X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=8d27614d06f9602b7aca7fcb4b7f23bedc6c157e;hb=refs%2Fheads%2Fbug%2FJAL-2374_JAL-2419_overlappinggroups_currentselection_popupmenu;hp=b23293f7a1f3f6a69882f6b81b76d7d4d2a6932a;hpb=d3d566fbf876a3511c06fecec695b2f59eb71169;p=jalview.git

diff --git a/build.xml b/build.xml
index b23293f..8d27614 100755
--- a/build.xml
+++ b/build.xml
@@ -27,7 +27,9 @@
     <echo message="build - compiles all necessary files for Application" />
     <echo message="makedist - compiles and places all necessary jar files into directory dist" />
     <echo message="makefulldist - signs all jar files and builds jnlp file for full distribution" />
-    <echo message="              this needs a keystore and key. Add -Dtimestamp to timestamp signed jars"/>
+    <echo message="              this needs a keystore and key."/>
+    <echo message="              Add -Dtimestamp to timestamp signed jars"/>
+    <echo message="              -Djalview.keyalg and -Djalview.keydig are SHA1/SHA1withRSA"/>
     <echo message="              See docs/building.html for more information." />
     <echo message="compileApplet - compiles all necessary files for Applet" />
     <echo message="makeApplet - compiles, then packages and obfuscates the Applet" />
@@ -88,6 +90,9 @@
     <!-- locally valid proxy for signing with external time server -->
     <property name="proxyPort" value="80"/>
     <property name="proxyHost" value="sqid"/>
+    <!-- key sign/digest algorithms -->
+    <property name="jalview.keyalg" value="SHA1withRSA" description="key algorithm for signing"/>
+    <property name="jalview.keydig" value="SHA1" description="algorithm for jar digest"/>
 
     <!-- default TestNG groups to run -->
     <property name="testng-groups" value="Functional" />
@@ -123,7 +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" />
@@ -374,7 +379,7 @@
   </target>
 
   <target name="-jarsignwithtsa" depends="makedist,preparejnlp" if="timestamp">
-    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA"
+    <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}">
         <include name="*.jar" />
@@ -382,7 +387,7 @@
     </signjar>
   </target>
   <target name="-jarsignnotsa" depends="makedist,preparejnlp" unless="timestamp">
-    <signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
+    <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="${packageDir}">
         <include name="*.jar" />
       </fileset>
@@ -421,13 +426,11 @@
         </information>
         <resources>
           <j2se version="${j2sev}" initial_heap_size="${inih}" max_heap_size="${maxh}" />
+          <jar main="true" href="jalview.jar"/>
           <fileset dir="${packageDir}">
-            <include name="jalview.jar" />
-          </fileset>
-          <fileset dir="${packageDir}">
+            <exclude name="jalview.jar" />
             <include name="*.jar" />
             <include name="*_*.jar" />
-            <exclude name="jalview.jar" />
             <exclude name="*jnilib.jar" />
           </fileset>
           <property name="jalview.version" value="${JALVIEW_VERSION}" />
@@ -518,7 +521,7 @@
   </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 -->
@@ -570,7 +573,7 @@
 
 <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">
@@ -613,14 +616,16 @@
     <pathelement location="appletlib/${jsoup}" />
     <pathelement location="appletlib/${jsonSimple}" />
     <pathelement location="appletlib/${javaJson}" />
-    <pathelement location="appletlib/plugin.jar" />
+    <fileset dir="${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" />
@@ -637,7 +642,7 @@
       <constructor/>
       <method name="*"/>
     </keep>
-   
+
     <keep access="public" type="class" name="MCview.PDBfile">
       <field access="public" />
       <method access="public" />
@@ -649,14 +654,14 @@
       <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 "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
@@ -692,8 +697,13 @@
 </target>
 <target name="sourcedist" description="create jalview source distribution" depends="init">
   <delete file="${source.dist.name}" />
-  <tar destfile="${source.dist.name}" compression="gzip">
-    <tarfileset dir="./" prefix="jalview" preserveLeadingSlashes="true">
+  <!-- temporary copy of source to update timestamps -->
+  <copy todir="_sourcedist">
+    <fileset dir=".">
+      <exclude name=".*" />
+      <exclude name="**/.*" />
+      <exclude name="*.class" />
+      <exclude name="**/*.class" />
       <include name="LICENSE" />
       <include name="README" />
       <include name="build.xml" />
@@ -718,14 +728,41 @@
       <exclude name="utils/InstallAnywhere/**Build.iap_xml" />
       <exclude name="utils/InstallAnywhere/**Build*/**" />
       <exclude name="utils/InstallAnywhere/**Build*/**" />
+      <exclude name="utils/InstallAnywhere/.build*.*/**" />
       <exclude name="utils/InstallAnywhere/**locale*" />
       <exclude name="utils/InstallAnywhere/**locale*/**" />
+      <exclude name="utils/InstallAnywhere/**locale*/**" />
       <include name="${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">
@@ -921,4 +958,11 @@
     </packageset>
   </javadoc>
 </target>
+<target name="linkcheck" depends="init,prepare">
+  <javac srcdir="utils" destdir="utils" includes="HelpLinksChecker.java"/>
+  <java fork="true" dir="${helpDir}" classpath="utils" classname="HelpLinksChecker" failonerror="true">
+    <arg file="${helpDir}"/>
+    <arg value="-nointernet"/>
+  </java>
+</target>
 </project>