X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=build.xml;h=dc93408a688636e94e85e0dc8355f055360c03e9;hb=80c223c45fde0899c9794e887801dd82fffd3452;hp=5b1066f63b20f1a090c8593eeeacb056c7cd092c;hpb=5aad8085fbd06d2e0f6a97d71e8ed58d0e02e6db;p=jalview.git

diff --git a/build.xml b/build.xml
index 5b1066f..dc93408 100755
--- a/build.xml
+++ b/build.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!--
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
  * 
  * This file is part of Jalview.
  * 
@@ -85,9 +85,22 @@
 		<!-- Key Password -->
 		<property name="jalview.key.pass" value="alignmentisfun" />
 
+		    
+		    
 		<!-- Don't change anything below here unless you know what you are doing! -->
 		<!-- 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"/>
+		<!-- J2SE version needed for webstart launch -->
+<!-- Anne's version needs 1.7 - should rebuild VARNA to java 1.6 for release -->
+		<property name="j2sev" value="1.7+"/>
+
+    <!-- Permissions for running Java applets and applications. Defaults are those suitable for deploying jalview webstart/jalviewLite at www.jalview.org -->
+    <property name="application.codebase" value="*.jalview.org"/>
+    <property name="applet.codebase" value="*.jalview.org"/>
+    <property name="applet.caller-codebase" value="${applet.codebase}"/>
+
 		<!-- build directory configuration -->
 		<property name="libDir" value="lib" />
 		<property name="resourceDir" value="resources" />
@@ -99,7 +112,8 @@
 		<property name="packageDir" value="dist" />
 		<property name="outputJar" value="jalview.jar" />
 		<!-- Jalview Applet JMol Jar Dependency -->
-		<property name="jmolJar" value="JmolApplet-12.1.13.jar" />
+		<property name="jmolJar" value="JmolApplet-12.2.4.jar" />
+		<property name="varnaJar" value="VARNAv3-9.jar" />
 		<property name="jalviewLiteJar" value="jalviewApplet.jar" />
 		<!-- switch to indicate if we should obfuscate jalviewLite -->
 		<!--<property name="donotobfuscate" value="true"/> -->
@@ -129,6 +143,7 @@
 				<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
 				-->
 				<include name="${jmolJar}" />
+				<include name="${varnaJar}" />
 			</fileset>
 
 		</path>
@@ -150,7 +165,11 @@
 				<include name="plugin.jar"/>
 			</fileset>
 			<pathelement location="appletlib/${jmolJar}" />
+      <pathelement location="lib/${varnaJar}" />
+
 		</path>
+    <!-- default location for outputting javadoc -->
+    <property name="javadocDir" value="${packageDir}/javadoc"/>
 	</target>
 
 
@@ -171,7 +190,7 @@
 
 	<target name="clean" depends="init">
 		<!-- not efficient yet. -->
-		<delete dir="${outputDir}" />
+		<delete dir="${outputDir}" includes="*,**/*"/>
 	</target>
 
 	<target name="distclean" depends="init, clean">
@@ -222,12 +241,18 @@
 
 	<target name="makefulldist" depends="makedist">
 		<!-- 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">
+		<signjar storepass="${jalview.keystore.pass}" keypass="${jalview.key.pass}" keystore="${jalview.keystore}" alias="${jalview.key}" lazy="false" verbose="false" sigalg="SHA1withRSA">
 
 			<fileset dir="${packageDir}">
 				<include name="*.jar" />
 			</fileset>
 		</signjar>
+		<copy todir="${packageDir}">
+			<fileset dir="${resourceDir}/images">
+				<include name="${WebStartImage}"/>
+			</fileset>
+					</copy>
+		
 		<taskdef classpathref="build.classpath" resource="com/roxes/tools/ant/taskdefs.properties" />
 
 		<!--    codebase="http://www.jalview.org/jalview/webstart" -->
@@ -239,22 +264,11 @@
 				<homepage href="http://www.jalview.org" />
 				<description>Jalview Multiple Alignment Editor</description>
 				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif" />
-				<offline_allowed />
-				<!--
-	<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="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"/>
-	-->
+				<icon href="${WebStartImage}" />
+				<offline_allowed/>
 			</information>
 			<resources>
-				<j2se version="1.5+" initial_heap_size="10M" />
+				<j2se version="${j2sev}" initial_heap_size="10M"  />
 				<fileset dir="${packageDir}">
 					<include name="jalview.jar" />
 				</fileset>
@@ -270,8 +284,7 @@
 			<security>
 				<all_permissions />
 			</security>
-		</jnlp>
-		<!-- the rest of these jnlp tasks are copy and pastes of the above but with different Vm args -->
+		</jnlp>		
 		<jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 			<information>
 				<title>Jalview</title>
@@ -279,22 +292,11 @@
 				<homepage href="http://www.jalview.org" />
 				<description>Jalview Multiple Alignment Editor</description>
 				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif" />
+				<icon href="${WebStartImage}" />
 				<offline_allowed />
-				<!--
-		<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="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"/>
-		-->
 			</information>
 			<resources>
-				<j2se version="1.5+" initial_heap_size="64M" max_heap_size="512M" />
+				<j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
 				<fileset dir="${packageDir}">
 					<include name="jalview.jar" />
 				</fileset>
@@ -318,22 +320,11 @@
 				<homepage href="http://www.jalview.org" />
 				<description>Jalview Multiple Alignment Editor</description>
 				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif" />
+				<icon href="${WebStartImage}" />
 				<offline_allowed />
-				<!--
-			<association mime-type="application-x/ext-file" extensions="fa"/>
-		        <association mime-type="application-x/ext-file" extensions="fasta"/>
-		        <association mime-type="application-x/ext-file" extensions="fastq"/>
-		        <association mime-type="application-x/ext-file" extensions="blc"/>
-		        <association mime-type="application-x/ext-file" extensions="msf"/>
-		        <association mime-type="application-x/ext-file" extensions="pfam"/>
-		        <association mime-type="application-x/ext-file" extensions="aln"/>
-		        <association mime-type="application-x/ext-file" extensions="pir"/>
-		        <association mime-type="application-x/ext-file" extensions="amsa"/>
-			-->
 			</information>
 			<resources>
-				<j2se version="1.5+" initial_heap_size="256M" max_heap_size="1024M" />
+				<j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
 				<fileset dir="${packageDir}">
 					<include name="jalview.jar" />
 				</fileset>
@@ -350,7 +341,27 @@
 				<all_permissions />
 			</security>
 		</jnlp>
-
+			<!-- finally, need to postprocess to add in associations at end of 'information' element 
+			
+			<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
+		
+		</xslt>
+			
+			
+			-->
+					<!--
+				<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="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="jar"/>-->
+	
 	</target>
 
 	<target name="runenv" depends="init">
@@ -414,9 +425,13 @@
 				<include name="*.jar"/>
 			</fileset>
 		</delete>
-		<jar destfile="${packageDir}/${outputJar}">
+		<jar destfile="${packageDir}/${outputJar}" index="true">
 			<manifest>
 				<attribute name="Main-Class" value="jalview.bin.Jalview" />
+        <attribute name="Permissions" value="all-permissions" />
+        <!--<attribute name="Trusted-Lib" value="true" /> -->
+        <attribute name="Application-Name" value="Jalview Desktop"/>
+        <attribute name="Codebase" value="${application.codebase}"/>
 			</manifest>
 			<fileset dir="${outputDir}/">
 				<exclude name="cache*/**" />
@@ -456,15 +471,22 @@
 		<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/**" />
+			excludes="ext/**,MCview/**,org/**,vamsas/**,jalview/ext/paradise/**" />
 	</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" />
-		<jar destfile="in.jar">
+		<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" />
+				<attribute name="Application-Name" value="JalviewLite Applet"/>
+				<!--        	<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>
 			<fileset dir="${outputDir}">
 				<include name="com/**" />
@@ -473,6 +495,7 @@
 				<include name=".build_properties" />
 				<include name="images/idwidth.gif" />
 				<include name="images/link.gif" />
+				<include name="lang/**" />
 			</fileset>
 		</jar>
 	</target>
@@ -494,11 +517,17 @@
 			<injar file="in.jar" />
 			<outjar file="${jalviewLiteJar}" />
 			<libraryjar refid="obfuscateDeps.path" />
+			<dontwarn/>
 			<keep access="public" type="class" name="jalview.bin.JalviewLite">
 				<field access="public" />
 				<method access="public" />
 				<constructor access="public" />
 			</keep>
+			<keep access="public" type="class" name="jalview.appletgui.AlignFrame">
+				<field access="public" />
+				<method access="public" />
+				<constructor access="public" />
+			</keep>
 			<!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
@@ -571,6 +600,8 @@
 	  <copy todir="${packageDir}/examples">
 	  <fileset dir="examples">
 	  	<include name="**/*"/>
+	  	<include name="javascript/*"/>
+      <include name="jmol/*"/>
 	  </fileset>
 	  	<fileset dir=".">
 	  	<include name="jalviewApplet.jar"/>
@@ -579,6 +610,27 @@
 	  	      <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="${packageDir}/examples">
+        <include name="*.jar" />
+      </fileset>
+    </signjar>
+	</target>
+	<target name="sourcedoc" description="Create jalview source documentation pages" depends="init">
+	 <javadoc destdir="${javadocDir}">
+	 	<packageset dir="${sourceDir}" includes="jalview/*,MCView/*">
+	 	</packageset>
+	 	</javadoc>
 	</target>
+	
 </project>