2FJAL-2909bamfiles;hp=d3685dd41a81b621cdbe6c44a00301ed194f755f;hpb=38dc674ce8f51bb3adaff35e362853272beb0727;p=jalview.git

diff --git a/build.xml b/build.xml
index d3685dd..4931cfb 100755
--- a/build.xml
+++ b/build.xml
@@ -128,7 +128,7 @@
     <property name="packageDir" value="dist" />
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
-    <property name="jmolJar" value="JmolApplet-14.2.14_2015.06.11.jar" />
+    <property name="jmolJar" value="JmolApplet-14.6.4_2016.10.26.jar" />
     <property name="varnaJar" value="VARNAv3-93.jar" />
     <property name="jsoup" value="jsoup-1.8.1.jar" />
     <property name="jsonSimple" value="json_simple-1.1.jar" />
@@ -302,7 +302,7 @@
     </testng>
   </target>
 
-  <target name="buildindices" depends="init, prepare,linkcheck" unless="help.uptodate">
+  <target name="buildindices" depends="init, prepare" unless="help.uptodate">
     <java classname="com.sun.java.help.search.Indexer" classpathref="build.classpath" fork="true" dir="${outputDir}/${helpDir}">
       <arg line="html" />
     </java>
@@ -425,7 +425,7 @@
           <offline_allowed />
         </information>
         <resources>
-          <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+          <j2se version="1.7+" />
           <jar main="true" href="jalview.jar"/>
           <fileset dir="${packageDir}">
             <exclude name="jalview.jar" />
@@ -450,7 +450,11 @@
     </presetdef>
 
     <jnlpf toFile="${jnlpFile}" />
-
+    <!-- add the add-modules j2se attribute for java 9 -->
+    <replace file="${jnlpFile}" value="j2se version=&quot;1.7+&quot; initial-heap-size=&quot;${inih}&quot; max-heap-size=&quot;${maxh}&quot; java-vm-args=&quot;--add-modules=java.se.ee --illegal-access=warn&quot;">
+          <replacetoken>j2se version="1.7+"</replacetoken>
+           
+        </replace>
   </target>
 
   <target name="-dofakejnlpfileassoc" depends="-generatejnlpf" if="nojnlpfileassocs">
@@ -521,7 +525,7 @@
   </axis-wsdl2java>
 </target>
 
-<target name="makedist" depends="build, buildPropertiesFile, buildindices">
+<target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
   <!-- make the package jar if not already existing -->
   <mkdir dir="${packageDir}" />
   <!-- clean dir if it already existed -->
@@ -573,7 +577,7 @@
 
 <target name="compileApplet" depends="init,clean">
   <mkdir dir="${outputDir}" />
-  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so" />
+  <javac source="${javac.source}" target="${javac.target}" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpathref="jalviewlite.deps" includes="jalview/appletgui/**" excludes="ext/**,gui/**,jbgui/**,MCview/**,org/**,vamsas/**,jalview/ext/rbvi/**,jalview/ext/paradise/**,jalview/ext/ensembl/**,jalview/ext/so/**" />
 </target>
 
 <target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -616,16 +620,16 @@
     <pathelement location="appletlib/${jsoup}" />
     <pathelement location="appletlib/${jsonSimple}" />
     <pathelement location="appletlib/${javaJson}" />
- 	<fileset dir="${java.home}/lib">
-        <include name="plugin.jar" />
+    <fileset dir="${java.home}/lib">
+      <include name="plugin.jar" />
     </fileset>
   </path>
   <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
 
   <proguard verbose="true" >
-    <injar file="in.jar" />    
-    <outjar file="${jalviewLiteJar}" />    
-    <libraryjar refid="obfuscateDeps.path" />    
+    <injar file="in.jar" />
+    <outjar file="${jalviewLiteJar}" />
+    <libraryjar refid="obfuscateDeps.path" />
     <dontwarn />
     <keep access="public" type="class" name="jalview.bin.JalviewLite">
       <field access="public" />
@@ -642,7 +646,7 @@
       <constructor/>
       <method name="*"/>
     </keep>
-   
+
     <keep access="public" type="class" name="MCview.PDBfile">
       <field access="public" />
       <method access="public" />
@@ -654,14 +658,14 @@
       <method access="public" />
       <constructor access="public" />
     </keep>
-    
+
     <keep access="public" type="class" name="jalview.ext.jmol.JmolParser">
       <field access="public" />
       <method access="public" />
       <constructor access="public" />
     </keep>
-    
-    
+
+
     <!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
@@ -697,8 +701,13 @@
 </target>
 <target name="sourcedist" description="create jalview source distribution" depends="init">
   <delete file="${source.dist.name}" />
-  <tar destfile="${source.dist.name}" compression="gzip">
-    <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+  <!-- temporary copy of source to update timestamps -->
+  <copy todir="_sourcedist">
+    <fileset dir=".">
+      <exclude name=".*" />
+      <exclude name="**/.*" />
+      <exclude name="*.class" />
+      <exclude name="**/*.class" />
       <include name="LICENSE" />
       <include name="README" />
       <include name="build.xml" />
@@ -723,14 +732,41 @@
       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
       <exclude name="utils/InstallAnywhere/**Build*/**" />
       <exclude name="utils/InstallAnywhere/**Build*/**" />
+      <exclude name="utils/InstallAnywhere/.build*.*/**" />
       <exclude name="utils/InstallAnywhere/**locale*" />
       <exclude name="utils/InstallAnywhere/**locale*/**" />
+      <exclude name="utils/InstallAnywhere/**locale*/**" />
       <include name="${schemaDir}/**/*" />
       <include name="utils/**/*" />
       <include name="${docDir}/**/*" />
       <include name="examples/**/*" />
+    </fileset>
+  </copy>
+
+  <tstamp prefix="build">
+    <format property="year" pattern="yyyy" />
+  </tstamp>
+  <!-- each replacetoken CDATA body must be on one line - 
+       otherwise the pattern doesn't match -->
+  <replace value="${JALVIEW_VERSION}">
+    <replacetoken><![CDATA[$$Version-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+  <replace dir="_sourcedist" value="${build.year}">
+    <replacetoken><![CDATA[$$Year-Rel$$]]></replacetoken>
+    <fileset dir="_sourcedist">
+      <include name="**/*" />
+    </fileset>
+  </replace>
+
+  <tar destfile="${source.dist.name}" compression="gzip">
+    <tarfileset dir="_sourcedist/" prefix="jalview" preserveLeadingSlashes="true">
     </tarfileset>
   </tar>
+
+  <delete dir="_sourcedist" />
 </target>
 <target name="prepubapplet_1" depends="makeApplet">
   <copy todir="${packageDir}/examples">
@@ -926,11 +962,10 @@
     </packageset>
   </javadoc>
 </target>
-<target name="linkcheck">
-  <!-- finally, publish the help files -->
+<target name="linkcheck" depends="init,prepare">
   <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
-  <java fork="true" dir="help" classpath="utils" classname="HelpLinksChecker" failonerror="true">
-    <arg file="help"/>
+  <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
+    <arg file="${helpDir}"/>
     <arg value="-nointernet"/>
   </java>
 </target>