X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=build.xml;h=beccd071474a8661f1d4f9d3647e69d61e1075be;hb=b3f065b1e4604502ef60a0d5c83ac43f07ccec0f;hp=fdefa363309b675770942c117d7b3deb70b31321;hpb=1b5f1de68f3f4dadcd4eecc80a5db17441eb7ab6;p=jalview.git

diff --git a/build.xml b/build.xml
index fdefa36..beccd07 100755
--- a/build.xml
+++ b/build.xml
@@ -1,20 +1,20 @@
 <?xml version="1.0"?>
 <!--
-   * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
-   * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
-   * 
-   * This file is part of Jalview.
-   * 
-   * Jalview is free software: you can redistribute it and/or
-   * modify it under the terms of the GNU General Public License 
-   * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
-   * 
-   * Jalview is distributed in the hope that it will be useful, but 
-   * WITHOUT ANY WARRANTY; without even the implied warranty 
-   * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
-   * PURPOSE.  See the GNU General Public License for more details.
-   * 
-   * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
 -->
 <project name="jalviewX" default="usage" basedir=".">
 	<!-- we use jalopy to format our sources -->
@@ -88,6 +88,8 @@
 		<!-- 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" />
+		<!-- J2SE version needed for webstart launch -->
+		<property name="j2sev" value="1.6+"/>
 		<!-- build directory configuration -->
 		<property name="libDir" value="lib" />
 		<property name="resourceDir" value="resources" />
@@ -99,7 +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"/> -->
@@ -122,6 +124,9 @@
 				<include name="*.jar" />
 				<include name="**/*.jar" />
 			</fileset>
+			<fileset dir="${java.home}/lib">
+				<include name="plugin.jar"/>
+			</fileset>
 			<fileset dir="appletlib">
 				<!-- the JmolApplet includes the JmolApplet console and the application javac seems to always try and build all packages 
 				-->
@@ -131,18 +136,25 @@
 		</path>
 		<property name="source.dist.name" value="${basedir}/jalview-src.tar.gz" />
 		<!-- The Location of the java 1.1.8 jdk -->
-		<property name="java118.home" value="C:\Sun\jdk1.1.8" />
-		<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
-		<!-- jre for 1.4 version
-		<property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+		<!--<property name="java118.home" value="C:\Sun\jdk1.1.8" />
 		-->
+		<property name="java118.home" value="${java.home}" />
+		    <!--<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip" />
+		--><!-- jre for 1.4 version -->
+		<property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+		
 		<!-- the classpath for building the 1.1 applet -->
 		<path id="jalviewlite.deps">
 			<fileset dir="${java118.home}">
 				<include name="lib/classes.zip" />
 			</fileset>
+			<fileset dir="${java.home}/lib">
+				<include name="plugin.jar"/>
+			</fileset>
 			<pathelement location="appletlib/${jmolJar}" />
 		</path>
+    <!-- default location for outputting javadoc -->
+    <property name="javadocDir" value="${packageDir}/javadoc"/>
 	</target>
 
 
@@ -163,7 +175,7 @@
 
 	<target name="clean" depends="init">
 		<!-- not efficient yet. -->
-		<delete dir="${outputDir}" />
+		<delete dir="${outputDir}" includes="*,**/*"/>
 	</target>
 
 	<target name="distclean" depends="init, clean">
@@ -233,20 +245,9 @@
 				<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"/>
-	-->
 			</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>
@@ -262,8 +263,7 @@
 			<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>
@@ -273,20 +273,9 @@
 				<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"/>
-		-->
 			</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>
@@ -312,20 +301,9 @@
 				<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"/>
-			-->
 			</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>
@@ -342,7 +320,26 @@
 				<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"/>-->
+	
 	</target>
 
 	<target name="runenv" depends="init">
@@ -442,11 +439,13 @@
 
 
 	<!-- Compile, package and obfuscate Jalview Applet -->
-	<target name="makeApplet" depends="obfuscate" />
+	<target name="makeApplet" depends="obfuscate" description="assemble the final jalviewLite applet jar with or without obfuscation"/>
 
 	<target name="compileApplet" depends="init,clean">
 		<mkdir dir="${outputDir}" />
-		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" classpath="appletlib/${jmolJar}" includes="jalview/appletgui/**" excludes="ext/**,MCview/**,org/**,vamsas/**" />
+		<javac source="1.5" target="1.5" srcdir="${sourceDir}" destdir="${outputDir}" debug="${javac.debug}" 
+			classpathref="jalviewlite.deps" includes="jalview/appletgui/**"
+			excludes="ext/**,MCview/**,org/**,vamsas/**" />
 	</target>
 
 	<target name="packageApplet" depends="compileApplet, buildPropertiesFile">
@@ -466,7 +465,7 @@
 			</fileset>
 		</jar>
 	</target>
-	<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally" description="construct the final jalviewLite applet jar with or without obfuscation">
+	<target name="obfuscate" depends="-obfuscatefake,-obfuscatereally">
 	</target>
 	<target name="-obfuscatefake" depends="packageApplet" if="donotobfuscate">
 		<copy file="in.jar" tofile="${jalviewLiteJar}" overwrite="true" />
@@ -532,6 +531,10 @@
 				<include name="jalview-jalopy.xml" />
 				<include name="JalviewApplet.jpx" />
 				<include name="JalviewX.jpx" />
+				<include name="nbbuild.xml"/>
+				<include name="nbproject/genfiles.properties"/>
+        <include name="nbproject/project.properties"/>
+        <include name="nbproject/project.xml"/>
 				<include name="${sourceDir}/*.java" />
 				<include name="${sourceDir}/**/*.java" />
 				<include name="${sourceDir}/**/*.cdr" />
@@ -549,7 +552,31 @@
 				<include name="${schemaDir}/**/*" />
 				<include name="utils/**/*" />
 				<include name="${docDir}/**/*" />
+				<include name="examples/**/*" />
 			</tarfileset>
 		</tar>
 	</target>
+	<target name="pubapplet" description="installs the jalviewLite applet and dependent jars into an applet examples directory built under ${outputDir}" depends="makeApplet">
+	  <copy todir="${packageDir}/examples">
+	  <fileset dir="examples">
+	  	<include name="**/*"/>
+	  	<include name="javascript/*"/>
+      <include name="jmol/*"/>
+	  </fileset>
+	  	<fileset dir=".">
+	  	<include name="jalviewApplet.jar"/>
+	  		</fileset>
+	  	<fileset dir="appletlib">
+	  	      <include name="**/*"/>
+	  	        </fileset>
+	  </copy>
+	  		
+	</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>