X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=ee0542d17af474f0a70403056bfcf1b70883e89f;hb=c118b1d02eeb6b1365ad3fae60509c082aa15650;hp=6cfaf4e5de36fde1f3de79de25b578fd5f467cac;hpb=205a4ac63d5d8ffcf5cf8d3556b5aca94f6cce06;p=jalview.git

diff --git a/build.xml b/build.xml
index 6cfaf4e..ee0542d 100755
--- a/build.xml
+++ b/build.xml
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <!--
  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -101,7 +101,7 @@
 		<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="jalviewLiteJar" value="jalviewApplet.jar" />
 		<!-- switch to indicate if we should obfuscate jalviewLite -->
 		<!--<property name="donotobfuscate" value="true"/> -->
@@ -236,45 +236,6 @@
 
 		<!--    codebase="http://www.jalview.org/jalview/webstart" -->
 		<!-- href="jalview.jnlp" prevent hard-wired pickup of jnlp in certain javaws versions -->
-		<jnlp toFile="${packageDir}/jalview_noa.jnlp" codebase="${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="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"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>-->
-			</information>
-			<resources>
-				<j2se version="${j2sev}" initial_heap_size="10M"  />
-				<fileset dir="${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>
 		<jnlp toFile="${packageDir}/jalview.jnlp" codebase="${WebStartLocation}">
 			<information>
 				<title>Jalview</title>
@@ -282,61 +243,11 @@
 				<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"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
+				<icon href="JalviewLogo_big.png" />
+				<offline_allowed/>
 			</information>
 			<resources>
-				<j2se version="${j2sev}" initial_heap_size="10M"/>
-				<fileset dir="${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>
-		
-		<jnlp toFile="${packageDir}/jalview_noa_1G.jnlp" codebase="${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="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"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>-->
-			</information>
-			<resources>
-				<j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
+				<j2se version="${j2sev}" initial_heap_size="10M"  />
 				<fileset dir="${packageDir}">
 					<include name="jalview.jar" />
 				</fileset>
@@ -352,7 +263,7 @@
 			<security>
 				<all_permissions />
 			</security>
-		</jnlp>
+		</jnlp>		
 		<jnlp toFile="${packageDir}/jalview_1G.jnlp" codebase="${WebStartLocation}">
 			<information>
 				<title>Jalview</title>
@@ -360,18 +271,8 @@
 				<homepage href="http://www.jalview.org" />
 				<description>Jalview Multiple Alignment Editor</description>
 				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif" />
+				<icon href="JalviewLogo_big.png" />
 				<offline_allowed />
-				<association mime-type="application-x/ext-file" extensions="fa"/>
-        <association mime-type="application-x/ext-file" extensions="fasta"/>
-        <association mime-type="application-x/ext-file" extensions="fastq"/>
-        <association mime-type="application-x/ext-file" extensions="blc"/>
-        <association mime-type="application-x/ext-file" extensions="msf"/>
-        <association mime-type="application-x/ext-file" extensions="pfam"/>
-        <association mime-type="application-x/ext-file" extensions="aln"/>
-        <association mime-type="application-x/ext-file" extensions="pir"/>
-        <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
 			</information>
 			<resources>
 				<j2se version="${j2sev}" initial_heap_size="128M" max_heap_size="512M" />
@@ -391,27 +292,15 @@
 				<all_permissions />
 			</security>
 		</jnlp>
-		<jnlp toFile="${packageDir}/jalview_noac_2G.jnlp" codebase="${WebStartLocation}">
+		<jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${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="logo_big.gif" />
+				<icon href="JalviewLogo_big.png" />
 				<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"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
-			-->
 			</information>
 			<resources>
 				<j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
@@ -431,15 +320,15 @@
 				<all_permissions />
 			</security>
 		</jnlp>
-		<jnlp toFile="${packageDir}/jalview_2G.jnlp" codebase="${WebStartLocation}">
-			<information>
-				<title>Jalview</title>
-				<vendor>The Barton Group</vendor>
-				<homepage href="http://www.jalview.org" />
-				<description>Jalview Multiple Alignment Editor</description>
-				<description kind="short">Jalview</description>
-				<icon href="logo_big.gif" />
-				<offline_allowed />
+			<!-- finally, need to postprocess to add in associations at end of 'information' element 
+			
+			<xslt in="${packageDir}/jalview_noa_1G.jnlp" out="${packageDir}/jalview_1G.jnlp">
+		
+		</xslt>
+			
+			
+			-->
+					<!--
 				<association mime-type="application-x/ext-file" extensions="fa"/>
         <association mime-type="application-x/ext-file" extensions="fasta"/>
         <association mime-type="application-x/ext-file" extensions="fastq"/>
@@ -449,27 +338,8 @@
         <association mime-type="application-x/ext-file" extensions="aln"/>
         <association mime-type="application-x/ext-file" extensions="pir"/>
         <association mime-type="application-x/ext-file" extensions="amsa"/>
-        <association mime-type="application-x/ext-file" extensions="stk"/>
-			</information>
-			<resources>
-				<j2se version="${j2sev}" initial_heap_size="256M" max_heap_size="1024M" />
-				<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>
-
+        <association mime-type="application-x/ext-file" extensions="stk"/>-->
+	
 	</target>
 
 	<target name="runenv" depends="init">