JAL-3111 drop hts-1.33 as a dependency (in favour of htsjdk-2.12)

[jalview.git] / build.xml

diff --git a/build.xml b/build.xml
index fd2b5dc..5ca105a 100755 (executable)
--- a/build.xml
+++ b/build.xml
@@ -136,7 +136,6 @@
     <property name="schemaDir" value="schemas" />
     <property name="outputDir" value="classes" unless:set="clover.jar"/>
     <property name="outputDir" value="cloverclasses" if:set="clover.jar"/>
-    <property name="outputDir" value="classes" />
     <property name="packageDir" value="dist" />
     <property name="outputJar" value="jalview.jar" />
     <!-- Jalview Applet JMol Jar Dependency -->
@@ -357,10 +356,15 @@
     </jar>
 
     <antcall target="writejnlpf">
-      <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
+      <param name="jnlpFile" value="${packageDir}/jalview_256M.jnlp" />
       <param name="inih" value="10M" />
       <param name="maxh" value="256M" />
     </antcall>
+    <antcall target="writejnlpf">
+      <param name="jnlpFile" value="${packageDir}/jalview.jnlp" />
+      <param name="inih" value="800M" />
+      <param name="maxh" value="1024M" />
+    </antcall>
 
     <antcall target="writejnlpf">
       <param name="jnlpFile" value="${packageDir}/jalview_1G.jnlp" />
@@ -370,7 +374,7 @@
 
     <antcall target="writejnlpf">
       <param name="jnlpFile" value="${packageDir}/jalview_2G.jnlp" />
-      <param name="inih" value="256M" />
+      <param name="inih" value="800M" />
       <param name="maxh" value="1024M" />
     </antcall>
 
@@ -397,7 +401,7 @@
         <association mime-type="application-x/ext-file" extensions="jar"/>-->
   </target>
 
-  <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
+  <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp" unless="nosign">
     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}"
       tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
       <fileset dir="${packageDir}">
@@ -405,7 +409,7 @@
       </fileset>
     </signjar>
   </target>
-  <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
+  <target name="-jarsignnotsa" depends="makedist,preparejnlp" if:blank="timestamp" unless="nosign">
     <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="${jalview.keyalg}" digestalg="${jalview.keydig}">
       <fileset dir="${packageDir}">
         <include name="*.jar" />
@@ -545,6 +549,9 @@
 </target>
 
 <target name="makedist" depends="build, buildPropertiesFile, linkcheck, buildindices">
+  <fail if="clover.jar">
+    Ignoring request to build jalview distribution with clover-instrumented classes
+  </fail>
   <!-- make the package jar if not already existing -->
   <mkdir dir="${packageDir}" />
   <!-- clean dir if it already existed -->
@@ -934,13 +941,13 @@
     <include name="ap_${jsonSimple}" />
   </fileset>
 </target>
-<target name="-signappletnotsa" unless="timestamp" depends="-signapplet">
+<target name="-signappletnotsa" if:blank="timestamp" depends="-signapplet" unless="nosign">
   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false">
     <fileset refid="signappletjarset" />
   </signjar>
 </target>
 
-<target name="-signapplettsa" if="timestamp" depends="-signapplet">
+<target name="-signapplettsa" if="timestamp" depends="-signapplet" unless="nosign">
   <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" tsaproxyhost="${proxyHost}" tsaproxyport="${proxyPort}" tsaurl="${jalview.tsaurl}">
     <fileset refid="signappletjarset" />
   </signjar>